diff --git a/.github/workflows/robot-validate.yml b/.github/workflows/robot-validate.yml
index 77b160e..9ad8dde 100644
--- a/.github/workflows/robot-validate.yml
+++ b/.github/workflows/robot-validate.yml
@@ -28,7 +28,7 @@ on:
jobs:
robot-smoke:
runs-on: ubuntu-latest
- timeout-minutes: 90
+ timeout-minutes: 30
env:
ROBOT_VERSION: v1.9.10
@@ -77,8 +77,9 @@ jobs:
ROBOT="java -jar $HOME/.local/share/robot/robot.jar"
$ROBOT merge \
--input "03_TECHNICAL_CORE/ontology/imports/bfo-2020.owl" \
- --input "03_TECHNICAL_CORE/ontology/imports/iao.owl" \
- --input "03_TECHNICAL_CORE/ontology/imports/ro.owl" \
+ --input "03_TECHNICAL_CORE/ontology/imports/iao_bot.owl" \
+ --input "03_TECHNICAL_CORE/ontology/imports/ro_bot.owl" \
+ --input "03_TECHNICAL_CORE/ontology/imports/cco_bot.owl" \
--input "03_TECHNICAL_CORE/ontology/ARCO_core.ttl" \
--input "03_TECHNICAL_CORE/ontology/ARCO_governance_extension.ttl" \
--input "03_TECHNICAL_CORE/ontology/ARCO_instances_sentinel.ttl" \
diff --git a/03_TECHNICAL_CORE/ontology/imports/cco_bot.owl b/03_TECHNICAL_CORE/ontology/imports/cco_bot.owl
new file mode 100644
index 0000000..9c63e52
--- /dev/null
+++ b/03_TECHNICAL_CORE/ontology/imports/cco_bot.owl
@@ -0,0 +1,5951 @@
+
+
+
+ BSD 3-Clause: https://github.com/CommonCoreOntology/CommonCoreOntologies/blob/master/LICENSE
+ CUBRC Inc., see full license.
+ This ontology is designed to represent agents, especially persons and organizations, and their roles.
+ Agent Ontology
+ Version 1.7
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+ 250-BFO
+
+ participates in
+ (Elucidation) participates in holds between some b that is either a specifically dependent continuant or generically dependent continuant or independent continuant that is not a spatial region & some process p such that b participates in p some way
+ Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 248-BFO
+
+ has participant
+ p has participant c =Def c participates in p
+ Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link>
+
+
+
+
+
+
+
+
+
+
+
+ 230-BFO
+
+ has member part
+ b has member part c =Def c member part of b
+ Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link>
+
+
+
+
+
+
+
+
+
+
+ 228-BFO
+
+ member part of
+ b member part of c =Def b is an object & c is a material entity & there is some time t such that b continuant part of c at t & there is a mutually exhaustive and pairwise disjoint partition of c into objects x1, ..., xn (for some n ≠ 1) with b = xi (for some 1 <= i <= n)
+ Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link>
+
+
+
+
+
+
+
+
+
+
+ 221-BFO
+
+ continuant part of
+ b continuant part of c =Def b and c are continuants & there is some time t such that b and c exist at t & b continuant part of c at t
+ Milk teeth continuant part of human; surgically removed tumour continuant part of organism
+ Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link>
+
+
+
+
+
+
+
+
+
+ 271-BFO
+
+ has continuant part
+ b has continuant part c =Def c continuant part of b
+ Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 260-BFO
+
+ specifically depended on by
+ s-depended on by
+ b specifically depended on by c =Def c specifically depends on b
+ Coloured object specifically depended on by colour
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 012-BFO
+
+ specifically depends on
+ s-depends on
+ (Elucidation) specifically depends on is a relation between a specifically dependent continuant b and specifically dependent continuant or independent continuant that is not a spatial region c such that b and c share no parts in common & b is of a nature such that at all times t it cannot exist unless c exists & b is not a boundary of c
+ A shape specifically depends on the shaped object; hue, saturation and brightness of a colour sample specifically depends on each other
+ The analogue of specifically depends on for occurrents is has participant.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 053-BFO
+
+ bearer of
+ b bearer of c =Def c inheres in b
+ A patch of ink is the bearer of a colour quality; an organism is the bearer of a temperature quality
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 051-BFO
+
+ inheres in
+ b inheres in c =Def b is a specifically dependent continuant & c is an independent continuant that is not a spatial region & b specifically depends on c
+ A shape inheres in a shaped object; a mass inheres in a material entity
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ designated by
+ x designated_by y iff y is an instance of Information Content Entity and x is an instance of Entity, such that given some context, y uniquely distinguishes x from other entities.
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ designates
+ x designates y iff x is an instance of an Information Content Entity, and y is an instance of an Entity, such that given some context, x uniquely distinguishes y from other entities.
+ a URL designates the location of a Web Page on the internet
+ a person's name designates that person
+ a vehicle identification number designates some vehicle
+ Given a stronger temporal interpretation, this property may be functional. For more info please refer to https://github.com/BFO-ontology/BFO-2020/tree/master/src/owl/temporal%20extensions.
+
+
+
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=IPO_model&oldid=1024398398
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/ExtendedRelationOntology
+
+ has output
+ y has_output x iff x is an instance of Continuant and y is an instance of Process, such that the presence of x at the end of y is a necessary condition for the completion of y.
+
+
+
+
+
+
+
+
+
+
+ http://purl.obolibrary.org/obo/IAO_0000136
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ is about
+ A primitive relationship between an Information Content Entity and some Entity.
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/ExtendedRelationOntology
+
+ is output of
+ x is_output_of y iff x is an instance of Continuant and y is an instance of Process, such that the presence of x at the end of y is a necessary condition for the completion of y.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ is subject of
+ A primitive relationship between an instance of an Entity and an instance of an Information Content Entity.
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ prescribed by
+ x prescribed_by y iff y is an instance of Information Content Entity and x is an instance of Entity, such that y serves as a rule or guide for x if x is an Occurrent, or y serves as a model for x if x is a Continuant.
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ prescribes
+ x prescribes y iff x is an instance of Information Content Entity and y is an instance of Entity, such that x serves as a rule or guide for y if y an Occurrent, or x serves as a model for y if y is a Continuant.
+ A blueprint prescribes some artifact or facility by being a model for it.
+ A professional code of conduct prescribes some realizations of a profession (role) by giving rules for how the bearer should act in those realizations.
+ An operations plan prescribes an operation by enumerating the tasks that need to be performed in order to achieve the objectives of the operation.
+
+
+
+
+
+
+
+
+
+
+
+
+ 001-BFO
+
+ entity
+ (Elucidation) An entity is anything that exists or has existed or will exist
+ Julius Caesar; the Second World War; your body mass index; Verdi's Requiem
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 008-BFO
+
+ continuant
+ (Elucidation) A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity
+ A human being; a tennis ball; a cave; a region of space; someone's temperature
+
+
+
+
+
+
+
+
+ 077-BFO
+
+ occurrent
+ (Elucidation) An occurrent is an entity that unfolds itself in time or it is the start or end of such an entity or it is a temporal or spatiotemporal region
+ As for process, history, process boundary, spatiotemporal region, zero-dimensional temporal region, one-dimensional temporal region, temporal interval, temporal instant.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 017-BFO
+
+ independent continuant
+ b is an independent continuant =Def b is a continuant & there is no c such that b specifically depends on c or b generically depends on c
+ An atom; a molecule; an organism; a heart; a chair; the bottom right portion of a human torso; a leg; the interior of your mouth; a spatial region; an orchestra
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 035-BFO
+
+ spatial region
+ (Elucidation) A spatial region is a continuant entity that is a continuant part of the spatial projection of a portion of spacetime at a given time
+ As for zero-dimensional spatial region, one-dimensional spatial region, two-dimensional spatial region, three-dimensional spatial region
+
+
+
+
+
+
+
+
+ 083-BFO
+
+ process
+ event
+ (Elucidation) p is a process means p is an occurrent that has some temporal proper part and for some time t, p has some material entity as participant
+ An act of selling; the life of an organism; a process of sleeping; a process of cell-division; a beating of the heart; a process of meiosis; the taxiing of an aircraft; the programming of a computer
+
+
+
+
+
+
+
+
+ 058-BFO
+
+ realizable entity
+ (Elucidation) A realizable entity is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region & which is of a type some instances of which are realized in processes of a correlated type
+ The role of being a doctor; the role of this boundary to delineate where Utah and Colorado meet; the function of your reproductive organs; the disposition of your blood to coagulate; the disposition of this piece of metal to conduct electricity
+
+
+
+
+
+
+
+
+ 050-BFO
+
+ specifically dependent continuant
+ b is a specifically dependent continuant =Def b is a continuant & there is some independent continuant c which is not a spatial region & which is such that b specifically depends on c
+ (with multiple bearers) John's love for Mary; the ownership relation between John and this statue; the relation of authority between John and his subordinates
+ (with one bearer) The mass of this tomato; the pink colour of a medium rare piece of grilled filet mignon at its centre; the smell of this portion of mozzarella; the disposition of this fish to decay; the role of being a doctor; the function of this heart to pump blood; the shape of this hole
+
+
+
+
+
+
+
+
+ 025-BFO
+
+ object aggregate
+ (Elucidation) An object aggregate is a material entity consisting exactly of a plurality (≥1) of objects as member parts which together form a unit
+ The aggregate of the musicians in a symphony orchestra and their instruments; the aggregate of bearings in a constant velocity axle joint; the nitrogen atoms in the atmosphere; a collection of cells in a blood biobank
+ 'Exactly' means that there are no parts of the object aggregate other than its member parts.
+ The unit can, at certain times, consist of exactly one object, for example, when a wolf litter loses all but one of its pups, but it must at some time have a plurality of member parts.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 034-BFO
+
+ site
+ (Elucidation) A site is a three-dimensional immaterial entity whose boundaries either (partially or wholly) coincide with the boundaries of one or more material entities or have locations determined in relation to some material entity
+ A hole in a portion of cheese; a rabbit hole; the Grand Canyon; the Piazza San Marco; the kangaroo-joey-containing hole of a kangaroo pouch; your left nostril (a fiat part - the opening - of your left nasal cavity); the lumen of your gut; the hold of a ship; the interior of the trunk of your car; hole in an engineered floor joist
+
+
+
+
+
+
+
+
+ 024-BFO
+
+ object
+ (Elucidation) An object is a material entity which manifests causal unity & is of a type instances of which are maximal relative to the sort of causal unity manifested
+ An organism; a fish tank; a planet; a laptop; a valve; a block of marble; an ice cube
+ A description of three primary sorts of causal unity is provided in Basic Formal Ontology 2.0. Specification and User Guide
+
+
+
+
+
+
+
+
+ 074-BFO
+
+ generically dependent continuant
+ g-dependent continuant
+ (Elucidation) A generically dependent continuant is an entity that exists in virtue of the fact that there is at least one of what may be multiple copies which is the content or the pattern that multiple copies would share
+ The pdf file on your laptop; the pdf file that is a copy thereof on my laptop; the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule; the content that is shared by a string of dots and dashes written on a page and the transmitted Morse code signal; the content of a sentence; an engineering blueprint
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 019-BFO
+
+ material entity
+ (Elucidation) A material entity is an independent continuant has some portion of matter as continuant part
+ A human being; the undetached arm of a human being; an aggregate of human beings
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 029-BFO
+
+ continuant fiat boundary
+ (Elucidation) A continuant fiat boundary b is an immaterial entity that is of zero, one or two dimensions & such that there is no time t when b has a spatial region as continuant part & whose location is determined in relation to some material entity
+ As for fiat point, fiat line, fiat surface
+
+
+
+
+
+
+
+
+ 028-BFO
+
+ immaterial entity
+ b is an immaterial entity =Def b is an independent continuant which is such that there is no time t when it has a material entity as continuant part
+ As for fiat point, fiat line, fiat surface, site
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Schlosser, Markus, "Agency", The Stanford Encyclopedia of Philosophy (Winter 2019 Edition), Edward N. Zalta (ed.), available at: https://plato.stanford.edu/archives/win2019/entries/agency/
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology
+
+ Agent
+ A Material Entity that bears an Agent Capability.
+
+
+
+
+
+
+
+
+ Schlosser, Markus, "Agency", The Stanford Encyclopedia of Philosophy (Winter 2019 Edition), Edward N. Zalta (ed.), available at: https://plato.stanford.edu/archives/win2019/entries/agency/
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology
+
+ Agent Capability
+ A Realizable Entity that inheres in a Material Entity in virtue of that Material Entity's capacity to realize it in some Planned Act.
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=Animal&oldid=1063873549
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology
+
+ Animal
+ An Organism that is multicellular, eukaryotic, heterotrophic, and capable of motility for part of its life.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Calendar System
+ A Temporal Reference System that is designed to organize and identify dates.
+ Calendars typically organize dates through the use of naming and temporal conventions based on Days, Weeks, Months, and Years.
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=Cartesian_coordinate_system&oldid=1058613323
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Cartesian Coordinate System
+ Rectangular Coordinate System
+ A Spatial Reference System that identifies each point in a spatial region of n-dimensions using an ordered n-tuple of numerical coordinates that are the signed (i.e. positive or negative) distances measured in the same unit of length from the zero point where the fixed perpendicular Coordinate System Axes meet.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ In traditional astronomical usage, civil time is mean solar time as calculated from midnight as the beginning of the Civil Day.
+ Note that Civil Time Reference System is more accurately represented as a Temporal Reference System that participates in an act of usage that is sanctioned by an appropriate civil authority. As such, it should be represented as a defined class.
+
+ Civil Time Reference System
+ A Temporal Reference System that is a statutory time scale as designated by civilian authorities to determine local time(s).
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ A single Clock Time System does not provide a complete means for identifying or measuring times. Depending on the particular Clock Time System, it may be compatible for use with one or more other Temporal Reference Systems.
+
+ Clock Time System
+ A Temporal Reference System that is a convention for keeping and displaying the Time of Day.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Measurement Unit of Currency
+ A Measurement Unit used in measurements of financial values.
+ U.S. Dollar, Euro, Yuan, South African Rand
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Descriptive Information Content Entity
+ Descriptive ICE
+ An Information Content Entity that consists of a set of propositions that describe some Entity.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Designative Information Content Entity
+ Designative ICE
+ An Information Content Entity that consists of a set of symbols that denote some Entity.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Directive Information Content Entity
+ Directive ICE
+ An Information Content Entity that consists of a set of propositions or images (as in the case of a blueprint) that prescribe some Entity.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Geospatial Coordinate Reference System
+ Geographic Coordinate System
+ A Spatial Reference System that is used to determine and identify the location of a point or object at or near the surface of the Earth.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Greenwich Mean Time (GMT) is the mean solar time at the Royal Observatory in Greenwich, London and has been superseded by Coordinated Universal Time (UTC).
+
+ Greenwich Mean Time Zone Identifier
+ A Time Zone Identifier that designates a spatial region where the local time is calculated according to the specified offset from Greenwich Mean Time.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology
+
+ Group of Agents
+ An Object Aggregate that has only Agents as parts.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ http://purl.obolibrary.org/obo/IAO_0000030
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Information Content Entity
+ ICE
+ A Generically Dependent Continuant that generically depends on some Information Bearing Entity and stands in relation of aboutness to some Entity.
+ Information Content Entity is here intended to be a class of Entities whose instances are the informational content of Information Bearing Entities. For example, three instances of information bearers -- such as a bar chart, color-coded map, and a written report -- each of which lists the GDP of Countries for the year 2010 are each different carriers of the same information content. It is this content that is generically dependent upon its carrier. This treatment of Informational Content Entity (cf. the Information Artifact Ontology) leads to a principle of subtyping based upon the relationship that ICE's have with the Entity they are about rather than characteristics such as format, language, measurement scale, or media. The latter are treated here as being Qualities of bearers.
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=Unit_of_measurement&oldid=1061038125
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Measurement Unit
+ A Descriptive Information Content Entity that describes a definite magnitude of a physical quantity, defined and adopted by convention and/or by law, that is used as a standard for measurement of the same physical quantity.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Acceleration
+ A Measurement Unit that is used as a standard for measurement of the rate at which objects change their velocities per unit of time.
+ feet per second per second, kilometers per second per second
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+ The type of particle quantified is typically either atoms or molecules, but may also be protons, neutrons, electrons, quarks, or other particles. The type of particle being measured should always be specified along with the measurement and its unit.
+
+ Measurement Unit of Amount of Substance
+ Measurement Unit of Chemical Amount
+ Measurement Unit of Enplethy
+ A Measurement Unit that is used as a standard for measurement of the number of a specified type of particle in a portion of matter.
+ mole, pound-mole
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Angle
+ A Measurement Unit that is used as a standard for measurement of the angle between two lines or planes in relation to a vertex.
+ degrees, radians
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Area
+ A Measurement Unit that is used as a standard for measurement of two-dimensional regions or Geospatial Regions.
+ square feet, square meters, acre, hectare
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Area Moment of Inertia
+ Measurement Unit of Second Area Moment
+ A Measurement Unit that is used as a standard for measurement of the distribution of Mass of an object with respect to an axis.
+ A measure of an object’s resistance to bending or deflection.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Density
+ A Measurement Unit that is used as a standard for measurement of the mass of an object per unit of its total volume.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Electromagnetic Force
+ A Measurement Unit that is used as a standard for measurement of the electromagnetic force between electrically charged entities.
+ volt, ampere, coulomb
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Energy
+ A Measurement Unit that is used as a standard for measurement of the Amount of work that is available in an object.
+ ft-lbs, calorie, horsepower, kilowatt
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Flow
+ A Measurement Unit that is used as a standard for measurement of the rate at which portions of a substance pass per unit of time.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Force
+ A Measurement Unit that is used as a standard for measurement of interactions in which the Motion or Velocity of an object is changed, unless the interaction is opposed.
+ newton, dyne, pound force
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Frequency
+ A Measurement Unit that is used as a standard for measurement of the number of times an event repeats per unit of time.
+ hertz, revolutions per minute
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Impulse
+ A Measurement Unit that is used as a standard for measurement of the integral of a Force applied to a portion of matter over a temporal interval.
+ N s, dyne second
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Length
+ A Measurement Unit that is used as a standard for measurement of one-dimensional regions or Geospatial Regions.
+ foot, meter, kilometer, mile
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Mass
+ A Measurement Unit that is used as a standard for measurement of an object's resistance to Acceleration when a Force is applied to the object.
+ ounce, gram, pound
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Mass Flow Rate
+ A Measurement Unit of Flow that is used as a standard for measurement of the rate at which the Mass of a substance passes per unit time.
+ kilogram per second, slug per second, pound per second
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Momentum
+ A Measurement Unit that is used as a standard for measurement of the Momentum of a portion of matter that is in Motion.
+ kg m/s, slug ft/s, g m/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Power
+ A Measurement Unit that is used as a standard for measurement of rates of work.
+ watt, horsepower
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Pressure
+ A Measurement Unit that is used as a standard for measurement of Force applied perpendicular to a surface per unit area.
+ pascal, atmosphere, pound-force per square inch
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Rotational Inertia
+ Measurement Unit of Moment of Inertia
+ Measurement Unit of Rotational Mass
+ A Measurement Unit that is used as a standard for measurement of the distribution of Mass of an object with respect to its axis of rotation.
+ A measure of an object’s resistance to change in its state of rotation.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Sound Level
+ A Measurement Unit that is used as a standard for measurement of the level (the loudness) of sounds.
+ decibels, sones
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Speed
+ A Measurement Unit that is used as a standard for measurement of the rates at which objects traverse distance.
+ miles per hour, kilometers per hour, knot, mach
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Temperature
+ A Measurement Unit that is used as a standard for measurement of the thermal energy in an object.
+ celsius, fahrenheit, kelvin
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Time
+ A Measurement Unit that is used as a standard for measurement of temporal regions.
+ second, minute, hour, day
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Torque
+ Measurement Unit of Moment of Force
+ Measurement Unit of Rotational Force
+ A Measurement Unit that is used as a standard for measurement of the rate of change of angular momentum of an object.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Volume
+ A Measurement Unit that is used as a standard for measurement of sites or three-dimensional regions or Geospatial Regions.
+ cubic feet, cubic meter, quart, liter
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Volumetric Flow Rate
+ A Measurement Unit of Flow that is used as a standard for measurement of the rate at which volumes of fluid pass per unit time.
+ cubic metres per second, standard cubic centimeters per minute, cubic feet per second, gallons per minute
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Measurement Unit of Work
+ A Measurement Unit that is used as a standard for measurement of displacements of points to which Forces have been applied.
+ joule, erg, kilowatt hour
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Military Time Zone Identifier
+ A Time Zone Identifier that designates a spatial region where the local time is calculated according to the specified offset from Zulu time, which has no offset from Coordinated Universal Time.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology
+
+ Organism
+ An Object that is an Animal or Plant.
+
+
+
+
+
+
+
+
+ http://purl.obolibrary.org/obo/OBI_0000245
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology
+ Members of organizations are either Organizations themselves or individual Persons. Members can bear specific Organization Member Roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the Organization by the organization members.
+
+ Organization
+ A Group of Agents which can be the bearer of roles, has members, and has a set of organization rules.
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=Human&oldid=1063145185
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology
+
+ Person
+ Human
+ An Animal that is a member of the species Homo sapiens.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Reference System
+ A Descriptive Information Content Entity that describes a set of standards for organizing and understanding data of the specified type or domain.
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=Solar_calendar&oldid=1058016588
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Solar Calendar System
+ A Calendar System that is designed to organize and identify dates based on the cycles of an Astronomical Body's Orbit around the Sun.
+ Unless otherwise specified, a Solar Calendar System is assumed to be relative to the Orbit of the Earth around the Sun.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Solar Time Reference System
+ A Temporal Reference System that is based on the position of the Sun in the sky.
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=Coordinate_system&oldid=1060461397
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Note that, while reference systems and reference frames are treated as synonyms here, some people treat them as related but separate entities. See: http://www.ggos-portal.org/lang_en/GGOS-Portal/EN/Topics/GeodeticApplications/GeodeticReferenceSystemsAndFrames/GeodeticReferenceSystemsAndFrames.html
+
+ Spatial Reference System
+ Coordinate System
+ Spatial Coordinate System
+ Spatial Reference Frame
+ A Reference System that describes a set of standards for uniquely identifying the position of an entity or the direction of a vector within a defined spatial region by means of measurements along one or more Coordinate System Axes.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Spatial Region Identifier
+ A Designative Information Content Entity that designates some Spatial Region.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Temporal Reference System
+ Temporal Reference Frame
+ Time Scale
+ A Reference System that describes a set of standards for measuring time as well as understanding the context of and organizing temporal data.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Standards of date, time, and time zone data formats:
+ISO/WD 8601-2 (http://www.loc.gov/standards/datetime/iso-tc154-wg5_n0039_iso_wd_8601-2_2016-02-16.pdf)
+W3C (https://www.w3.org/TR/NOTE-datetime)
+ There is no class 'Time Zone' (the region), only 'Time Zone Identifier' (the designator for some region). Instances of 'Time Zone Identifier' should be related to instances of 'Information Bearing Entity' by means of the object properites 'uses time zone identifier' and 'time zone identifier used by' as appropriate. This is supposed to be analogous to the way we represent the relationship between measurement values and measurement units, where the relevant instance of Information Bearing Entity 'uses measurement unit' some instance of Measurement Unit (i.e., an instance of Information Content Entity).
+
+ Time Zone Identifier
+ A Spatial Region Identifier that designates the region associated with some uniform standard time for legal, commercial, or social purposes.
+
+
+
+
+
+
+
+
+ UT
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Universal Time Reference System
+ A Solar Time Reference System that is based on the average speed of the Earth's rotation and which uses the prime meridian at 0° longitude as a reference point.
+ A Solar Time Reference System that is based on the average speed of the Earth's rotation and which uses the prime meridian at 0� longitude as a reference point.
+
+
+
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Acre Measurement Unit
+ acre
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Afghanistan Afghani
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Albania Lek
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Algerian Dinar
+
+
+
+
+
+
+
+
+ A
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+1
+
+ Alpha Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Angolan Kwanza
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Angstrom Measurement Unit
+ Angstrom
+ Å
+ Ångström
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Argentine Peso
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Armenian Dram
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Atmosphere Measurement Unit
+ atm
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Australian Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Azerbaijan Manat
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Bangladesh Taka
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Bar Measurement Unit
+ bar
+
+
+
+
+
+
+
+
+ TCB
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ "Barycentric Coordinate Time (TCB, from the French Temps-coordonnée barycentrique) is a coordinate time standard intended to be used as the independent variable of time for all calculations pertaining to orbits of planets, asteroids, comets, and interplanetary spacecraft in the Solar system. It is equivalent to the proper time experienced by a clock at rest in a coordinate frame co-moving with the barycenter of the Solar system: that is, a clock that performs exactly the same movements as the Solar system but is outside the system's gravity well. It is therefore not influenced by the gravitational time dilation caused by the Sun and the rest of the system."
+From: (https://en.wikipedia.org/wiki/Barycentric_Coordinate_Time)
+ "Barycentric Coordinate Time (TCB, from the French Temps-coordonn�e barycentrique) is a coordinate time standard intended to be used as the independent variable of time for all calculations pertaining to orbits of planets, asteroids, comets, and interplanetary spacecraft in the Solar system. It is equivalent to the proper time experienced by a clock at rest in a coordinate frame co-moving with the barycenter of the Solar system: that is, a clock that performs exactly the same movements as the Solar system but is outside the system's gravity well. It is therefore not influenced by the gravitational time dilation caused by the Sun and the rest of the system."
+From: (https://en.wikipedia.org/wiki/Barycentric_Coordinate_Time)
+
+ Barycentric Coordinate Time
+
+
+
+
+
+
+
+
+ TDB
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ TDB is a linear scaling of Barycentric Coordinate Time (TCB) and is a relativistic coordinate time scale used in astronomy as a time standard that accounts for time dilation when calculating Orbits and Ephemerides of Astronomical Bodies and interplanetary Spacecraft in the Solar System. TDB is a successor of Ephemeris Time (ET) and is nearly equivalent to the time scale Teph used for DE405 planetary and lunar ephemerides generated by the Jet Propulsion Laboratory.
+
+ Barycentric Dynamical Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Bayre Measurement Unit
+ ba
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Belarussian Ruble
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Bhutan Ngultrum
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Binary Degree Measurement Unit
+ Binary Radian
+ Brad
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Bolivia Boliviano
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Bosnia And Herzegovina Convertible Mark
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Botswana Pula
+
+
+
+
+
+
+
+
+ B
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+2
+
+ Bravo Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Brazilian Real
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ British Thermal Unit Measurement Unit
+ BTU
+ Btu
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Brunei Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Bulgarian Lev
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Burundi Franc
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ CFA Franc
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ CFP Franc
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Calorie Measurement Unit
+ cal
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Cambodian Riel
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Canadian Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Cape Verde Escudo
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Centigram Measurement Unit
+ cg
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Centiliter Measurement Unit
+ cL
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Centimeter Measurement Unit
+ cm
+
+
+
+
+
+
+
+
+ C
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+3
+
+ Charlie Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Chilean Peso
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Chinese Renminbi
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Colombian Peso
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Comoros Franc
+
+
+
+
+
+
+
+
+
+ UTC
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ UTC is a variant of Universal Time that is calculated by combining Universal Time 1 with International Atomic Time by occasionally adding leap seconds to TAI in order to maintain UTC within 0.9 seconds of UT1. The difference between UTC and UT1 is called DUT1 and always has a value between -0.9 seconds and +0.9 seconds. Coordinated Universal Time is the current basis for civil time and is the reference time for time zones, whose local times are defined based on an offset from UTC.
+
+ Coordinated Universal Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Costa Rica Colon
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Croatia Kuna
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Cubic Centimeter Measurement Unit
+ cm^3
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Cubic Decimeter Measurement Unit
+ dm^3
+
+
+
+
+
+
+
+
+ cusec
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Cubic Feet Per Second Measurement Unit
+ ft^3/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Cubic Foot Measurement Unit
+ ft^3
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Cubic Inch Measurement Unit
+ in^3
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Cubic Meter Measurement Unit
+ m^3
+
+
+
+
+
+
+
+
+ m^3/s
+ cumec
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Cubic Meter Per Second Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Cubic Millimeter Measurement Unit
+ mm^3
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Cubic Yard Measurement Unit
+ yrd^3
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Czech Koruna
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Danish Krone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Day Measurement Unit
+
+
+
+
+
+
+
+
+ Donna Jones
+ Olivia Hobai
+ dBi
+ https://shopdelta.eu/dbi-power-gain-of-isotropic-antenna_l2_aid836.html
+ https://www.techtarget.com/whatis/definition/decibels-relative-to-isotropic-radiator-dBi
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Decibel Isotropic Measurement Unit
+ Decibels Over Isotropic
+ Decibels Over Isotropic Antenna
+ Decibels Relative to Isotrope
+ Decibels Relative to Isotropic Radiator
+ Decibels Relative to an Isotropic Reference Antenna
+
+
+
+
+
+
+
+
+ dB
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Decibel Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Decigram Measurement Unit
+ dg
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Deciliter Measurement Unit
+ dL
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Decimeter Measurement Unit
+ dm
+
+
+
+
+
+
+
+
+ degree Celsius
+ °C
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Degree Celsius Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Degree Fahrenheit Measurement Unit
+ °F
+
+
+
+
+
+
+
+
+ °
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Degree Measurement Unit
+
+
+
+
+
+
+
+
+ D
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+4
+
+ Delta Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Democratic Republic Of Congo Franc
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Dominican Peso
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Dyne Measurement Unit
+ dyn
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Dyne Second Measurement Unit
+ dyne s
+ dyne second
+
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=Earth-centered,_Earth-fixed_coordinate_system&oldid=1062678600
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Earth-Centered Earth-Fixed Coordinate System
+ Conventional Terrestrial Coordinate System
+ ECEF
+ ECR
+ Earth Centered Earth Fixed
+ Earth Centered Rotational Coordinate System
+ Earth-Centered Earth-Fixed
+ Earth-Centered, Earth-Fixed
+ A Geospatial and Cartesian Coordinate System that identifies positions using an x-axis, y-axis, and z-axis coordinate where the zero point is the center of the Earth, the z-Axis extends toward the North Pole but does not always coincide exactly with the Earth's Axis of Rotation, the x-Axis extends through the intersection of the Prime Meridian and the Equator, the y-Axis completes the right-handed system, and all three axes are fixed to the Earth such that they rotate along with the Earth.
+
+
+
+
+
+
+
+
+ E
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+5
+
+ Echo Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Egyptian Pound
+
+
+
+
+
+
+
+
+ ET
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ ET is an astronomical time scale that was adopted as a standard in 1952 by the IAU but has since been superseded and is no longer actively used. ET is based on the ephemeris second, which was defined as a fraction of the tropical year for 1900 January 01 as calculated using Newcomb's 1895 tables of the Sun. ET was designed to avoid problems caused by variations in Earth's rotational period and was used for Solar System ephemeris calculations until being replaced by Terrestrial Dynamical Time (TDT) in 1979.
+
+ Ephemeris Time
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Erg Measurement Unit
+ erg
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Ethiopian Birr
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Euro
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Feet Per Second Measurement Unit
+ ft/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Feet Per Second Per Second Measurement Unit
+ ft/s/s
+ ft/s^2
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Fiji Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Foot Measurement Unit
+ ft
+
+
+
+
+
+
+
+
+ F
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+6
+
+ Foxtrot Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+0
+
+ GMT
+ Greenwich Mean Time
+
+
+
+
+
+
+
+
+ NST
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-3:30
+ Newfoundland Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-1
+ CAT
+ Central African Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-10
+ HST
+ Hawaii Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-11
+ MIT
+ Midway Islands Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-2
+ BET
+ Brazil Eastern Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-3
+ AGT
+ Argentina Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-4
+ PRT
+ Puerto Rico and US Virgin Islands Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-5
+ EST
+ Eastern Standard Time
+ IET
+ Indiana Eastern Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-6
+ CST
+ Central Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-7
+ MST
+ Mountain Standard Time
+ PNT
+ Phoenix Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-8
+ PST
+ Pacific Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT-9
+ AST
+ Alaska Standard Time
+
+
+
+
+
+
+
+
+ IRST
+ IT
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+3:30
+ Iran Standard Time
+ Iran Time
+
+
+
+
+
+
+
+
+ IST
+ SLST
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+5:30
+ Indian Standard Time
+ Sri Lanka Standard Time
+
+
+
+
+
+
+
+
+ ACST
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+9:30
+ Australian Central Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+1
+ ECT
+ European Central Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+10
+ AET
+ Australia Eastern Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+11
+ SST
+ Solomon Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+12
+ NST
+ New Zealand Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+2
+ EET
+ Eastern European Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+3
+ EAT
+ Eastern African Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+4
+ NET
+ Near East Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+5
+ PLT
+ Pakistan Lahore Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+6
+ BST
+ Bangladesh Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+7
+ VST
+ Vietnam Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+8
+ CTT
+ China Taiwan Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ GMT+9
+ JST
+ Japan Standard Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Gallon Measurement Unit
+ gal
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Gallon Per Minute Measurement Unit
+ gal/min
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Gambian Dalasi
+
+
+
+
+
+
+
+
+ TCG
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ "TCG is a coordinate time standard intended to be used as the independent variable of time for all calculations pertaining to precession, nutation, the Moon, and artificial satellites of the Earth. It is equivalent to the proper time experienced by a clock at rest in a coordinate frame co-moving with the center of the Earth: that is, a clock that performs exactly the same movements as the Earth but is outside the Earth's gravity well. It is therefore not influenced by the gravitational time dilation caused by the Earth."
+From: (https://en.wikipedia.org/wiki/Geocentric_Coordinate_Time)
+
+ Geocentric Coordinate Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Georgian Lari
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Ghana Cedi
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Gigahertz Measurement Unit
+ GHz
+
+
+
+
+
+
+
+
+ GARS
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Global Area Reference System
+
+
+
+
+
+
+
+
+ G
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+7
+
+ Golf Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Gradian Measurement Unit
+ Gon
+ Grad
+ Grade
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Gram Measurement Unit
+ g
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Gram-Mole Measurement Unit
+ g-mol
+ gram-mole
+
+
+
+
+
+
+
+
+ g/cm^3
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Gram Per Cubic Centimeter Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Gram Per Second Measurement Unit
+ g/s
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=Gregorian_calendar&oldid=1062360692
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ The Gregorian Calendar was instituted by Pope Gregory XIII via papal bull on 24 February 1582 as a reform of the Julian Calendar to stop the drift of the calendar with respect to the equinoxes and solstices. The Gregorian Calendar is currently the most widely used civil Calendar System in the world and is 13 days ahead of the Julian Calendar Date.
+
+ Gregorian Calendar
+ A Solar Calendar System that has a regular Year of 365 24-Hour Days divided into 12 Months with a leap day added at the end of February every 4 Years except Years that are evenly divisible by 100 but not 400 such that there are 97 leap Years every 400 Years and the average length of a Gregorian Year is 365.2425 Days (365 Days 5 Hours 49 Minutes 12 Seconds).
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Guatemala Quetzal
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Guinean Franc
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Guyana Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Haiti Gourde
+
+
+
+
+
+
+
+
+ hertz
+ Hz
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Hertz Measurement Unit
+ cycles per second
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Honduras Lempira
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ HongKong Dollar
+
+
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Horsepower Measurement Unit
+ hp
+
+
+
+
+
+
+
+
+ H
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+8
+
+ Hotel Time Zone
+
+
+
+
+
+
+
+
+ h
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Hour Measurement Unit
+ hr
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Hungary Forint
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Iceland Krona
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Inch Measurement Unit
+ in
+
+
+
+
+
+
+
+
+ I
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+9
+
+ India Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Indian Rupee
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Indonesia Rupiah
+
+
+
+
+
+
+
+
+ TAI
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ TAI is a time standard the values of which are generated by calculating the weighted average of the measurements of more than 400 atomic clocks and is based on the International System of Units (SI) definition of one second equals the time it takes a Cesium-133 atom at the ground state to oscillate exactly 9,192,631,770 times. TAI is extremely precise, but does not perfectly synchronize with Earth times, which is why TAI and UT1 are both used to determine UTC. TAI serves as the main realization of TT.
+
+ International Atomic Time
+
+
+
+
+
+
+
+
+ Alken, P., Thébault, E., Beggan, C.D. et al. International Geomagnetic Reference Field: the thirteenth generation. Earth Planets Space 73, 49 (2021). https://doi.org/10.1186/s40623-020-01288-x , https://www.iaga-aiga.org/
+ Alken, P., Th�bault, E., Beggan, C.D. et al. International Geomagnetic Reference Field: the thirteenth generation. Earth Planets Space 73, 49 (2021). https://doi.org/10.1186/s40623-020-01288-x , https://www.iaga-aiga.org/
+ This global main field model provides magnetic field values for any location on Earth, e.g. for navigational purposes (declination) or as a standard for core field subtraction for aeromagnetic surveys. An updated version is adopted by International Association of Geomagnetism and Aeronomy (IAGA) every 5 years).
+
+ International Geomagnetic Reference Field
+
+
+
+
+
+
+
+
+ ITRS
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ The ITRS definition fulfills the following conditions:
+1. It is geocentric, the center of mass being defined for the whole earth, including oceans and atmosphere.
+2. The unit of length is the metre (SI). This scale is consistent with the TCG time coordinate for a geocentric local frame, in agreement with IAU and IUGG (1991) resolutions. This is obtained by appropriate relativistic modelling.
+3. Its orientation was initially given by the BIH orientation at 1984.0.
+4. The time evolution of the orientation is ensured by using a no-net-rotation condition with regards to horizontal tectonic motions over the whole earth.
+From: (https://www.iers.org/IERS/EN/Science/ITRS/ITRS.html)
+
+ International Terrestrial Reference System
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Iranian Rial
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Israel Shekel
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Jamaican Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Japanese Yen
+
+
+
+
+
+
+
+
+ Teph
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Teph (the 'eph' is written as subscript) is an ephemeris time argument developed and calculated at the Jet Propulsion Laboratory (JPL) and implemented in a series of numerically integrated Development Ephemerides (DE), including the currently used DE405. Teph is characterized as a relativistic coordinate time that is nearly equivalent to the IAU's definition of TCB, though Teph is not currently an IAU time standard. Teph is used by the JPL to generate the ephemerides it publishes to support spacecraft navigation and astronomy.
+
+ Jet Propulsion Laboratory Ephemeris Time Argument
+ JPL Ephemeris Time
+
+
+
+
+
+
+
+
+
+
+ joule
+ J
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Joule Measurement Unit
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=Julian_calendar&oldid=1063127575
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ The Julian Calendar was proposed by Julius Caesar as a reform of the Roman Calendar, took effect on 1 January 46 BC, and was the predominant Calendar System in Europe until being largely replaced by the Gregorian Calendar.
+
+ Julian Calendar
+ A Solar Calendar System that has a regular Year of 365 24-Hour Days divided into 12 Months with a leap day added at the end of February every 4 Years such that the average length of a Julian Year is 365.25 Days.
+
+
+
+
+
+
+
+
+ J
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Juliet time is used as an indexical to refer to local time without otherwise specifying the time zone.
+
+ Juliet Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Kazakhstan Tenge
+
+
+
+
+
+
+
+
+ kelvin
+ K
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kelvin Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Kenyan Shilling
+
+
+
+
+
+
+
+
+ K
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+10
+
+ Kilo Time Zone
+
+
+
+
+
+
+
+
+ kg/cm^2
+ kgf/cm^2
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilogram Force Per Centimeter Square Measurement Unit
+ Kilogram Per Square Centimeter Measurement Unit
+ Kilopond Per Centimeter Square Measurement Unit
+
+
+
+
+
+
+
+
+ kilogram
+ kg
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilogram Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilogram Meter Per Second Measurement Unit
+ kg m/s
+
+
+
+
+
+
+
+
+ kg-m^2
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilogram Meter Square Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilogram-Mole Measurement Unit
+ kg-mol
+ kilogram-mole
+
+
+
+
+
+
+
+
+ kg/m^3
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilogram Per Cubic Meter Measurement Unit
+
+
+
+
+
+
+
+
+ kg/L
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilogram Per Liter Measurement Unit
+
+
+
+
+
+
+
+
+ kg/s
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilogram Per Second Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilohertz Measurement Unit
+ kHz
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kiloliter Measurement Unit
+ kL
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilometer Measurement Unit
+ km
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilometers Per Hour Measurement Unit
+ km/h
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilometers Per Second Measurement Unit
+ km/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilometers Per Second Per Second Measurement Unit
+ km/s/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilomole Measurement Unit
+ kilomole
+ kmol
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilonewton Measurement Unit
+ kN
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilopond Measurement Unit
+ Kilogram Force Measurement Unit
+ Kilogram-Force
+ kgf
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Kilovolt Ampere Measurement Unit
+ kVA
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Knot Measurement Unit
+ kn
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Kuwaiti Dinar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Kyrgyzstan Som
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Laos Kip
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Lebanese Pound
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Lesotho Loti
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Liberian Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Libyan Dinar
+
+
+
+
+
+
+
+
+ L
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+11
+
+ Lima Time Zone
+
+
+
+
+
+
+
+
+ L
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Liter Measurement Unit
+ Litre
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Liter Per Second Measurement Unit
+ l/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Long Ton Measurement Unit
+ Displacement Ton
+ Gross Ton
+ Imperial Ton
+ Weight Ton
+ ton (UK)
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Macao Pataca
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Macedonian Denar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Mach Measurement Unit
+ M
+ Ma
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Madagascar Malagasy Ariary
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Malawi Kwacha
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Malaysia Ringgit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Mauritania Ouguiya
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Mauritius Rupee
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Megahertz Measurement Unit
+ MHz
+
+
+
+
+
+
+
+
+ meter
+ m
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Meter Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Meters Per Second Measurement Unit
+ m/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Meters Per Second Per Second Measurement Unit
+ m/s/s
+ m/s^2
+
+
+
+
+
+
+
+
+ t
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Metric Ton Measurement Unit
+ tonne
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Mexican Peso
+
+
+
+
+
+
+
+
+ M
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Mike Time Zone is the same local time as Yankee Time Zone, but is 1 Day (i.e. 24 Hours) ahead of Yankee Time Zone as they are on opposite sides of the International Date Line.
+ Offset from Universal Coordinated Time = UTC+12
+
+ Mike Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Mile Measurement Unit
+ mi
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Miles Per Hour Measurement Unit
+ mi/h
+ mph
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Miles Per Second Measurement Unit
+ mi/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Miles Per Second Per Second Measurement Unit
+ mi/s/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Milliampere Measurement Unit
+ mA
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Millibar Measurement Unit
+ mb
+ mbar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Milligram Measurement Unit
+ mg
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Milliliter Measurement Unit
+ mL
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Millimeter Measurement Unit
+ mm
+
+
+
+
+
+
+
+
+ min
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Minute Measurement Unit
+
+
+
+
+
+
+
+
+ '
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Minute of Arc Measurement Unit
+ Arcminute
+ MOA
+ am
+ amin
+ arcmin
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Moldovan Leu
+
+
+
+
+
+
+
+
+ mole
+ mol
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+ One mole contains exactly 6.02214076×10^23 elementary entities.
+
+ Mole Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Mongolia Tugrik
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Month Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Morocco Dirham
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Mozambique Metical
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Myanmar Kyat
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Namibia Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Nanometer Measurement Unit
+ Nanometre
+ nm
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Nautical Mile Measurement Unit
+ M
+ NM
+ nmi
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Nepalese Rupee
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ New Zealand Dollar
+
+
+
+
+
+
+
+
+ newton
+ N
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Newton Measurement Unit
+
+
+
+
+
+
+
+
+ N-m
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Newton Meter Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Newton Second Measurement Unit
+ N s
+ Newton second
+ Ns
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Newton Second Per Kilogram Measurement Unit
+ Ns/kg
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Nicaragua Cordoba Oro
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Nigeria Naira
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ North Korean Won
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Norwegian Krone
+
+
+
+
+
+
+
+
+ N
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-1
+
+ November Time Zone
+
+
+
+
+
+
+
+
+ O
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-2
+
+ Oscar Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Ounce Measurement Unit
+ oz
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Pakistani Rupee
+
+
+
+
+
+
+
+
+ P
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-3
+
+ Papa Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Papua New Guinea Kina
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Paraguay Guarani
+
+
+
+
+
+
+
+
+ pascal
+ Pa
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Pascal Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Peru Nuevo Sol
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Philippine Peso
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Phon Measurement Unit
+ phon
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Pint Measurement Unit
+ pt
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Poland Zloty
+
+
+
+
+
+
+
+
+ lb ft
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Pound Foot Measurement Unit
+
+
+
+
+
+
+
+
+ lb ft s^2
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Pound Foot Second Square Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Pound Force Measurement Unit
+ lbf
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Pound Measurement Unit
+ lb
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Pound-Mole Measurement Unit
+ lb-mol
+ lbmol
+ pound-mole
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Pound Per Second Measurement Unit
+ lb/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Pounds Per Square Inch Measurement Unit
+ psi
+
+
+
+
+
+
+
+
+ qt
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Quart Measurement Unit
+
+
+
+
+
+
+
+
+ m^4
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Quartic Meter Measurement Unit
+
+
+
+
+
+
+
+
+ Q
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-4
+
+ Quebec Time Zone
+
+
+
+
+
+
+
+
+ radian
+ rad
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Radian Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Revolutions Per Day Measurement Unit
+ r/day
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Revolutions Per Minute Measurement Unit
+ r/min
+ rpm
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Romanian Leu
+
+
+
+
+
+
+
+
+ R
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-5
+
+ Romeo Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Russian Rouble
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Rwanda Franc
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Samoa Tala
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Sao Tome Principe Dobra
+
+
+
+
+
+
+
+
+ second
+ s
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Second Measurement Unit
+
+
+
+
+
+
+
+
+ "
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Second of Arc Measurement Unit
+ Arcsecond
+ arcsec
+ as
+ asec
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Serbian Dinar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Seychelles Rupee
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Shaft Horsepower Measurement Unit
+ shp
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Short Ton Measurement Unit
+ Net Ton
+ ton (US)
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Sierra Leone Leone
+
+
+
+
+
+
+
+
+ S
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-6
+
+ Sierra Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Singapore Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Slug Foot Per Second Measurement Unit
+ slug ft/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Slug Measurement Unit
+ slug
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Slug Per Second Measurement Unit
+ slug/s
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Solomon Island Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Sone Measurement Unit
+ sone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ South Africa Rand
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ South Korean Won
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ South Sudanese Pound
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Square Centimeter Measurement Unit
+ cm^2
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Square Decimeter Measurement Unit
+ dm^2
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Square Foot Measurement Unit
+ ft^2
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Square Inch Measurement Unit
+ in^2
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Square Kilometer Measurement Unit
+ km^2
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Square Meter Measurement Unit
+ m^2
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Square Mile Measurement Unit
+ mi^2
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Square Millimeter Measurement Unit
+ mm^2
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Square Yard Measurement Unit
+ yd^2
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Sri Lanka Rupee
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ St Helena Pound
+
+
+
+
+
+
+
+
+ sccm
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Standard Cubic Centimeter Per Minute Measurement Unit
+ cm^3/min
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Sudanese Pound
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Surinamese Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Swaziland Lilangeni
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Swedish Krona
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Swiss Franc
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Syrian Pound
+
+
+
+
+
+
+
+
+ T
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Tablespoon Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Tajikistan Somoni
+
+
+
+
+
+
+
+
+ T
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-7
+
+ Tango Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Tanzania Shilling
+
+
+
+
+
+
+
+
+ t
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Teaspoon Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Terahertz Measurement Unit
+ THz
+
+
+
+
+
+
+
+
+ TT
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ TT is an astronomical time standard that is a theoretical ideal designed to be free of the irregularities in Earth's rotation and is primarily used for time measurements of astronomical observations made from the surface of Earth. It was formerly called Terrestrial Dynamical Time (TDT), which was formulated to replace Ephemeris Time (ET).
+
+ Terrestrial Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Thai Baht
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Tonga Pa anga
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Trinidad and Tobago Dollar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Tunisian Dinar
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Turkish Lira
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Turkmenistan Manat
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Turn Measurement Unit
+ Cycle
+ Full Circle
+ Revolution
+ Rotation
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=12-hour_clock&oldid=1057602523
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Twelve-Hour Clock Time System
+ 12-Hour Clock
+ 12-Hour Clock Time System
+ Twelve Hour Clock
+ Twelve Hour Clock Time System
+ Twelve-Hour Clock
+ A Clock Time System for keeping the Time of Day in which the Day runs from midnight to midnight and is divided into two intervals of 12 Hours each, where: the first interval begins at midnight, ends at noon, and is indicated by the suffix 'a.m.'; the second interval begins at noon, ends at midnight, and is indicated by the suffix 'p.m.'; and the midnight and noon Hours are numbered 12 with subsequent Hours numbered 1-11.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Twenty Foot Equivalent Unit
+
+
+
+
+
+
+
+
+ https://en.wikipedia.org/w/index.php?title=24-hour_clock&oldid=1063744105
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Twenty-Four-Hour Clock Time System
+ 24-Hour Clock
+ 24-Hour Clock Time System
+ Military Time
+ Military Time System
+ Twenty-Four Hour Clock Time System
+ Twenty-Four-Hour Clock
+ A Clock Time System for time keeping in which the Day runs from midnight to midnight and is divided into 24 Hours, indicated by the Hours passed since midnight, from 0 to 23.
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Uganda Shilling
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Ukraine Hryvnia
+
+
+
+
+
+
+
+
+ U
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-8
+
+ Uniform Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ United Kingdom Pound
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ United States Dollar
+
+
+
+
+
+
+
+
+ UT0
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ UT0 is a variant of Universal Time that is measured by observing the diurnal motion of stars or extragalactic radio sources at a specific location on Earth. It does not take into consideration distorting factors, in particular polar motion, such that its value will differ based on the location it is measured at.
+
+ Universal Time 0
+
+
+
+
+
+
+
+
+ UT1
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ UT1 is a derivation of UT0 that takes into account distortions caused by polar motion and is proportional to the rotation angle of the Earth with respect to distant quasars, specifically, the International Celestial Reference Frame (ICRF). UT1 is currently the most widely used variant of Universal Time and has the same value everywhere on Earth.
+
+ Universal Time 1
+ Astronomical Time
+
+
+
+
+
+
+
+
+ UT1A
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Universal Time 1 A
+
+
+
+
+
+
+
+
+ UT1D
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Universal Time 1 D
+
+
+
+
+
+
+
+
+ UT1F
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Universal Time 1 F
+
+
+
+
+
+
+
+
+ UT1R
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ UT1R is a variant of Universal Time that is a smoothed version of UT1 by filtering out periodic variations due to tidal waves.
+
+ Universal Time 1 R
+
+
+
+
+
+
+
+
+ UT2
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ UT2 is a variant of Universal Time that smooths UT1 by accounting for both polar motion and variations in Earth's rotation due to seasonal factors, such as changes in vegetation and water or snow distribution.
+
+ Universal Time 2
+
+
+
+
+
+
+
+
+ UTM
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ Universal Transverse Mercator Reference System
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Unix Time is a Temporal Reference System for describing a point in time, defined as the number of seconds that have elapsed since 00:00:00 Coordinated Universal Time (UTC) Thursday, 1 January 1970 minus the number of leap seconds that have taken place since then.
+(See: https://en.wikipedia.org/wiki/Unix_time)
+
+ Unix Time
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Uruguay Peso
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Uzbekistan Sum
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Vanuatu Vatu
+
+
+
+
+
+
+
+
+ V
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-9
+
+ Victor Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Viet Nam Dong
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Volt Ampere Measurement Unit
+ VA
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Volt Measurement Unit
+ V
+
+
+
+
+
+
+
+
+ watt
+ W
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Watt Measurement Unit
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Week Measurement Unit
+
+
+
+
+
+
+
+
+ W
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-10
+
+ Whiskey Time Zone
+
+
+
+
+
+
+
+
+ WGS 84
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ "WGS 84 is an Earth-centered, Earth-fixed terrestrial reference system and geodetic datum. WGS 84 is based on a consistent set of constants and model parameters that describe the Earth's size, shape, and gravity and geomagnetic fields. WGS 84 is the standard U.S. Department of Defense definition of a global reference system for geospatial information and is the reference system for the Global Positioning System (GPS). It is compatible with the International Terrestrial Reference System (ITRS)."
+From: (http://www.unoosa.org/pdf/icg/2012/template/WGS_84.pdf)
+
+ World Geodetic System 1984
+
+
+
+
+
+
+
+
+ WGRS
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+
+ World Geographic Reference System
+
+
+
+
+
+
+
+
+ X
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-11
+
+ X-ray Time Zone
+
+
+
+
+
+
+
+
+ Y
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC-12
+ Yankee Time Zone is the same local time as Mike Time Zone, but is 1 Day (i.e. 24 Hours) behind Mike Time Zone as they are on opposite sides of the International Date Line.
+
+ Yankee Time Zone
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Yard Measurement Unit
+ yrd
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/UnitsOfMeasureOntology
+
+ Year Measurement Unit
+ yr
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Yemeni Rial
+
+
+
+
+
+
+
+
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/CurrencyUnitOntology
+
+ Zambia Kwacha
+
+
+
+
+
+
+
+
+ Z
+ http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
+ Offset from Universal Coordinated Time = UTC+0
+
+ Zulu Time Zone
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/03_TECHNICAL_CORE/ontology/imports/iao.owl b/03_TECHNICAL_CORE/ontology/imports/iao.owl
deleted file mode 100644
index 14b867d..0000000
--- a/03_TECHNICAL_CORE/ontology/imports/iao.owl
+++ /dev/null
@@ -1,8532 +0,0 @@
-
-
-
-
- en
- Adam Goldstein
- Alan Ruttenberg
- Albert Goldfain
- Barry Smith
- Bjoern Peters
- Carlo Torniai
- Charles Tapley Hoyt
- Chris Mungall
- Chris Stoeckert
- Christian A. Boelling
- Clint Dowland
- Darren Natale
- David Osumi-Sutherland
- Gwen Frishkoff
- Holger Stenzhorn
- James A. Overton
- James Malone
- Jennifer Fostel
- Jie Zheng
- Jonathan Rees
- Larisa Soldatova
- Lawrence Hunter
- Mathias Brochhausen
- Matt Brush
- Melanie Courtot
- Michel Dumontier
- Paolo Ciccarese
- Pat Hayes
- Philippe Rocca-Serra
- Randy Dipert
- Ron Rudnicki
- Satya Sahoo
- Sivaram Arabandi
- Werner Ceusters
- William Duncan
- William Hogan
- Yongqun (Oliver) He
- The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.
- Information Artifact Ontology (IAO)
-
- An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO
- IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999
- IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999
-
- 2026-03-30
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
- Really of interest to developers only
- BFO OWL specification label
-
-
-
-
-
-
-
-
- Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
- Person:Alan Ruttenberg
- Really of interest to developers only
- BFO CLIF specification label
-
-
-
-
-
-
-
-
- editor preferred term
-
- The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
-
- editor preferred term
-
-
-
-
-
-
-
- example of usage
-
- A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
-
- example of usage
-
-
-
-
-
-
-
- in branch
- An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
- GROUP:OBI
- OBI_0000277
- in branch
-
-
-
-
-
-
-
- has curation status
- PERSON:Alan Ruttenberg
- PERSON:Bill Bug
- PERSON:Melanie Courtot
- has curation status
-
-
-
-
-
-
-
- definition
-
- The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
- 2012-04-05:
-Barry Smith
-
-The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
-
-Can you fix to something like:
-
-A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
-
-Alan Ruttenberg
-
-Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
-
-On the specifics of the proposed definition:
-
-We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
-
-Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
-
-We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
-
- definition
-
-
-
-
-
-
-
- editor note
-
- An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
-
- editor note
-
-
-
-
-
-
-
- term editor
-
- Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
- 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
-
- term editor
-
-
-
-
-
-
-
- alternative label
-
- A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
- OBO Operations committee
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
-
- alternative label
-
-
-
-
-
-
-
- definition source
-
- Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
- PERSON:Daniel Schober
- Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
-
- definition source
-
-
-
-
-
-
-
- has obsolescence reason
- Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
- PERSON:Alan Ruttenberg
- PERSON:Melanie Courtot
- has obsolescence reason
-
-
-
-
-
-
-
- curator note
-
- An administrative note of use for a curator but of no use for a user
- PERSON:Alan Ruttenberg
-
- curator note
-
-
-
-
-
-
-
- term tracker item
- the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588
-
- A URL for a request or discussion of an ontology term.
- Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
- Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
- The 'tracker item' can associate a tracker with a specific ontology term.
- term tracker item
-
-
-
-
-
-
-
-
- ontology term requester
-
- The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
- Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
- Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
- The 'term requester' can credit the person, organization or project who request the ontology term.
- ontology term requester
-
-
-
-
-
-
-
- is denotator type
- Relates an class defined in an ontology, to the type of it's denotator
- In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
- Alan Ruttenberg
- is denotator type
-
-
-
-
-
-
-
- imported from
-
- For external terms/classes, the ontology from which the term was imported
- PERSON:Alan Ruttenberg
- PERSON:Melanie Courtot
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
-
- imported from
-
-
-
-
-
-
-
- expand expression to
- ObjectProperty: RO_0002104
-Label: has plasma membrane part
-Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
-
- A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
- Chris Mungall
- expand expression to
-
-
-
-
-
-
-
- expand assertion to
- ObjectProperty: RO???
-Label: spatially disjoint from
-Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
-
- A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
- Chris Mungall
- expand assertion to
-
-
-
-
-
-
-
- first order logic expression
- PERSON:Alan Ruttenberg
- first order logic expression
-
-
-
-
-
-
-
- antisymmetric property
- part_of antisymmetric property xsd:true
- Use boolean value xsd:true to indicate that the property is an antisymmetric property
- Alan Ruttenberg
- antisymmetric property
-
-
-
-
-
-
-
-
- OBO foundry unique label
-
- An alternative name for a class or property which is unique across the OBO Foundry.
- The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
- PERSON:Alan Ruttenberg
- PERSON:Bjoern Peters
- PERSON:Chris Mungall
- PERSON:Melanie Courtot
- GROUP:OBO Foundry <http://obofoundry.org/>
- OBO foundry unique label
-
-
-
-
-
-
-
- has ID digit count
- Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
- Annotations:
- 'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
- 'has ID digit count' : 7,
- rdfs:label "RO id policy"
- 'has ID policy for': "RO"
- Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
- Person:Alan Ruttenberg
- has ID digit count
-
-
-
-
-
-
-
- has ID range allocated
- Datatype: idrange:1
-Annotations: 'has ID range allocated to': "Chris Mungall"
-EquivalentTo: xsd:integer[> 2151 , <= 2300]
-
- Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
- Person:Alan Ruttenberg
- has ID range allocated to
-
-
-
-
-
-
-
- has ID policy for
- Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
- Annotations:
- 'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
- 'has ID digit count' : 7,
- rdfs:label "RO id policy"
- 'has ID policy for': "RO"
- Relating an ontology used to record id policy to the ontology namespace whose policy it manages
- Person:Alan Ruttenberg
- has ID policy for
-
-
-
-
-
-
-
- has ID prefix
- Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
- Annotations:
- 'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
- 'has ID digit count' : 7,
- rdfs:label "RO id policy"
- 'has ID policy for': "RO"
- Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
- Person:Alan Ruttenberg
- has ID prefix
-
-
-
-
-
-
-
- elucidation
- person:Alan Ruttenberg
- Person:Barry Smith
- Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
-
- elucidation
-
-
-
-
-
-
-
- has associated axiom(nl)
- Person:Alan Ruttenberg
- Person:Alan Ruttenberg
- An axiom associated with a term expressed using natural language
-
- has associated axiom(nl)
-
-
-
-
-
-
-
- has associated axiom(fol)
- Person:Alan Ruttenberg
- Person:Alan Ruttenberg
- An axiom expressed in first order logic using CLIF syntax
-
- has associated axiom(fol)
-
-
-
-
-
-
-
- is allocated id range
- Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
- PERSON:Alan Ruttenberg
- Add as annotation triples in the granting ontology
- is allocated id range
-
-
-
-
-
-
-
- retired from use as of
- relates a class of CRID to the date after which further instances should not be made, according to the central authority
- In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
- Alan Ruttenberg
- retired from use as of
-
-
-
-
-
-
-
- has ontology root term
- Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
- Nicolas Matentzoglu
- has ontology root term
-
-
-
-
-
-
-
- may be identical to
- A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
- David Osumi-Sutherland
- #40
- VFB
- Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
- may be identical to
-
-
-
-
-
-
-
- scheduled for obsoletion on or after
- Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
- Chris Mungall, Jie Zheng
- https://github.com/geneontology/go-ontology/issues/15532
- https://github.com/information-artifact-ontology/ontology-metadata/issues/32
- GO ontology
- scheduled for obsoletion on or after
-
-
-
-
-
-
-
-
- has axiom id
- Person:Alan Ruttenberg
- Person:Alan Ruttenberg
- A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
-
- has axiom label
-
-
-
-
-
-
-
- term replaced by
-
- Use on obsolete terms, relating the term to another term that can be used as a substitute
- Person:Alan Ruttenberg
- Person:Alan Ruttenberg
- Add as annotation triples in the granting ontology
- term replaced by
-
-
-
-
-
-
-
- This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
- OBO Operations call
-
- logical characteristic of object property
-
-
-
-
-
-
-
- 'part disjoint with' 'defined by construct' """
- PREFIX owl: <http://www.w3.org/2002/07/owl#>
- PREFIX : <http://example.org/
- CONSTRUCT {
- [
- a owl:Restriction ;
- owl:onProperty :part_of ;
- owl:someValuesFrom ?a ;
- owl:disjointWith [
- a owl:Restriction ;
- owl:onProperty :part_of ;
- owl:someValuesFrom ?b
- ]
- ]
- }
- WHERE {
- ?a :part_disjoint_with ?b .
- }
- Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
-
-
-
- defined by construct
-
-
-
-
-
-
-
- The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing).
- A provenance property that denotes a synonym to be the preferred one for a specific community.
-
-
- 2025-06-02
- preferred label for community
-
-
-
-
-
-
-
- CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
- A synonym type for describing abbreviations or initialisms
-
-
- 2023-03-03
- abbreviation
-
-
-
-
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-
-
-
- A synonym type for describing ambiguous synonyms
-
-
- 2023-03-03
- ambiguous synonym
-
-
-
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-
-
-
- A synonym type for describing dubious synonyms
-
-
- 2023-03-03
- dubious synonym
-
-
-
-
-
-
-
-
- EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
- A synonym type for describing layperson or colloquial synonyms
-
-
- 2023-03-03
- layperson synonym
-
-
-
-
-
-
-
-
- CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
- A synonym type for describing pluralization synonyms
-
-
- 2023-03-03
- plural form
-
-
-
-
-
-
-
-
- CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
- A synonym type for describing UK spelling variants
-
-
- 2023-03-03
- UK spelling synonym
-
-
-
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-
-
- A synonym type for common misspellings
-
-
- 2023-03-03
- misspelling
-
-
-
-
-
-
-
-
- A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
-
-
- 2023-03-03
- misnomer
-
-
-
-
-
-
-
-
- MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
- A synonym type for names that have been used as primary labels in the past.
-
-
- 2023-07-25
- previous name
-
-
-
-
-
-
-
-
- The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
- A synonym type for the legal entity name
-
-
- 2023-07-27
- legal name
-
-
-
-
-
-
-
-
- CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label
- The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.
-
-
- 2023-09-30
- INN
- International Nonproprietary Name
-
-
-
-
-
-
-
-
- nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
- A synonym type for describing Latin term synonyms.
-
-
- 2023-10-12
- latin term
-
-
-
-
-
-
-
-
- NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
- A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
-
-
- 2023-11-01
- acronym
-
-
-
-
-
-
-
-
- The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: `<https://purl.brain-bican.org/ontology/dmbao/dmbao.owl> a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`.
- Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf.
-
-
- 2025-09-17
- has ontology hierarchical property
-
-
-
-
-
-
-
- A serial number such as "12324X"; a stop sign; a written proper name such as "OBI
- An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
-
-
- 2024-03-25
- has symbol
-
-
-
-
-
-
-
- An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
- temporal interpretation
-
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-
- An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
-
- https://github.com/information-artifact-ontology/ontology-metadata/issues/18
- has broad synonym
- https://github.com/information-artifact-ontology/ontology-metadata/issues/18
-
-
-
-
-
-
-
-
- disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
- An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
-
-
- 2024-03-18
- has cross-reference
-
-
-
-
-
-
-
- An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
-
- https://github.com/information-artifact-ontology/ontology-metadata/issues/20
- has exact synonym
- https://github.com/information-artifact-ontology/ontology-metadata/issues/20
-
-
-
-
-
-
-
-
- An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
-
- https://github.com/information-artifact-ontology/ontology-metadata/issues/19
- has narrow synonym
- https://github.com/information-artifact-ontology/ontology-metadata/issues/19
-
-
-
-
-
-
-
-
- An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
-
- https://github.com/information-artifact-ontology/ontology-metadata/issues/21
- has related synonym
- https://github.com/information-artifact-ontology/ontology-metadata/issues/21
-
-
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- is part of
- my brain is part of my body (continuant parthood, two material entities)
- my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
- this day is part of this year (occurrent parthood)
- a core relation that holds between a part and its whole
- Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
- Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
- Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
-
-A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
- part_of
-
- part of
- http://www.obofoundry.org/ro/#OBO_REL:part_of
-
-
-
-
-
-
-
-
- has part
- my body has part my brain (continuant parthood, two material entities)
- my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
- this year has part this day (occurrent parthood)
- a core relation that holds between a whole and its part
- Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
- Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
- Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
-
-A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
- has_part
-
- has part
-
-
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-
- realized in
- this disease is realized in this disease course
- this fragility is realized in this shattering
- this investigator role is realized in this investigation
- is realized by
- realized_in
- [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
- Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
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- realized in
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- realizes
- this disease course realizes this disease
- this investigation realizes this investigator role
- this shattering realizes this fragility
- to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
- Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
-
- realizes
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- occurs in
- b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
- occurs_in
- unfolds in
- unfolds_in
- Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
-
- occurs in
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- site of
- [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
- Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
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- contains process
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- One of my mental representations is directed towards the Pacific Ocean.
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- A relationship between a quality and a portion of reality such that the quality refers to or is cognitively directed towards the portion of reality.
- person: William Hogan
- https://ceur-ws.org/Vol-1515/regular10.pdf
-
- In the definition source, the relation is called 'is_about'. To avoid confusion with the existing "is about" relation in IAO, we called it 'is directed towards' per Alan Ruttenberg's suggestion.
- is directed towards
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- has measurement unit label
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- The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink.
-
-Here the ink + paper is the independent continuant and the carrier is the pattern in the ink.
-
-c = pattern in the ink
-b = paper + ink
-r = friend
-
- c specifically denotes r =def
-r is a portion of reality
-& c is a particular quality
-& c depends specifically on some independent continuant b
-& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly.
-
-Marked means there is a changed or additional quality of the bearer - the quality is the information carrier.
-
-Case 1
-Memory trace as mark created when reading some description of some friend. The trace can denote.
-
-Case 2
-Pattern of ink arrayed on paper as mark when writing down a friend's name
-
-Case 3
-Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
- 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
- see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
- Alan Ruttenberg
- Smith, Ceusters, Ruttenberg, 2000 years of philosophy
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- obsolete_specifically denotes
- true
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- This document is about information artifacts and their representations
-
- A (currently) primitive relation that relates an information artifact to an entity.
- 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
-
-We will try to build it back up by elaborating the various subproperties that are more precisely defined.
-
-Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
- person:Alan Ruttenberg
- Smith, Ceusters, Ruttenberg, 2000 years of philosophy
- is about
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- An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
- 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
- 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
- PERSON: Jonathan Rees
- Person: Alan Ruttenberg
- mentions
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- Inverse of the relation 'mentions'
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- 2022-01-28T07:20:08Z
- mentioned by
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- A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
- A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
- 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.
-g denotes r =def
-r is a portion of reality
-there is some c that is a concretization of g
-every c that is a concretization of g specifically denotes r
- person:Alan Ruttenberg
- Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
-
- denotes
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- see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
-
- obsolete_materially denotes
- true
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- m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
- 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
- From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]
-
-This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
-
-Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
---
-From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]
-
-unit of measure is a quality, e.g. the length of a ruler.
-
-[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]
-
-[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]
-
-a represents b means either a denotes b or a describes
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-describe:
-a describes b means a is about b and a allows an inference of at least one quality of b
-
-We have had a long discussion about denotes versus describes.
- From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.
-
-a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
- From the second meeting on IAO:
-
-An attempt at defining assay using Barry's "reliability" wording
-
-assay:
-process and has_input some material entity
-and has_output some information content entity
-and which is such that instances of this process type reliably generate
-outputs that describes the input.
- This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
-
-Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
- Alan Ruttenberg
- is quality measurement of
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- obsolete_describes
- true
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- obsolete_represents
- true
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- inverse of the relation 'denotes'
- Person: Jie Zheng, Chris Stoeckert, Mike Conlon
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- denoted by
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- relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
- has coordinate unit label
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- relates a process to a time-measurement-datum that represents the duration of the process
- Person:Alan Ruttenberg
- is duration of
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- inverse of the relation of is quality measurement of
- 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
- Person:Alan Ruttenberg
- is quality measured as
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- A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
- Person:Alan Ruttenberg
- Person:Bjoern Peters
- is quality specification of
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- inverse of the relation of is quality specification of
- 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
- Person:Alan Ruttenberg
- Person:Bjoern Peters
- quality is specified as
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- relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
- Alan Ruttenberg
- has time stamp
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- relates a time stamped measurement datum to the measurement datum that was measured
- Alan Ruttenberg
- has measurement datum
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- has specified input
- see is_input_of example_of_usage
-
- The inverse property of is specified input of
- 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
- PERSON: Alan Ruttenberg
- PERSON: Bjoern Peters
- PERSON: Larry Hunter
- PERSON: Melanie Coutot
-
- has specified input
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- is specified input of
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- has specified output
-
- The inverse property of is specified output of
- PERSON: Alan Ruttenberg
- PERSON: Bjoern Peters
- PERSON: Larry Hunter
- PERSON: Melanie Courtot
-
- has specified output
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- is specified output of
-
- A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
- Alan Ruttenberg
- PERSON:Bjoern Peters
-
- is specified output of
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- inheres in
- this fragility is a characteristic of this vase
- this red color is a characteristic of this apple
- a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
- inheres_in
-
- Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
- characteristic of
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- bearer of
- this apple is bearer of this red color
- this vase is bearer of this fragility
- Inverse of characteristic_of
- A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
- bearer_of
- is bearer of
-
- has characteristic
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- participates in
- this blood clot participates in this blood coagulation
- this input material (or this output material) participates in this process
- this investigator participates in this investigation
- a relation between a continuant and a process, in which the continuant is somehow involved in the process
- participates_in
- participates in
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- has participant
- this blood coagulation has participant this blood clot
- this investigation has participant this investigator
- this process has participant this input material (or this output material)
- a relation between a process and a continuant, in which the continuant is somehow involved in the process
- Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
- has_participant
- http://www.obofoundry.org/ro/#OBO_REL:has_participant
- has participant
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- A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
- An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
- A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.
- is concretized as
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- A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
- An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
- A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.
- concretizes
-
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- this catalysis function is a function of this enzyme
- a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
- A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
- function_of
- is function of
- This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
- function of
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- this red color is a quality of this apple
- a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
- A quality inheres in its bearer at all times for which the quality exists.
- is quality of
- quality_of
- This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
- quality of
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- this investigator role is a role of this person
- a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
- A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
- is role of
- role_of
- This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
- role of
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- this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
- a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
- A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
- has_function
- has function
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- this apple has quality this red color
- a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
- A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
- has_quality
- has quality
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- this person has role this investigator role (more colloquially: this person has this role of investigator)
- a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
- A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
- has_role
- has role
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- a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
- has disposition
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- This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
- disposition of
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- this cell derives from this parent cell (cell division)
- this nucleus derives from this parent nucleus (nuclear division)
-
- a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
- This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
- derives_from
- derives from
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- this parent cell derives into this cell (cell division)
- this parent nucleus derives into this nucleus (nuclear division)
-
- a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
- This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
- derives_into
- derives into
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- is location of
- my head is the location of my brain
- this cage is the location of this rat
- a relation between two independent continuants, the location and the target, in which the target is entirely within the location
- Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
- location_of
-
- location of
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- located in
- my brain is located in my head
- this rat is located in this cage
- a relation between two independent continuants, the target and the location, in which the target is entirely within the location
- Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
- Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
- located_in
-
- http://www.obofoundry.org/ro/#OBO_REL:located_in
- located in
-
-
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-
- This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
-
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-
- This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
-
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- the surface of my skin is a 2D boundary of my body
- a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
- A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
- Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
- 2D_boundary_of
- boundary of
- is 2D boundary of
- is boundary of
-
- 2D boundary of
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- my body has 2D boundary the surface of my skin
- a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
- A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
- Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
- has boundary
- has_2D_boundary
-
- has 2D boundary
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- An organism that is a member of a population of organisms
- is member of is a mereological relation between a item and a collection.
- is member of
- member part of
- SIO
-
- member of
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- has member is a mereological relation between a collection and an item.
- SIO
-
- has member
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- DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
- DEPRECATED inheres in
- true
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- DEPRECATED bearer of
- true
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- has measurement value
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- has x coordinate value
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- has z coordinate value
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- has y coordinate value
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- A planned process that has specified output a software product and that involves the creation of source code.
- Mathias Brochhausen
- William R. Hogan
- http://en.wikipedia.org/wiki/Software_development
- A planned process resulting in a software product involving the creation of source code.
- software development
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- A measurement datum that is the output of counting.
- Mathias Brochhausen
- A measurement datum that is the output of counting.
- count
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- The planned process of finding the number of elements in a finite set of objects.
- Mathias Brochhausen
- http://en.wikipedia.org/wiki/Counting
- The planned process of finding the number of elements in a finite set of objects.
- counting
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- software source code version control repository
- A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc.
- William R. Hogan
- Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based
- source code repository
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- process of compiling software
- A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions.
- William R. Hogan
- It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
- Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.
- compiling software
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- creating a data set
- A planned process that has a data set as its specified output.
- William R. Hogan
- data set creation
- dataset creation
- dataset creating
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- entity
- Entity
- Julius Caesar
- Verdi’s Requiem
- the Second World War
- your body mass index
- BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
- Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
- An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
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- entity
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- Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
-
- per discussion with Barry Smith
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- An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
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- continuant
- Continuant
- An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
- BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
- Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
- A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
- if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
- if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
- if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
- (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
- (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
- (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
- (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
-
- continuant
-
-
-
-
- Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
-
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- A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
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- if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
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- if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
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- if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
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- (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
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- (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
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- (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
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- (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
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- occurrent
- Occurrent
- An entity that has temporal parts and that happens, unfolds or develops through time.
- BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
- BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
- Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
- Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
- An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
- Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
- b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
- (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
- (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
-
- occurrent
-
-
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-
- Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
-
- per discussion with Barry Smith
-
-
-
-
- Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
-
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- An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
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- Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
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- b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
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- (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
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- (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
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- ic
- IndependentContinuant
- a chair
- a heart
- a leg
- a molecule
- a spatial region
- an atom
- an orchestra.
- an organism
- the bottom right portion of a human torso
- the interior of your mouth
- b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
- For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
- For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
- (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
- (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
- (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
- A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
-
- independent continuant
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- b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
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- For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
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- For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
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- (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
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- (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
-
-
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- (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
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- s-region
- SpatialRegion
- BFO 2 Reference: Spatial regions do not participate in processes.
- Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
- A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
- All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
- (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
- (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
-
- spatial region
-
-
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-
- Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
-
- per discussion with Barry Smith
-
-
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- A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
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- All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
-
-
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- (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
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- (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
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- t-region
- TemporalRegion
- Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
- A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
- All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
- Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
- (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
- (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
- (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
-
- temporal region
-
-
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-
- Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
-
- per discussion with Barry Smith
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-
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- A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
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- All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
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- Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
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- (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
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- (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
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- (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
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- 2d-s-region
- TwoDimensionalSpatialRegion
- an infinitely thin plane in space.
- the surface of a sphere-shaped part of space
- A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
- (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
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- two-dimensional spatial region
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-
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- A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
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- (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
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- st-region
- SpatiotemporalRegion
- the spatiotemporal region occupied by a human life
- the spatiotemporal region occupied by a process of cellular meiosis.
- the spatiotemporal region occupied by the development of a cancer tumor
- A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
- All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
- Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
- Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
- Every spatiotemporal region occupies_spatiotemporal_region itself.
- Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
- (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
- (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
- (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
- (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
- (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
-
- spatiotemporal region
-
-
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-
- Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
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-
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-
- Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
-
-
-
-
-
- Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
-
-
-
-
-
- (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
-
-
-
-
-
- (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
-
-
-
-
-
- (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
-
-
-
-
-
- (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
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-
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-
-
- (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
-
-
-
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-
- A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
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- All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
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-
- process
- Process
- a process of cell-division, \ a beating of the heart
- a process of meiosis
- a process of sleeping
- the course of a disease
- the flight of a bird
- the life of an organism
- your process of aging.
- p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
- BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
- (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
- An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
-
- process
-
-
-
-
- p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
-
-
-
-
-
- (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
-
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- disposition
- Disposition
- an atom of element X has the disposition to decay to an atom of element Y
- certain people have a predisposition to colon cancer
- children are innately disposed to categorize objects in certain ways.
- the cell wall is disposed to filter chemicals in endocytosis and exocytosis
- BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
- b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
- If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
- (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
- (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
-
- disposition
-
-
-
-
- b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
-
-
-
-
-
- If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
-
-
-
-
-
- (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
-
-
-
-
-
- (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
-
-
-
-
-
-
-
-
-
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- realizable
- RealizableEntity
- the disposition of this piece of metal to conduct electricity.
- the disposition of your blood to coagulate
- the function of your reproductive organs
- the role of being a doctor
- the role of this boundary to delineate where Utah and Colorado meet
- A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
- To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
- All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
- (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
- (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
-
- realizable entity
-
-
-
-
- To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
-
-
-
-
-
- All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
-
-
-
-
-
- (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
-
-
-
-
-
- (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
-
-
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- 0d-s-region
- ZeroDimensionalSpatialRegion
- A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
- (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
-
- zero-dimensional spatial region
-
-
-
-
- A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
-
-
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-
- (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
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- quality
- Quality
- the ambient temperature of this portion of air
- the color of a tomato
- the length of the circumference of your waist
- the mass of this piece of gold.
- the shape of your nose
- the shape of your nostril
- a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
- If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
- (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
- (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
-
- quality
-
-
-
-
- a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
-
-
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-
- If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
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-
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-
-
- (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
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-
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-
-
- (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
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- sdc
- SpecificallyDependentContinuant
- Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
- of one-sided specifically dependent continuants: the mass of this tomato
- of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
- the disposition of this fish to decay
- the function of this heart: to pump blood
- the mutual dependence of proton donors and acceptors in chemical reactions [79
- the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
- the pink color of a medium rare piece of grilled filet mignon at its center
- the role of being a doctor
- the shape of this hole.
- the smell of this portion of mozzarella
- b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
- Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
- (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
- A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
-
- specifically dependent continuant
-
-
-
-
- b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
-
-
-
-
-
- Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
-
- per discussion with Barry Smith
-
-
-
-
- (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
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- role
- Role
- John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
- the priest role
- the role of a boundary to demarcate two neighboring administrative territories
- the role of a building in serving as a military target
- the role of a stone in marking a property boundary
- the role of subject in a clinical trial
- the student role
- A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
- BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
- b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
- (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
-
- role
-
-
-
-
- b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
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-
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-
- (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
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- fiat-object-part
- FiatObjectPart
- or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
- the FMA:regional parts of an intact human body.
- the Western hemisphere of the Earth
- the division of the brain into regions
- the division of the planet into hemispheres
- the dorsal and ventral surfaces of the body
- the upper and lower lobes of the left lung
- BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
- b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
- (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
-
- fiat object part
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-
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-
- b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
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- (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
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- 1d-s-region
- OneDimensionalSpatialRegion
- an edge of a cube-shaped portion of space.
- A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
- (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
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- one-dimensional spatial region
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-
- A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
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- (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
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- object-aggregate
- ObjectAggregate
- a collection of cells in a blood biobank.
- a swarm of bees is an aggregate of members who are linked together through natural bonds
- a symphony orchestra
- an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
- defined by fiat: the aggregate of members of an organization
- defined through physical attachment: the aggregate of atoms in a lump of granite
- defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
- defined via attributive delimitations such as: the patients in this hospital
- the aggregate of bearings in a constant velocity axle joint
- the aggregate of blood cells in your body
- the nitrogen atoms in the atmosphere
- the restaurants in Palo Alto
- your collection of Meissen ceramic plates.
- An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
- BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
- ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
- b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
- (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
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- object aggregate
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- An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
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- An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
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- ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
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- b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
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- (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
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- 3d-s-region
- ThreeDimensionalSpatialRegion
- a cube-shaped region of space
- a sphere-shaped region of space,
- A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
- (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
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- three-dimensional spatial region
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- A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
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- (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
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- site
- Site
- Manhattan Canyon)
- a hole in the interior of a portion of cheese
- a rabbit hole
- an air traffic control region defined in the airspace above an airport
- the Grand Canyon
- the Piazza San Marco
- the cockpit of an aircraft
- the hold of a ship
- the interior of a kangaroo pouch
- the interior of the trunk of your car
- the interior of your bedroom
- the interior of your office
- the interior of your refrigerator
- the lumen of your gut
- your left nostril (a fiat part – the opening – of your left nasal cavity)
- b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
- (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
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- site
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- b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
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- (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
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- object
- Object
- atom
- cell
- cells and organisms
- engineered artifacts
- grain of sand
- molecule
- organelle
- organism
- planet
- solid portions of matter
- star
- BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
- BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
- BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
- BFO 2 Reference: an object is a maximal causally unified material entity
- BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
- b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
-
- object
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-
- b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
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- gdc
- GenericallyDependentContinuant
- The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
- the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
- the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
- b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
- (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
- A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
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- generically dependent continuant
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- b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
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- (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
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- function
- Function
- the function of a hammer to drive in nails
- the function of a heart pacemaker to regulate the beating of a heart through electricity
- the function of amylase in saliva to break down starch into sugar
- BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
- A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
- (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
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- function
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- A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
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- (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
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- p-boundary
- ProcessBoundary
- the boundary between the 2nd and 3rd year of your life.
- p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
- Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
- (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
- (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
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- process boundary
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- p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
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- Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
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- (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
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- (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
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- 1d-t-region
- OneDimensionalTemporalRegion
- the temporal region during which a process occurs.
- BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
- A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
- (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
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- one-dimensional temporal region
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- A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
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- (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
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- material
- MaterialEntity
- a flame
- a forest fire
- a human being
- a hurricane
- a photon
- a puff of smoke
- a sea wave
- a tornado
- an aggregate of human beings.
- an energy wave
- an epidemic
- the undetached arm of a human being
- An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
- BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
- BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
- BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
- A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
- Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
- every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
- (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
- (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
- (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
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- material entity
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- A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
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- Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
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- every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
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- (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
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- (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
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- (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
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- cf-boundary
- ContinuantFiatBoundary
- b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
- BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
- BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
- Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
- Every continuant fiat boundary is located at some spatial region at every time at which it exists
- (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
-
- continuant fiat boundary
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- b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
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- Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
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-
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- (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
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- immaterial
- ImmaterialEntity
- BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
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- immaterial entity
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- 1d-cf-boundary
- OneDimensionalContinuantFiatBoundary
- The Equator
- all geopolitical boundaries
- all lines of latitude and longitude
- the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
- the median sulcus of your tongue
- a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
- (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
-
- one-dimensional continuant fiat boundary
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- a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
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- (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
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- process-profile
- ProcessProfile
- On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
- One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
- The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
- b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
- b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
- (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
- (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
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- process profile
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- b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
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- b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
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- (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
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- (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
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- r-quality
- RelationalQuality
- John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
- a marriage bond, an instance of requited love, an obligation between one person and another.
- b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
- (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
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- relational quality
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- b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
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- (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
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- 2d-cf-boundary
- TwoDimensionalContinuantFiatBoundary
- a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
- (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
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- two-dimensional continuant fiat boundary
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- a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
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- (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
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- 0d-cf-boundary
- ZeroDimensionalContinuantFiatBoundary
- the geographic North Pole
- the point of origin of some spatial coordinate system.
- the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
- zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
- a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
- (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
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- zero-dimensional continuant fiat boundary
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- zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
-
- requested by Melanie Courtot
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- a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
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- (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
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- 0d-t-region
- ZeroDimensionalTemporalRegion
- a temporal region that is occupied by a process boundary
- right now
- the moment at which a child is born
- the moment at which a finger is detached in an industrial accident
- the moment of death.
- temporal instant.
- A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
- (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
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- zero-dimensional temporal region
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- A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
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- (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
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- history
- History
- A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
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- history
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- A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
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- completely executed planned process
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- completely executed planned process
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- planned process
- A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification.
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- planned process
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- conditional specification
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- A directive information entity that specifies what should happen if the trigger condition is fulfilled.
- PlanAndPlannedProcess Branch
- OBI branch derived
- OBI_0000349
- conditional specification
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- measurement unit label
- Examples of measurement unit labels are liters, inches, weight per volume.
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- A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
- 2009-03-16: provenance: a term measurement unit was
-proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and
-Cristian Cocos, and subsequently moved to IAO where the objective for
-which the original term was defined was satisfied with the definition
-of this, different, term.
- 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
- PERSON: Alan Ruttenberg
- PERSON: Melanie Courtot
- measurement unit label
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- objective specification
- In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
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- A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
- 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
- 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
- Answers the question, why did you do this experiment?
- PERSON: Alan Ruttenberg
- PERSON: Barry Smith
- PERSON: Bjoern Peters
- PERSON: Jennifer Fostel
- goal specification
- OBI Plan and Planned Process/Roles Branch
- OBI_0000217
- objective specification
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- narrative object
- Examples of narrative objects are reports, journal articles, and patents submission.
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- A narrative object is an information content entity that is a set of propositions.
- 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
- agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
- person:Chris Stoeckert
- OBI_0000013
- group:OBI
- narrative object
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- Pour the contents of flask 1 into flask 2
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- A directive information entity that describes an action the bearer will take.
- Alan Ruttenberg
- OBI Plan and Planned Process branch
- action specification
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- obsolete_artifact
- true
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-
-
-
-
-
- datum label
-
- A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
- http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
- GROUP: IAO
- 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
-
- datum label
-
-
-
-
-
-
-
-
- software
-
- Software is a plan specification composed of a series of instructions that can be
-interpreted by or directly executed by a processing unit.
- see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
- PERSON: Alan Ruttenberg
- PERSON: Bjoern Peters
- PERSON: Chris Stoeckert
- PERSON: Melanie Courtot
- GROUP: OBI
- software
-
-
-
-
-
-
-
-
- obsolete_digital entity
- A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
- 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
-
-Superclass was 'digitial quality'
- person:Chris Stoeckert
- OBI_0000261
- group:OBI
-
- obsolete2_digital entity
- true
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- journal article
- Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
-
- A report that is published in a journal.
- PERSON: Alan Ruttenberg
- PERSON: Chris Stoeckert
- OBI_0000159
- group:OBI
- journal article
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- information carrier
- In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
-
- A quality of an information bearer that imparts the information content
- 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
- 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
- PERSON: Alan Ruttenberg
- Smith, Ceusters, Ruttenberg, 2000 years of philosophy
- information carrier
-
-
-
-
-
-
-
-
- model number
-
- A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
- manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
- Person: Alan Ruttenberg
- model number
-
-
-
-
-
-
-
-
-
- obsolete_material_entity
- true
-
-
-
-
-
-
-
-
- binary digital entity
- MS Word document, ZIP file, DICOM file, JPEG file
- A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
- 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
-Superclass was 'digital entity'
- digital_entity
- person:Chris Stoeckert
- OBI_0000244
- group:OBI
-
- obsolete2_binary digital entity
- true
-
-
-
-
-
-
-
-
- The length of a ruler.
- a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
- Alan Ruttenberg
- Smith, Ceusters, Ruttenberg, 2000 years of philosophy
-
- obsolete_unit of measure
- true
-
-
-
-
-
-
-
-
- programming language
- R, Perl, Java
-
- A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
- person:Alan Ruttenberg
- person:Chris Stoeckert
- OBI_0000058
- group:OBI
- programming language
-
-
-
-
-
-
-
-
- data entity
- Data items include counts of things, analyte concentrations, and statistical summaries.
-
- An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
- 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
- 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
- 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
- 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
- JAR: datum -- well, this will be very tricky to define, but maybe some
-information-like stuff that might be put into a computer and that is
-meant, by someone, to denote and/or to be interpreted by some
-process... I would include lists, tables, sentences... I think I might
-defer to Barry, or to Brian Cantwell Smith
-
-JAR: A data item is an approximately justified approximately true approximate belief
- PERSON: Alan Ruttenberg
- PERSON: Chris Stoeckert
- PERSON: Jonathan Rees
- data
- data item
- data entity
-
-
-
-
-
-
-
-
- symbol
- a serial number such as "12324X"
- a stop sign
- a written proper name such as "OBI"
-
- An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
- 20091104, MC: this needs work and will most probably change
- 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
- PERSON: James A. Overton
- PERSON: Jonathan Rees
- based on Oxford English Dictionary
- symbol
-
-
-
-
-
-
-
-
- numeral
-
- A symbol that denotes a number.
- PERSON: Jonathan Rees
- numeral
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- information content entity
- Examples of information content entites include journal articles, data, graphical layouts, and graphs.
-
- A generically dependent continuant that is about some thing.
- 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
- information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
-
-Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
- PERSON: Chris Stoeckert
- OBI_0000142
- information content entity
-
-
-
-
-
-
-
-
- integer numeral
-
- A numeral that denotes an integer
- PERSON: Jonathan Rees
- integer numeral
-
-
-
-
-
-
-
-
-
-
-
- 1
-
-
-
-
-
- 1
-
-
- 10 feet. 3 ml.
-
- A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
- 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
-this case we explicitly refer to the singular form
- Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
- PERSON: Alan Ruttenberg
- PERSON: Melanie Courtot
- scalar measurement datum
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- An information content entity whose concretizations indicate to their bearer how to realize them in a process.
- 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
- 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
- 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
- Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
- PERSON: Alan Ruttenberg
- PERSON: Bjoern Peters
- directive information entity
-
-
-
-
-
-
-
-
- time trigger
-
- PlanAndPlannedProcess Branch
- time trigger
-
-
-
-
-
-
-
-
- obsolete_study interpretation
-
- A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
- 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
- 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
- The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
- Lawrence Hunter
- PERSON: Alan Ruttenberg
- PERSON: Jennifer Fostel
- PERSON: Melanie Courtot
- conclusion
- OBI_0000005
-
- obsolete_study interpretation
- true
-
-
-
-
-
-
-
-
- dot plot
- Dot plot of SSC-H and FSC-H.
-
- A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
- person:Allyson Lister
- person:Chris Stoeckert
- OBI_0000123
- group:OBI
- dot plot
-
-
-
-
-
-
-
-
- graph
-
- A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
- PERSON: Lawrence Hunter
- person:Alan Ruttenberg
- person:Allyson Lister
- OBI_0000240
- group:OBI
- graph
-
-
-
-
-
-
-
-
- text based digital entity
- XML file, C++ source code file
- A text based digital entity is a digital entity that is encoded so that it only contains text characters.
- 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
-superclass was 'digital document'
- digital_entity
- person:Chris Stoeckert
- OBI_0000132
- group:OBI
-
- obsolete2_text based digital entity
- true
-
-
-
-
-
-
-
-
- rule
- example to be added
-
- A rule is an executable which guides, defines, restricts actions.
- MSI
- PRS
- OBI_0500021
- PRS
- rule
-
-
-
-
-
-
-
-
- contour plot
- Contour plot of SSC-H, FSC-H, and FL1-H.
-
- generically_dependent_continuants
- person:Allyson Lister
- person:Chris Stoeckert
- OBI_0000246
- group:Flow Cytometry community
- contour plot
-
-
-
-
-
-
-
-
- report figure
-
- A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
- I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
- Replaced by defined version of figure
- person:Alan Ruttenberg
- person:Allyson Lister
- OBI_0000027
- group:OBI
-
- obsolete2_report figure
- true
-
-
-
-
-
-
-
-
- algorithm
- PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
-
- A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
- Philippe Rocca-Serra
- PlanAndPlannedProcess Branch
- OBI_0000270
- adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
- algorithm
-
-
-
-
-
-
-
-
- software interpreter
- R program, Perl interpreter, Java virtual machine
-
- A software interpreter is a software application that executes some specified input software.
- Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
- person:Alan Ruttenberg
- person:Chris Stoeckert
- OBI_0000199
- group:OBI
- software interpreter
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- curation status specification
-
- The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
- Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
- PERSON:Bill Bug
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- OBI_0000266
- curation status specification
-
-
-
-
-
-
-
-
- density plot
- Density plot of SSC-H and FSC-H.
-
- A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
- person:Allyson Lister
- person:Chris Stoeckert
- OBI_0000179
- group:Flow Cytometry community
- density plot
-
-
-
-
-
-
-
-
- report
- Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
-
- A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record).
- 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on
-something that has completed." Should it be restricted to those things
-that are completed? For example, a progress report is (usually) about
-something that definitely has *not* been completed, or may include
-(only) projections. I think the definition would not suffer if the
-whole sentence is deleted.
- 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
- 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
- 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
- disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
- PERSON: Alan Ruttenberg
- PERSON: Chris Stoeckert
- PERSON: Melanie Courtot
- GROUP: OBI
- OBI_0000099
- report
-
-
-
-
-
-
-
-
- report element
-
- A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
- 2009-03-16: needs some more work (clarify relations).
- 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
- 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
- 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
- Replaced by textual entity and figure
- There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
- PERSON: Alan Ruttenberg
- PERSON: Allyson Lister
- PERSON: Melanie Courtot
- GROUP:OBI
- OBI_0000001
-
- obsolete_report element
- true
-
-
-
-
-
-
-
-
- binary executable
- Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
- 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
-superclass was 'digital entity'
- person:Jennifer Fostel
- OBI_0000222
- group:OBI
-
- obsolete2_binary executable
- true
-
-
-
-
-
-
-
-
- source code module
- The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
-
- A source code module is a directive information entity that specifies, using a programming language, some algorithm.
- person:Alan Ruttenberg
- person:Chris Stoeckert
- OBI_0000039
- group:OBI
- source code module
-
-
-
-
-
-
-
-
- report table
-
- A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
- 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
- person:Alan Ruttenberg
- person:Allyson Lister
- OBI_0000265
- group:OBI
-
- obsolete_report table
- true
-
-
-
-
-
-
-
-
- data format specification
-
- A data format specification is the information content borne by the document published defining the specification.
-Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
- 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes
-information. Example: The ISO document specifying what encompasses an
-XML document; The instructions in a XSD file"
- PERSON: Alan Ruttenberg
- PlanAndPlannedProcess Branch
- OBI branch derived
- OBI_0000187
-
- data format specification
-
-
-
-
-
-
-
-
- homogenous data collection
- Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
-
- A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
- 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
- 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
- person:Allyson Lister
- person:Chris Stoeckert
- data set
- group:OBI
- homogenous data collection
-
-
-
-
-
-
-
-
- image
-
- An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
- person:Alan Ruttenberg
- person:Allyson
- person:Chris Stoeckert
- OBI_0000030
- group:OBI
- image
-
-
-
-
-
-
-
-
- data about an ontology part
- Data about an ontology part is a data item about a part of an ontology, for example a term
- Person:Alan Ruttenberg
- data about an ontology part
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- plan specification
- PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
-
- A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
- 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
- 2014-03-31: A plan specification can have other parts, such as conditional specifications.
- 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
- Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
- Alan Ruttenberg
- Clint Dowland
- OBI Plan and Planned Process branch
- OBI_0000344
- 2/3/2009 Comment from OBI review.
-
-Action specification not well enough specified.
-Conditional specification not well enough specified.
-Question whether all plan specifications have objective specifications.
-
-Request that IAO either clarify these or change definitions not to use them
- plan specification
- https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131
-
-
-
-
-
-
-
-
- digital document
- A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
- 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
-superclass was 'digial entity'
- person:Jennifer Fostel
- OBI_0000195
- group:OBI
-
- obsolete2_digital document
- true
-
-
-
-
-
-
-
-
- measurement datum
- Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
-
- A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
- 2/2/2009 is_specified_output of some assay?
- person:Chris Stoeckert
- OBI_0000305
- group:OBI
- measurement datum
-
-
-
-
-
-
-
-
-
- _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
-
-Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
-
- obsolete_identifier
- true
-
-
-
-
-
-
-
-
- version number
-
- A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
- Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
- GROUP: IAO
- version number
-
-
-
-
-
-
-
-
- serial number
-
- A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
- Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
- GROUP: IAO
- serial number
-
-
-
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-
- lot number
-
- A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
- GROUP: IAO
- batch number
- lot number
-
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-
- A settings datum is a datum that denotes some configuration of an instrument.
- 2/3/2009 Feedback from OBI
-
-This should be a "setting specification". There is a question of whether it is information about a realizable or not.
-
-Pro other specification are about realizables.
-Cons sometimes specifies a quality which is not a realizable.
- Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
- setting datum
-
-
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-
- 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
- Need to rework digital entity. Digital quality was suggested by Barry.
-
- obsolete_digital quality
- true
-
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-
- conclusion textual entity
- that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
-
- A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
- 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
- 2009/10/23 Alan Ruttenberg: We need to work on the definition still
- Person:Alan Ruttenberg
- conclusion textual entity
-
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- material information bearer
- A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
- a brain
- a hard drive
-
- A material entity in which a concretization of an information content entity inheres.
- GROUP: IAO
- material information bearer
-
-
-
-
-
-
-
-
- histogram
-
- A histogram is a report graph which is a statistical description of a
-distribution in terms of occurrence frequencies of different event classes.
- PERSON:Chris Stoeckert
- PERSON:James Malone
- PERSON:Melanie Courtot
- GROUP:OBI
- histogram
-
-
-
-
-
-
-
-
- heatmap
-
- A heatmap is a report graph which is a graphical representation of data
-where the values taken by a variable(s) are shown as colors in a
-two-dimensional map.
- PERSON:Chris Stoeckert
- PERSON:James Malone
- PERSON:Melanie Courtot
- GROUP:OBI
- heatmap
-
-
-
-
-
-
-
-
- Venn diagram
-
- A Venn diagram is a report graph showing all hypothetically possible
-logical relations between a finite collection of sets.
- PERSON:Chris Stoeckert
- PERSON:James Malone
- PERSON:Melanie Courtot
- WEB: http://en.wikipedia.org/wiki/Venn_diagram
- Venn diagram
-
-
-
-
-
-
-
-
- obsolete_survival curve
-
- A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
- PERSON:Chris Stoeckert
- PERSON:James Malone
- PERSON:Melanie Courtot
- WEB: http://www.graphpad.com/www/book/survive.htm
-
- obsolete_survival curve
- true
-
-
-
-
-
-
-
-
- dendrogram
- Dendrograms are often used in computational biology to
-illustrate the clustering of genes.
-
- A dendrogram is a report graph which is a tree diagram
-frequently used to illustrate the arrangement of the clusters produced by a
-clustering algorithm.
- PERSON:Chris Stoeckert
- PERSON:James Malone
- PERSON:Melanie Courtot
- WEB: http://en.wikipedia.org/wiki/Dendrogram
- dendrogram
-
-
-
-
-
-
-
-
- scatter plot
- Comparison of gene expression values in two samples can be displayed in a scatter plot
-
- A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
- PERSON:Chris Stoeckert
- PERSON:James Malone
- PERSON:Melanie Courtot
- scattergraph
- WEB: http://en.wikipedia.org/wiki/Scatterplot
- scatter plot
-
-
-
-
-
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-
-
- A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
- PERSON:Alan Ruttenberg
- PERSON:Joanne Luciano
- PERSON:Melanie Courtot
- WEB: http://en.wiktionary.org/wiki/photograph
- photograph
-
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- photographic print
-
- A photographic print is a material entity upon which a photograph generically depends.
- PERSON:Alan Ruttenberg
- PERSON:Melanie Courtot
- photographic print
-
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-
- obsolescence reason specification
-
- The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
- The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
- PERSON: Alan Ruttenberg
- PERSON: Melanie Courtot
- obsolescence reason specification
-
-
-
-
-
-
-
-
- textual entity
- Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
-
- A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
- AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
- MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
- PERSON: Lawrence Hunter
- text
- textual entity
-
-
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-
- citation
- Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
-
- A textual entity intended to identify a particular publication.
- PERSON: Lawrence Hunter
- citation
-
-
-
-
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-
-
- author identification
- L. Hunter
-
- A textual entity intended to identify a particular author
- PERSON: Lawrence Hunter
- author identification
-
-
-
-
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-
- institutional identification
- University of Colorado Denver School of Medicine
-
- A textual entity intended to identify a particular institution
- PERSON: Lawrence Hunter
- institutional identification
-
-
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-
- caption
- Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
-
- A textual entity that describes a figure
- PERSON: Lawrence Hunter
- caption
-
-
-
-
-
-
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-
- document title
- Textual characteristics of traditional and Open Access scientific journals are similar
-
- A textual entity that names a document
- PERSON: Lawrence Hunter
- document title
-
-
-
-
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-
- table
- | T F
---+-----
-T | T F
-F | F F
-
- A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
- PERSON: Lawrence Hunter
- table
-
-
-
-
-
-
-
-
- table of abbreviations
- IAO information artifact ontology
-OBI ontology of biomedical investiations
-GO gene ontology
-
- A table where the constituent texts are abbreviations and their expansions
- PERSON: Lawrence Hunter
- table of abbreviations
-
-
-
-
-
-
-
-
- figure
- Any picture, diagram or table
-
- An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
- PERSON: Lawrence Hunter
- figure
-
-
-
-
-
-
-
-
- diagram
- A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
-
- A figure that expresses one or more propositions
- PERSON: Lawrence Hunter
- diagram
-
-
-
-
-
-
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-
- document
- A journal article, patent application, laboratory notebook, or a book
-
- A collection of information content entities intended to be understood together as a whole
- PERSON: Lawrence Hunter
- document
-
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- publication
- journal article, newspaper story, book, etc.
-
- A document that is the output of a publishing process.
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- PERSON: Lawrence Hunter
- published document
-
- Revisit the term in Octorber 2020. Improve the defintion.
- publication
-
-
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-
- publication about an investigation
- Most scientific journal articles
-
- A publication that is about an investigation
- PERSON: Lawrence Hunter
- scientific publication
- publication about an investigation
-
-
-
-
-
-
-
-
- patent
- US Patent 6,449,603
-
- A document that has been accepted by a patent authority
- PERSON: Lawrence Hunter
- patent
-
-
-
-
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-
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-
-
-
- document part
- An abstract, introduction, method or results section.
-
- An information content entity that is part of a document.
- PERSON: Lawrence Hunter
- document part
-
-
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-
- abstract
- The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
-
- A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
- PERSON: Lawrence Hunter
- precis
-
- abstract
-
-
-
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-
-
- introduction to a publication about an investigation
- Section labelled 'introduction' of a typical scientific journal article
-
- A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
- PERSON: Lawrence Hunter
- background
- introduction
- overview
-
- introduction to a publication about an investigation
-
-
-
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-
-
-
- methods section
- The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
-
- A part of a publication about an investigation that is about the study design of the investigation
- PERSON: Lawrence Hunter
- experimental
- experimental methods
- experimental procedures
- experimental section
- method
- methodology
- methods
-
- methods section
-
-
-
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-
-
- results section
- The section labelled 'results' in a typical scientific journal article
-
- A part of a publication about an investigation that is about a study design execution
- PERSON: Lawrence Hunter
- results
- results section
-
-
-
-
-
-
-
-
- discussion section of a publication about an investigation
-
- A part of a publication about an investigation that is about the study interpretation of the investigation
- PERSON: Lawrence Hunter
- discussion
- discussion section
- discussions
-
- discussion section of a publication about an investigation
-
-
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-
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-
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-
- references section
- The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
-
- A part of a document that has citations as parts
- PERSON: Lawrence Hunter
- literature cited
- reference
- reference list
- references
-
- references section
-
-
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- author list
- Lawrence Hunter and Kevin Brettonel Cohen
-
- A part of a document that enumerates the authors of the document
- PERSON: Lawrence Hunter
- author list
-
-
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-
- institution list
- The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
-
- A part of a document that has parts that are institution identifications associated with the authors of the document
- PERSON: Lawrence Hunter
- institution list
-
-
-
-
-
-
-
-
- author contributions section
- LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
-
- A part of a publication that is about the specific contributions of each author
- PERSON: Lawrence Hunter
- author contributions
- authors' contribution
- authors' contributions
- authors' roles
- contributions by the authors
- contributorship
-
- author contributions section
-
-
-
-
-
-
-
-
- acknowledgements section
- The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
-
- Part of a publication that is about the contributions of people or institutions other than the authors.
- PERSON: Lawrence Hunter
- acknowledgement
- acknowledgements
- acknowledgment
- acknowledgments
-
- acknowledgements section
-
-
-
-
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-
-
- footnote
- The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
-
- A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
- PERSON: Lawrence Hunter
- endnote
- footnotes
-
- footnote
-
-
-
-
-
-
-
-
- supplementary material to a document
-
- A part of a document that is segregated from the rest of the document due to its size
- PERSON: Lawrence Hunter
- additional file
- additional files
- additional information
- appendix
- electronic supplementary material
- electronic supplementary materials
- supplemental data
- supplemental information
- supplemental material
- supplementary data
- supplementary files
- supplementary information
- supplementary material
- supplementary materials
- supporting information
-
- supplementary material to a document
-
-
-
-
-
-
-
-
- table of contents
-
- A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
- PERSON: Lawrence Hunter
- table of contents
-
-
-
-
-
-
-
-
- table of figures
-
- A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
- PERSON: Lawrence Hunter
- table of figures
-
-
-
-
-
-
-
-
- running title
-
- A shorter version of a document title
- PERSON: Lawrence Hunter
- running title
-
-
-
-
-
-
-
-
- copyright section
- This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
-
- A document part that describes legal restrictions on making or distributing copies of the document
- PERSON: Lawrence Hunter
- copyright section
-
-
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- 1
-
-
-
- A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
- 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
- Alan Ruttenberg
- AR notes: We need to discuss whether it should include site.
- cartesian spatial coordinate datum
- http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
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- 1
-
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-
- A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
- Alan Ruttenberg
- one dimensional cartesian spatial coordinate datum
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- 1
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- 1
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- A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
- Alan Ruttenberg
- two dimensional cartesian spatial coordinate datum
-
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- 1
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- 1
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- 1
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- A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
- Alan Ruttenberg
- three dimensional cartesian spatial coordinate datum
-
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- A scalar measurement datum that is the result of measurement of length quality
- Alan Ruttenberg
- length measurement datum
-
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- denotator type
- The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
- A denotator type indicates how a term should be interpreted from an ontological perspective.
- Alan Ruttenberg
- Barry Smith, Werner Ceusters
- denotator type
-
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- A scalar measurement datum that is the result of measurement of mass quality
- 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
- Person:Alan Ruttenberg
- mass measurement datum
-
-
-
-
-
-
-
-
- hypothesis textual entity
- that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
-
- A textual entity that expresses an assertion that is intended to be tested.
- 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
- Person:Alan Ruttenberg
- hypothesis textual entity
-
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- A scalar measurement datum that is the result of measuring a temporal interval
- 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
- Person:Alan Ruttenberg
- time measurement datum
-
-
-
-
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-
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-
- A textual entity that is used as directive to deliver something to a person, or organization
- 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59
- postal address
-
-
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- email address
-
- Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
- Person:Alan Ruttenberg
- Person:Chris Stoeckart
- email address
-
-
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-
- author role
-
- A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
- PERSON: Alan Ruttenberg
- PERSON: Melanie Courtot
- author role
-
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- A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
- Person:Alan Ruttenberg
- data item extraction from journal article
-
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- A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
- Person: Jie Zheng
- https://en.wikipedia.org/wiki/Publishing
-
- VEuPathDB
- publishing process
-
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- A document that is in preparation for submission to be published.
- PERSON: Jie Zheng
- EFO_0001795 in preparation
-
- VEuPathDB
- document in preparation for publication
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- Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
-
- A planned process in which a document is created or added to by including the specified input in it.
- 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
- Bjoern Peters
- wikipedia http://en.wikipedia.org/wiki/Documenting
- documenting
-
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- line graph
-
- A line graph is a type of graph created by connecting a series of data
-points together with a line.
- PERSON:Chris Stoeckert
- PERSON:Melanie Courtot
- line chart
- GROUP:OBI
- WEB: http://en.wikipedia.org/wiki/Line_chart
- line graph
-
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- A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
-
- A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
- 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
- Person:Alan Ruttenberg
- Person:Bjoern Peters
- Person:Melanie Courtot
- assigning a CRID
- assigning a centrally registered identifier
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- Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
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- A planned process in which a CRID registry associates an information content entity with a CRID symbol
- PERSON:Alan Ruttenberg
- associating information with a CRID in the CRID registry
- associating information with a centrally registered identifier in its registry
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- a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
- MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
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- obsolete_establishing a CRID registry
- true
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- The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
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- A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
- PERSON: Alan Ruttenberg
- PERSON: Bill Hogan
- PERSON: Bjoern Peters
- PERSON: Melanie Courtot
- CRID symbol
- Original proposal from Bjoern, discussions at IAO calls
- centrally registered identifier symbol
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- The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
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- An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
- 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
- Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
- Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
- PERSON: Alan Ruttenberg
- PERSON: Bill Hogan
- PERSON: Bjoern Peters
- PERSON: Melanie Courtot
- CRID
- Original proposal from Bjoern, discussions at IAO calls
- centrally registered identifier
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- PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
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- A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
- Justin Whorton
- PERSON: Alan Ruttenberg
- PERSON: Bill Hogan
- PERSON: Bjoern Peters
- PERSON: Melanie Courtot
- CRID registry
- Original proposal from Bjoern, discussions at IAO calls
- https://github.com/information-artifact-ontology/IAO/issues/237
- centrally registered identifier registry
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- Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
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- A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
- PERSON: Alan Ruttenberg
- PERSON: Bill Hogan
- PERSON: Bjoern Peters
- PERSON: Melanie Courtot
- looking up a CRID
- looking up a centrally registered identifier
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- time stamped measurement datum
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- pmid:20604925 - time-lapse live cell microscopy
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- A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
- Alan Ruttenberg
- experimental time series
- time sampled measurement data set
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- written name
- "Bill Clinton"
- "The Eiffel Tower"
- "United States of America"
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- A textual entity that denotes a particular in reality.
- PERSON: Bill Hogan
- https://github.com/information-artifact-ontology/IAO/issues/114
- The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
- written name
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- A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
- PERSON: Melanie Courtot
- PERSON: Michel Dumontier
- https://github.com/information-artifact-ontology/IAO/issues/80
- software method
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- A software module is software composed of a collection of software methods.
- PERSON: Melanei Courtot
- PERSON: Michel Dumontier
- https://github.com/information-artifact-ontology/IAO/issues/80
- software module
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- A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
- PERSON: Melanie Courtot
- PERSON: Michel Dumontier
- https://github.com/information-artifact-ontology/IAO/issues/80
- software library
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- A software application is software that can be directly executed by some processing unit.
- PERSON: Melanie Courtot
- PERSON: Michel Dumontier
- https://github.com/information-artifact-ontology/IAO/issues/80
- software application
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- A software script is software whose instructions can be executed using a software interpreter.
- PERSON: Melanie Courtot
- PERSON: Michel Dumontier
- https://github.com/information-artifact-ontology/IAO/issues/80
- software script
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- abbreviation textual entity
- From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):
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-BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.
- A textual entity listing abbreviations and their expansions that are used in a document.
- PERSON: Bill Baumgartner
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- abbreviation textual entity
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- abbreviations section
- The section labelled 'abbreviations' in a typical scientific journal article.
- A part of a document where abbreviations and their long-forms used within the document are listed.
- PERSON: Bill Baumgartner
- abbreviation and acronyms
- abbreviation list
- abbreviations
- abbreviations and acronyms
- abbreviations list
- abbreviations used
- definitions for abbreviations
- list of abbreviations
- list of abbreviations used
- non-standard abbreviations
- nonstandard abbreviations
- nonstandard abbreviations and acronyms
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- abbreviations section
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- author information section
- The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)
- A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
- PERSON: Bill Baumgartner
- author information
- authors’ information
- biographies
- contributor information
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- author information section
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- author information textual entity
- From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/):
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-IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
- A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
- PERSON: Bill Baumgartner
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- author information textual entity
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- author summary section
- The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)
- A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers.
- PERSON: Bill Baumgartner
- author summary
- summary
- synopsis
- Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)
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- author summary section
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- author summary textual entity
- From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/):
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-The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX.
- A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
- PERSON: Bill Baumgartner
- Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
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- author summary textual entity
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- availability section
- The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
- A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained.
- PERSON: Bill Baumgartner
- availability
- availability of data
- data archiving
- data availability
- data availability statement
- data sharing statement
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- availability section
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- availability textual entity
- From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):
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-Project home page:http://krux.googlecode.com
- A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
- PERSON: Bill Baumgartner
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- availability textual entity
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- case report section
- The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
- A part of a document about the medical history of a specific patient as it relates to the topic of the document.
- PERSON: Bill Baumgartner
- case presentation
- case report
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- case report section
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- case report textual entity
- Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/):
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-The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
- A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
- PERSON: Bill Baumgartner
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- case report textual entity
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- conclusion section
- The section labelled 'conclusion' in a typical scientific journal article.
- A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document.
- PERSON: Bill Baumgartner
- concluding remarks
- conclusion
- conclusions
- findings
- summary
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- conclusion section
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- conflict of interest section
- The section labelled 'conflict of interest statement' in a typical scientific journal article.
- A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document.
- PERSON: Bill Baumgartner
- authors' disclosures of potential conflicts of interest
- competing financial interests
- competing interests
- conflict of interest
- conflict of interest statement
- conflict of interests
- conflicts of interest
- declaration of competing interest
- declaration of competing interests
- declaration of interest
- declaration of interests
- disclosure of conflict of interest
- disclosure of potential conflicts of interest
- duality of interest
- statement of interest
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- conflict of interest section
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- conflict of interest statement
- SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)]
- A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document.
- PERSON: Bill Baumgartner
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- conflict of interest textual entity
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- consent section
- The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
- A part of a document about the consent process that was used to enroll patients in a study.
- PERSON: Bill Baumgartner
- consent
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- consent section
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- consent textual entity
- From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):
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-Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.
- A textual entity that documents the consenting process used to enroll patients in a study.
- PERSON: Bill Baumgartner
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- consent textual entity
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- ethical approval section
- The section labelled 'ethical approval' in a typical scientific journal article.
- A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
- PERSON: Bill Baumgartner
- ethical approval
- ethical requirements
- ethics
- ethics statement
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- ethical approval section
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- ethical approval textual entity
- From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
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-The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review.
- A textual entity that documents the ethical approval of some study design.
- PERSON: Bill Baumgartner
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- ethical approval textual entity
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- figures section
- The section labelled 'figures' in a typical scientific journal article.
- A part of a document that contains one or more figures.
- PERSON: Bill Baumgartner
- figures
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- figures section
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- funding source declaration section
- The section labelled 'funding' in a typical scientific journal article.
- A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
- PERSON: Bill Baumgartner
- financial support
- funding
- funding information
- funding sources
- funding statement
- funding/support
- grants
- role of the funding source
- source of funding
- sources of funding
- study funding
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- funding source declaration section
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- funding souce declaration textual entity
- From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/):
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-This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication.
- A textual entity documenting the source of funding that supported some study.
- PERSON: Bill Baumgartner
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- funding source declaration textual entity
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- future directions section
- The section labelled 'future directions' in a typical scientific journal article.
- A part of a document detailing extensions of the described work that may be implemented at some future point in time.
- PERSON: Bill Baumgartner
- future challenges
- future considerations
- future developments
- future directions
- future outlook
- future perspectives
- future plans
- future prospects
- future research
- future research directions
- future studies
- future work
- outlook
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- future directions section
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- future directions textual entity
- Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/):
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-In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members.
- A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
- PERSON: Bill Baumgartner
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- future directions textual entity
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- genome announcement section
- The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)
- A document part announcing the publication of a novel draft genome sequence.
- PERSON: Bill Baumgartner
- genome announcement
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- genome announcement section
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- genome announcement textual entity
- Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/):
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-Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB).
- A textual entity that describes the generation and public release of a novel, draft genome sequence.
- PERSON: Bill Baumgartner
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- genome announcement textual entity
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- keyword textual entity
- From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/):
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-Exon orthology; alternative splicing; exon duplication; intron-exon structure.
- A textual entity listing keywords indicating the major theme(s) of a document.
- PERSON: Bill Baumgartner
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- keyword textual entity
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- keywords section
- The section labelled 'keywords' in a typical scientific journal article.
- A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
- PERSON: Bill Baumgartner
- keywords
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- keywords section
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- study limitations section
- The section labelled 'limitations' in a typical scientific journal article.
- A part of a document about biases or short comings related to the study design and execution.
- PERSON: Bill Baumgartner
- limitations
- study limitations
- Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
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- study limitations section
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- study limitations textual entity
- Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/).
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-Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out.
- A textual entity addressing a shortcoming or bias of a study design or execution.
- PERSON: Bill Baumgartner
- Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
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- study limitations textual entity
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- materials section
- The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
- A part of a document about the materials required to reproduce the content of the document.
- PERSON: Bill Baumgartner
- materials
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- materials section
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- notes section
- The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
- A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
- PERSON: Bill Baumgartner
- notes
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- notes section
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- patients section
- The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)
- A part of a document about the patients that participated in a study.
- PERSON: Bill Baumgartner
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- patients section
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- patients textual entity
- Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/):
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-Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred.
- A textual entity expressing information regarding the patients used in a study.
- PERSON: Bill Baumgartner
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- patients textual entity
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- pre-publication history section
- The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)
- A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors.
- PERSON: Bill Baumgartner
- notice of republication
- pre-publication history
-
- pre-publication history section
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- pre-publication history textual entity
- From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/):
-
-The pre-publication history for this paper can be accessed here:
-http://www.biomedcentral.com/1471-2253/13/33/prepub
- A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information.
- PERSON: Bill Baumgartner
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- pre-publication history textual entity
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- related work section
- The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)
- A part of a document about work in other publications that is relevant to the content of the document.
- PERSON: Bill Baumgartner
- related literature
- related work
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- related work section
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- related work textual entity
- Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/):
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-Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
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- A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
- PERSON: Bill Baumgartner
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- related work textual entity
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- requirements section
- The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
- A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
- PERSON: Bill Baumgartner
- requirements
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- requirements section
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- requirements textual entity
- From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):
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-• Operating systems: Platform independent
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-• Programming language: Matlab, R, Python
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-• Other requirements: None
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-• License: GNU GPL v3
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-• Any restrictions to use by non-academics: None
- A textual entity that expresses the requirements necessary to use a resource, e.g. software.
- PERSON: Bill Baumgartner
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- requirements textual entity
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- statistical analysis textual entity
- From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/):
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-Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant.
- A textual entity documenting statistical analysis tools and techniques employed.
- PERSON: Bill Baumgartner
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- statistical analysis textual entity
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- statistical analysis section
- The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
- A part of the document used to describe the statistical methodologies employed in the work presented in the document.
- PERSON: Bill Baumgartner
- statistical analysis
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- statistical analysis section
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- tables section
- The section labelled 'tables' in a typical scientific journal article.
- A part of a document that contains one or more tables.
- PERSON: Bill Baumgartner
- tables
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- tables section
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- An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail.
- Mathias Brochhausen
- postal code
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- A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region.
- Mathias Brochhausen
- Postal delivery route
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- A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes.
- Mathias Brochhausen
- ZIP code
- zone improvement plan code
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- database extract, transform, and load process
- A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
- Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second
- Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.
- PERSON:Alan Ruttenberg
- ETL
- WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load
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- database extract, transform, and load process
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- the section of the document where the title appears
- This term should not be confused with dc:title - this term represents the component of the document where the title appears, and not the value of the title itself.
- Charles Tapley Hoyt
- https://github.com/information-artifact-ontology/IAO/issues/286
- title section
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- descriptive data section
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- A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made.
- PERSON: Chen Yang
- PERSON: Jie Zheng
- https://www.equator-network.org/reporting-guidelines/prisma/
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- ONE ontology
- descriptive data section
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- additional results section
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- A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)
- PERSON: Chen Yang
- PERSON: Jie Zheng
- https://www.equator-network.org/reporting-guidelines/consort/
- https://www.equator-network.org/reporting-guidelines/prisma/
- https://www.equator-network.org/reporting-guidelines/strobe/
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- ONE ontology
- additional results section
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- research participants section
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- A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.).
- PERSON: Chen Yang
- PERSON: Jie Zheng
- https://www.equator-network.org/reporting-guidelines/consort/
- https://www.equator-network.org/reporting-guidelines/prisma/
- https://www.equator-network.org/reporting-guidelines/strobe-nut/
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- ONE ontology
- research participants section
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- measurement methods section
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- A methods section that describes details of data assessment methods (data measurement).
- PERSON: Chen Yang
- PERSON: Jie Zheng
- https://www.equator-network.org/reporting-guidelines/strobe/
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- ONE ontology
- measurement methods section
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- research settings section
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- A document part that describes the physical/social/cultural conditions around a research trial.
- PERSON: Chen Yang
- PERSON: Jie Zheng
- https://www.ncbi.nlm.nih.gov/books/NBK262175/
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- ONE ontology
- research settings section
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- study bias section
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- A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others.
- PERSON: Chen Yang
- PERSON: Jie Zheng
- DOI: 10.1097/PRS.0b013e3181de24bc
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- ONE ontology
- study bias section
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- graphical abstract
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- An abstract that is pictorial summary of the main findings described in the document.
- PERSON: Jie Zheng
- PERSON: Tim Beck
- visual abstract
- https://www.elsevier.com/authors/journal-authors/graphical-abstract
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- Biomedical literature NLP project
- graphical abstract
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- A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor.
- "You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/]
- This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25)
- http://orcid.org/0000-0002-1595-3213
- ORCID ID
- ORCiD
- Open Researcher and Contributor ID
- Open Researcher and Contributor Identifier
- https://orcid.org/
- https://github.com/information-artifact-ontology/IAO/issues/259
- ORCID identifier
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- data collection
- A data entity that consists of multiple data entities.
- Sebastian Duesing
- data set
- https://github.com/information-artifact-ontology/IAO/issues/283
- https://github.com/obi-ontology/obi/issues/1877
- data collection
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- identifier
- An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
- Justin Whorton
- Mathias Brochhausen
- proper name
- https://github.com/information-artifact-ontology/IAO/issues/237
- Mathias Brochhausen
- Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
- identifier
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- alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems
- An information content entity that is a fundamental unit in a written language.
- Justin Whorton
- http://en.wikipedia.org/wiki/Grapheme
- https://github.com/information-artifact-ontology/IAO/issues/237
- Mathias Brochhausen
- Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there.
- grapheme
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- A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
- Justin Whorton
- Mathias Brochhausen
- dubbing process
- naming
- https://github.com/information-artifact-ontology/IAO/issues/237
- Mathias Brochhausen
- identifier creating process
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- An identifier referring to an individual entity that is ascribed personhood by the user of the identifier.
- Justin Whorton
- Mathias Brochhausen
- http://en.wikipedia.org/wiki/Personal_name
- https://github.com/information-artifact-ontology/IAO/issues/237
- Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
- Personal names to not include names of fictional characters, e.g. Sherlock Holmes.
- Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)
- personal name
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- A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name
- Justin Whorton
- Mathias Brochhausen
- first name
- http://en.wikipedia.org/wiki/Given_name
- https://github.com/information-artifact-ontology/IAO/issues/237
- given name
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- An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children.
- Justin Whorton
- Mathias Brochhausen
- last name
- surname
- http://en.wikipedia.org/wiki/Family_name
- https://github.com/information-artifact-ontology/IAO/issues/237
- family name
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- An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.
- Alan Ruttenberg
- Justin Whorton
- Mathias Brochhausen
- code map
- code system
- codeset
- coding system
- controlled vocabulary
- https://github.com/information-artifact-ontology/IAO/issues/237
- Alan Ruttenberg
- Clint Dowland
- Matt Diller
- Sarah Bost
- William R. Hogan
- Code sets might include non-entities/things (e.g. missing thumbs).
- Does not imply absence vs. presence of any taxonomy.
- Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.
- Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.
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-When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
- For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
- For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
- Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.
- The information content entities do not denote each other.
- code set
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- ontology module
- I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
- ontology file
- This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
- ontology module
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- base ontology module
- An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
- base ontology module
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- editors ontology module
- An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
- source ontology module
- editors ontology module
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- main release ontology module
- An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
- TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
- main release ontology module
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- bridge ontology module
- An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
- bridge ontology module
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- import ontology module
- A subset ontology module that is intended to be imported from another ontology.
- TODO: add axioms that indicate this is the output of a module extraction process.
- import file
- import ontology module
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- subset ontology module
- An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
- ontology slim
- subset ontology
- subset ontology module
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- curation subset ontology module
- A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
- curation subset ontology module
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- analysis ontology module
- An ontology module that is intended for usage in analysis or discovery applications.
- analysis subset ontology module
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- single layer ontology module
- A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
- ribbon subset
- single layer subset ontology module
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- exclusion subset ontology module
- A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
- antislim
- exclusion subset ontology module
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- external import ontology module
- An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
- external import
- external import ontology module
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- species subset ontology module
- A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
- taxon subset
- species subset ontology module
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- reasoned ontology module
- An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
- reasoned ontology module
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- generated ontology module
- An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
- TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
- generated ontology module
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- template generated ontology module
- An ontology module that is automatically generated from a template specification and fillers for slots in that template.
- template generated ontology module
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- taxonomic bridge ontology module
- taxonomic bridge ontology module
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- ontology module subsetted by expressivity
- ontology module subsetted by expressivity
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- obo basic subset ontology module
- A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.
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-Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).
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-An ontology is OBO Basic if and only if it has the following characteristics:
-DAG
-Unidirectional
-No Dangling Clauses
-Fully Asserted
-Fully Labeled
-No equivalence axioms
-Singly labeled edges
-No qualifier lists
-No disjointness axioms
-No owl-axioms header
-No imports
- obo basic subset ontology module
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- ontology module subsetted by OWL profile
- ontology module subsetted by OWL profile
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- EL++ ontology module
- EL++ ontology module
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- investigation
- a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
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- investigation
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- study design execution
- a planned process that carries out a study design
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- study design execution
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- data transformation
- A completely executed planned process that produces output data from input data.
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- data transformation
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- study design
- A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
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- study design
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- morphology
- A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
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- morphology
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- length
- A 1-D extent quality which is equal to the distance between two points.
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- length
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- mass
- A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
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- mass
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- physical quality
- A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
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- physical quality
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- physical object quality
- A quality which inheres in a continuant.
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- physical object quality
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- length unit
- A unit which is a standard measure of the distance between two points.
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- length unit
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- mass unit
- A unit which is a standard measure of the amount of matter/energy of a physical object.
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- mass unit
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- time unit
- A unit which is a standard measure of the dimension in which events occur in sequence.
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- time unit
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- example to be eventually removed
- example to be eventually removed
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- failed exploratory term
- The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job.
- Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification.
- Person:Alan Ruttenberg
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- failed exploratory term
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-
-
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- metadata complete
- Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
- metadata complete
-
-
-
-
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-
-
- organizational term
- The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release.
- organizational term
-
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-
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- ready for release
- Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
- ready for release
-
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- metadata incomplete
- Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
- metadata incomplete
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- uncurated
- Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
- uncurated
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- pending final vetting
- All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
- pending final vetting
-
-
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-
-
-
-
- Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
- PERSON: Alan Ruttenberg
- PERSON: Melanie Courtot
-
- obsolete_core
- true
-
-
-
-
-
-
-
-
-
- placeholder removed
- The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined.
- This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider.
-
-
- placeholder removed
-
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- terms merged
- The term has been combined with one or more other terms to create a more encompassing (merged) term.
- The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge.
-
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- terms merged
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- term imported
- The term has been replaced by a term imported from another ontology.
- This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001.
-
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- term imported
-
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- term split
- The term has been split into two or more new terms.
- This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001.
-
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- term split
-
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-
- This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
- We expect to be able to mine these new reasons and add instances as required.
- obsolete_other
- true
-
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- universal
- Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
- Alan Ruttenberg
- A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
- universal
-
-
-
-
-
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- defined class
- A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
- "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
- Alan Ruttenberg
- defined class
-
-
-
-
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- named class expression
- A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
- named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
- Alan Ruttenberg
- named class expression
-
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- to be replaced with external ontology term
- Terms with this status should eventually replaced with a term from another ontology.
- Alan Ruttenberg
- group:OBI
- to be replaced with external ontology term
-
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- requires discussion
- A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
- Alan Ruttenberg
- group:OBI
- requires discussion
-
-
-
-
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-
- The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
- This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype.
-
- https://github.com/information-artifact-ontology/ontology-metadata/issues/77
- https://orcid.org/0000-0001-5208-3432
-
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- out of scope
-
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-
- The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality.
- This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore).
-
- https://github.com/information-artifact-ontology/ontology-metadata/issues/136
- https://orcid.org/0000-0002-4142-7153
- domain entity does not exist
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diff --git a/03_TECHNICAL_CORE/ontology/imports/iao_bot.owl b/03_TECHNICAL_CORE/ontology/imports/iao_bot.owl
new file mode 100644
index 0000000..c9476c7
--- /dev/null
+++ b/03_TECHNICAL_CORE/ontology/imports/iao_bot.owl
@@ -0,0 +1,1621 @@
+
+
+
+ en
+ Adam Goldstein
+ Alan Ruttenberg
+ Albert Goldfain
+ Barry Smith
+ Bjoern Peters
+ Carlo Torniai
+ Charles Tapley Hoyt
+ Chris Mungall
+ Chris Stoeckert
+ Christian A. Boelling
+ Clint Dowland
+ Darren Natale
+ David Osumi-Sutherland
+ Gwen Frishkoff
+ Holger Stenzhorn
+ James A. Overton
+ James Malone
+ Jennifer Fostel
+ Jie Zheng
+ Jonathan Rees
+ Larisa Soldatova
+ Lawrence Hunter
+ Mathias Brochhausen
+ Matt Brush
+ Melanie Courtot
+ Michel Dumontier
+ Paolo Ciccarese
+ Pat Hayes
+ Philippe Rocca-Serra
+ Randy Dipert
+ Ron Rudnicki
+ Satya Sahoo
+ Sivaram Arabandi
+ Werner Ceusters
+ William Duncan
+ William Hogan
+ Yongqun (Oliver) He
+ The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.
+ Information Artifact Ontology (IAO)
+
+ An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO
+ IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999
+ IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999
+
+ 2026-03-30
+
+
+
+
+
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+
+ This document is about information artifacts and their representations
+
+ A (currently) primitive relation that relates an information artifact to an entity.
+ 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
+
+We will try to build it back up by elaborating the various subproperties that are more precisely defined.
+
+Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
+ person:Alan Ruttenberg
+ Smith, Ceusters, Ruttenberg, 2000 years of philosophy
+
+ is about
+
+
+
+
+
+
+
+
+
+ inheres in
+ this fragility is a characteristic of this vase
+ this red color is a characteristic of this apple
+ a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
+ inheres_in
+
+ Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
+
+ characteristic of
+
+
+
+
+
+
+
+
+
+ bearer of
+ this apple is bearer of this red color
+ this vase is bearer of this fragility
+ Inverse of characteristic_of
+ A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
+ bearer_of
+ is bearer of
+
+
+ has characteristic
+
+
+
+
+
+
+
+
+
+
+ this catalysis function is a function of this enzyme
+ a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
+ A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
+ function_of
+ is function of
+ This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
+
+ function of
+
+
+
+
+
+
+
+
+
+ this red color is a quality of this apple
+ a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
+ A quality inheres in its bearer at all times for which the quality exists.
+ is quality of
+ quality_of
+ This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
+
+ quality of
+
+
+
+
+
+
+
+
+
+ this investigator role is a role of this person
+ a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
+ A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
+ is role of
+ role_of
+ This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
+
+ role of
+
+
+
+
+
+
+
+
+
+
+ this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
+ a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
+ A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
+ has_function
+
+ has function
+
+
+
+
+
+
+
+
+
+ this apple has quality this red color
+ a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
+ A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
+ has_quality
+
+ has quality
+
+
+
+
+
+
+
+
+
+
+ this person has role this investigator role (more colloquially: this person has this role of investigator)
+ a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
+ A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
+ has_role
+
+ has role
+
+
+
+
+
+
+
+
+
+
+
+ a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
+
+ has disposition
+
+
+
+
+
+
+
+
+ This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
+
+ disposition of
+
+
+
+
+
+
+
+
+
+
+
+
+ entity
+ Entity
+ Julius Caesar
+ Verdi’s Requiem
+ the Second World War
+ your body mass index
+ BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
+ Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
+ An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
+
+ entity
+
+
+
+
+ Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
+
+ per discussion with Barry Smith
+
+
+
+
+
+ An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
+
+
+
+
+
+
+
+
+
+ continuant
+ Continuant
+ An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
+ BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
+ Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
+ A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
+ if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
+ if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
+ if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
+ (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
+ (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
+ (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
+ (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
+
+ continuant
+
+
+
+
+ (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
+
+
+
+
+
+ (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
+
+
+
+
+
+ Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
+
+
+
+
+
+ A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
+
+
+
+
+
+ if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
+
+
+
+
+
+ if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
+
+
+
+
+
+ if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
+
+
+
+
+
+ (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
+
+
+
+
+
+ (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
+
+
+
+
+
+
+
+
+
+
+
+ ic
+ IndependentContinuant
+ a chair
+ a heart
+ a leg
+ a molecule
+ a spatial region
+ an atom
+ an orchestra.
+ an organism
+ the bottom right portion of a human torso
+ the interior of your mouth
+ b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
+ For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
+ For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
+ (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
+ (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
+ (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
+ A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
+
+ independent continuant
+
+
+
+
+ b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
+
+
+
+
+
+ For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
+
+
+
+
+
+ For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
+
+
+
+
+
+ (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
+
+
+
+
+
+ (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
+
+
+
+
+
+ (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
+
+
+
+
+
+
+
+
+
+
+ disposition
+ Disposition
+ an atom of element X has the disposition to decay to an atom of element Y
+ certain people have a predisposition to colon cancer
+ children are innately disposed to categorize objects in certain ways.
+ the cell wall is disposed to filter chemicals in endocytosis and exocytosis
+ BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
+ b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
+ If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
+ (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
+ (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
+
+ disposition
+
+
+
+
+ b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
+
+
+
+
+
+ If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
+
+
+
+
+
+ (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
+
+
+
+
+
+ (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
+
+
+
+
+
+
+
+
+
+
+ realizable
+ RealizableEntity
+ the disposition of this piece of metal to conduct electricity.
+ the disposition of your blood to coagulate
+ the function of your reproductive organs
+ the role of being a doctor
+ the role of this boundary to delineate where Utah and Colorado meet
+ A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
+ To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
+ All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
+ (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
+ (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
+
+ realizable entity
+
+
+
+
+ To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
+
+
+
+
+
+ All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
+
+
+
+
+
+ (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
+
+
+
+
+
+ (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
+
+
+
+
+
+
+
+
+
+ quality
+ Quality
+ the ambient temperature of this portion of air
+ the color of a tomato
+ the length of the circumference of your waist
+ the mass of this piece of gold.
+ the shape of your nose
+ the shape of your nostril
+ a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
+ If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
+ (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
+ (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
+
+ quality
+
+
+
+
+ a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
+
+
+
+
+
+ If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
+
+
+
+
+
+ (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
+
+
+
+
+
+ (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
+
+
+
+
+
+
+
+
+
+
+ sdc
+ SpecificallyDependentContinuant
+ Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
+ of one-sided specifically dependent continuants: the mass of this tomato
+ of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
+ the disposition of this fish to decay
+ the function of this heart: to pump blood
+ the mutual dependence of proton donors and acceptors in chemical reactions [79
+ the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
+ the pink color of a medium rare piece of grilled filet mignon at its center
+ the role of being a doctor
+ the shape of this hole.
+ the smell of this portion of mozzarella
+ b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
+ Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
+ (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
+ A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
+
+ specifically dependent continuant
+
+
+
+
+ b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
+
+
+
+
+
+ Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
+
+ per discussion with Barry Smith
+
+
+
+
+ (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
+
+
+
+
+
+
+
+
+
+ role
+ Role
+ John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
+ the priest role
+ the role of a boundary to demarcate two neighboring administrative territories
+ the role of a building in serving as a military target
+ the role of a stone in marking a property boundary
+ the role of subject in a clinical trial
+ the student role
+ A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
+ BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
+ b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
+ (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
+
+ role
+
+
+
+
+ b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
+
+
+
+
+
+ (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
+
+
+
+
+
+
+
+
+
+ gdc
+ GenericallyDependentContinuant
+ The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
+ the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
+ the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
+ b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
+ (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
+ A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
+
+ generically dependent continuant
+
+
+
+
+ b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
+
+
+
+
+
+ (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
+
+
+
+
+
+
+
+
+
+ function
+ Function
+ the function of a hammer to drive in nails
+ the function of a heart pacemaker to regulate the beating of a heart through electricity
+ the function of amylase in saliva to break down starch into sugar
+ BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
+ A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
+ (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
+
+ function
+
+
+
+
+ A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
+
+
+
+
+
+ (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
+
+
+
+
+
+
+
+
+
+ data entity
+ Data items include counts of things, analyte concentrations, and statistical summaries.
+
+ An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
+ 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
+ 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
+ 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
+ 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
+ JAR: datum -- well, this will be very tricky to define, but maybe some
+information-like stuff that might be put into a computer and that is
+meant, by someone, to denote and/or to be interpreted by some
+process... I would include lists, tables, sentences... I think I might
+defer to Barry, or to Brian Cantwell Smith
+
+JAR: A data item is an approximately justified approximately true approximate belief
+ PERSON: Alan Ruttenberg
+ PERSON: Chris Stoeckert
+ PERSON: Jonathan Rees
+ data
+ data item
+
+ data entity
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ information content entity
+ Examples of information content entites include journal articles, data, graphical layouts, and graphs.
+
+ A generically dependent continuant that is about some thing.
+ 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
+ information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
+
+Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
+ PERSON: Chris Stoeckert
+ OBI_0000142
+
+ information content entity
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ curation status specification
+
+ The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
+ Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
+ PERSON:Bill Bug
+ GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
+ OBI_0000266
+
+ curation status specification
+
+
+
+
+
+
+
+
+ data about an ontology part
+ Data about an ontology part is a data item about a part of an ontology, for example a term
+ Person:Alan Ruttenberg
+
+ data about an ontology part
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ obsolescence reason specification
+
+ The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
+ The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
+ PERSON: Alan Ruttenberg
+ PERSON: Melanie Courtot
+
+ obsolescence reason specification
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ denotator type
+ The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
+ A denotator type indicates how a term should be interpreted from an ontological perspective.
+ Alan Ruttenberg
+ Barry Smith, Werner Ceusters
+
+ denotator type
+
+
+
+
+
+
+
+
+
+
+
+
+
+ example to be eventually removed
+
+ example to be eventually removed
+
+
+
+
+
+
+
+
+ failed exploratory term
+ The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job.
+ Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification.
+ Person:Alan Ruttenberg
+
+
+
+ failed exploratory term
+
+
+
+
+
+
+
+
+ metadata complete
+ Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
+
+ metadata complete
+
+
+
+
+
+
+
+
+ organizational term
+ The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release.
+
+ organizational term
+
+
+
+
+
+
+
+
+ ready for release
+ Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
+
+ ready for release
+
+
+
+
+
+
+
+
+ metadata incomplete
+ Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
+
+ metadata incomplete
+
+
+
+
+
+
+
+
+ uncurated
+ Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
+
+ uncurated
+
+
+
+
+
+
+
+
+ pending final vetting
+ All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
+
+ pending final vetting
+
+
+
+
+
+
+
+
+ placeholder removed
+ The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined.
+ This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider.
+
+
+
+ placeholder removed
+
+
+
+
+
+
+
+
+ terms merged
+ The term has been combined with one or more other terms to create a more encompassing (merged) term.
+ The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge.
+
+
+
+ terms merged
+
+
+
+
+
+
+
+
+ term imported
+ The term has been replaced by a term imported from another ontology.
+ This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001.
+
+
+
+ term imported
+
+
+
+
+
+
+
+
+ term split
+ The term has been split into two or more new terms.
+ This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001.
+
+
+
+ term split
+
+
+
+
+
+
+
+
+ universal
+ Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
+ Alan Ruttenberg
+ A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
+
+ universal
+
+
+
+
+
+
+
+
+ defined class
+ A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
+ "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
+ Alan Ruttenberg
+
+ defined class
+
+
+
+
+
+
+
+
+ named class expression
+ A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
+ named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
+ Alan Ruttenberg
+
+ named class expression
+
+
+
+
+
+
+
+
+ to be replaced with external ontology term
+ Terms with this status should eventually replaced with a term from another ontology.
+ Alan Ruttenberg
+ group:OBI
+
+ to be replaced with external ontology term
+
+
+
+
+
+
+
+
+ requires discussion
+ A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
+ Alan Ruttenberg
+ group:OBI
+
+ requires discussion
+
+
+
+
+
+
+
+
+ The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
+ This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype.
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/77
+ https://orcid.org/0000-0001-5208-3432
+
+
+
+ out of scope
+
+
+
+
+
+
+
+
+ The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality.
+ This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore).
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/136
+ https://orcid.org/0000-0002-4142-7153
+
+ domain entity does not exist
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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diff --git a/03_TECHNICAL_CORE/ontology/imports/ro.owl b/03_TECHNICAL_CORE/ontology/imports/ro.owl
deleted file mode 100644
index fff2d40..0000000
--- a/03_TECHNICAL_CORE/ontology/imports/ro.owl
+++ /dev/null
@@ -1,19040 +0,0 @@
-
-
-
-
- The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
-
- OBO Relations Ontology
- 2025-12-17
- https://github.com/oborel/obo-relations/
-
-
-
-
-
-
-
-
-
-
-
-
- editor preferred term
-
- The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- editor preferred term
-
-
-
-
-
-
-
- example of usage
-
- A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- example of usage
- example of usage
-
-
-
-
-
-
-
- has curation status
- PERSON:Alan Ruttenberg
- PERSON:Bill Bug
- PERSON:Melanie Courtot
- has curation status
-
-
-
-
-
-
-
- definition
-
- The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
- 2012-04-05:
-Barry Smith
-
-The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
-
-Can you fix to something like:
-
-A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
-
-Alan Ruttenberg
-
-Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
-
-On the specifics of the proposed definition:
-
-We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
-
-Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
-
-We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- definition
- definition
-
-
-
-
-
-
-
- editor note
-
- An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
- editor note
-
-
-
-
-
-
-
- term editor
-
- Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
- 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- term editor
-
-
-
-
-
-
-
- alternative label
-
- A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
- OBO Operations committee
- PERSON:Daniel Schober
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
- alternative label
-
-
-
-
-
-
-
- definition source
-
- Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
- PERSON:Daniel Schober
- Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- definition source
-
-
-
-
-
-
-
- curator note
-
- An administrative note of use for a curator but of no use for a user
- PERSON:Alan Ruttenberg
- curator note
-
-
-
-
-
-
-
- term tracker item
- the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
-
- An IRI or similar locator for a request or discussion of an ontology term.
- Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
- Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
- The 'tracker item' can associate a tracker with a specific ontology term.
- term tracker item
-
-
-
-
-
-
-
- imported from
-
- For external terms/classes, the ontology from which the term was imported
- PERSON:Alan Ruttenberg
- PERSON:Melanie Courtot
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- imported from
-
-
-
-
-
-
-
- expand expression to
- ObjectProperty: RO_0002104
-Label: has plasma membrane part
-Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
-
- A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
- Chris Mungall
- expand expression to
-
-
-
-
-
-
-
- expand assertion to
- ObjectProperty: RO???
-Label: spatially disjoint from
-Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
-
- A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
- Chris Mungall
- expand assertion to
-
-
-
-
-
-
-
- first order logic expression
- An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.
- PERSON:Alan Ruttenberg
- first order logic expression
-
-
-
-
-
-
-
-
- OBO foundry unique label
-
- An alternative name for a class or property which is unique across the OBO Foundry.
- The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
- PERSON:Alan Ruttenberg
- PERSON:Bjoern Peters
- PERSON:Chris Mungall
- PERSON:Melanie Courtot
- GROUP:OBO Foundry <http://obofoundry.org/>
- OBO foundry unique label
-
-
-
-
-
-
-
- elucidation
- person:Alan Ruttenberg
- Person:Barry Smith
- Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
- elucidation
-
-
-
-
-
-
-
- term replaced by
-
- Use on obsolete terms, relating the term to another term that can be used as a substitute
- Person:Alan Ruttenberg
- Person:Alan Ruttenberg
- Add as annotation triples in the granting ontology
- term replaced by
-
-
-
-
-
-
-
- 'part disjoint with' 'defined by construct' """
- PREFIX owl: <http://www.w3.org/2002/07/owl#>
- PREFIX : <http://example.org/
- CONSTRUCT {
- [
- a owl:Restriction ;
- owl:onProperty :part_of ;
- owl:someValuesFrom ?a ;
- owl:disjointWith [
- a owl:Restriction ;
- owl:onProperty :part_of ;
- owl:someValuesFrom ?b
- ]
- ]
- }
- WHERE {
- ?a :part_disjoint_with ?b .
- }
- Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
-
-
-
- defined by construct
-
-
-
-
-
-
-
- An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
- temporal interpretation
-
-
-
-
-
-
-
-
-
- tooth SubClassOf 'never in taxon' value 'Aves'
- x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
-
-
-
- Class: ?X DisjointWith: RO_0002162 some ?Y
- PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
-PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
-CONSTRUCT {
- in_taxon: a owl:ObjectProperty .
- ?x owl:disjointWith [
- a owl:Restriction ;
- owl:onProperty in_taxon: ;
- owl:someValuesFrom ?taxon
- ] .
- ?x rdfs:subClassOf [
- a owl:Restriction ;
- owl:onProperty in_taxon: ;
- owl:someValuesFrom [
- a owl:Class ;
- owl:complementOf ?taxon
- ]
- ] .
-}
-WHERE {
- ?x never_in_taxon: ?taxon .
-}
- never in taxon
-
-
-
-
-
-
-
-
-
- A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
- non-overlapping with
- shares no parts with
-
- Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
- PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050>
-PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171>
-CONSTRUCT {
- part_of: a owl:ObjectProperty .
- [
- a owl:Restriction ;
- owl:onProperty part_of: ;
- owl:someValuesFrom ?x ;
- owl:disjointWith [
- a owl:Restriction ;
- owl:onProperty part_of: ;
- owl:someValuesFrom ?y
- ]
- ]
-}
-WHERE {
- ?x mutually_spatially_disjoint_with: ?y .
-}
- mutually spatially disjoint with
-
- https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
-
-
-
-
-
-
-
-
- An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
- taxonomic class assertion
-
-
-
-
-
-
-
-
-
- S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]
- ambiguous for taxon
-
-
-
-
-
-
-
-
-
- S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
-
-
- This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
- dubious for taxon
-
-
-
-
-
-
-
-
-
- S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
-
-
- PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
-PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
-CONSTRUCT {
- in_taxon: a owl:ObjectProperty .
- ?witness rdfs:label ?label .
- ?witness rdfs:subClassOf ?x .
- ?witness rdfs:subClassOf [
- a owl:Restriction ;
- owl:onProperty in_taxon: ;
- owl:someValuesFrom ?taxon
- ] .
-}
-WHERE {
- ?x present_in_taxon: ?taxon .
- BIND(IRI(CONCAT(
- "http://purl.obolibrary.org/obo/RO_0002175#",
- MD5(STR(?x)),
- "-",
- MD5(STR(?taxon))
- )) as ?witness)
- BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label)
-}
- The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.
- present in taxon
-
-
-
-
-
-
-
-
-
- defined by inverse
-
-
-
-
-
-
-
-
- An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
- logical macro assertion
- http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/
-
-
-
-
-
-
-
- An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.
- annotation property cardinality
-
-
-
-
-
-
-
-
-
- A logical macro assertion whose domain is an IRI for a class
- The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
- logical macro assertion on a class
-
-
-
-
-
-
-
-
- A logical macro assertion whose domain is an IRI for a property
- logical macro assertion on a property
-
-
-
-
-
-
-
-
- Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
- logical macro assertion on an object property
-
-
-
-
-
-
-
-
- logical macro assertion on an annotation property
-
-
-
-
-
-
-
-
- An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.
- dispositional interpretation
-
-
-
-
-
-
-
-
- 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
- A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
- shares no connection with
- Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
- has no connections with
-
-
-
-
-
-
-
-
- inherited annotation property
-
-
-
-
-
-
-
- Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)
- curator guidance link
-
-
-
-
-
-
-
-
- brain always_present_in_taxon 'Vertebrata'
- forelimb always_present_in_taxon Euarchontoglires
- S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S
- This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed.
- never lost in
- always present in taxon
-
-
-
-
-
-
-
-
- This property was originally created for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans.
- temporal logical macro assertion on a class
-
-
-
-
-
-
-
-
- measurement property has unit
-
-
-
-
-
-
-
-
- has start time value
- http://purl.obolibrary.org/obo/ro/docs/temporal-durations/
-
-
-
-
-
-
-
-
- has end time value
-
-
-
-
-
-
-
-
-
- Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.
- start, days post fertilization
-
-
-
-
-
-
-
-
-
- Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.
- end, days post fertilization
-
-
-
-
-
-
-
-
-
- Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.
- start, years post birth
-
-
-
-
-
-
-
-
-
- Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2
- end, years post birth
-
-
-
-
-
-
-
-
-
- Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.
- start, months post birth
-
-
-
-
-
-
-
-
-
- Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2
- end, months post birth
-
-
-
-
-
-
-
-
-
- Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.
- month of gestation
-
-
-
-
-
-
-
-
-
- A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process
- has developmental stage marker
-
-
-
-
-
-
-
-
-
- Count of number of days intervening between the start of the stage and the time of coitum.
- For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)
- start, days post coitum
-
-
-
-
-
-
-
-
-
- Count of number of days intervening between the end of the stage and the time of coitum.
- end, days post coitum
-
-
-
-
-
-
-
-
-
- start, weeks post birth
-
-
-
-
-
-
-
-
-
- end, weeks post birth
-
-
-
-
-
-
-
-
-
- If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p
- is asymmetric relational form of process class
- http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
-
-
-
-
-
-
-
-
- If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p
- is symmetric relational form of process class
- http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
-
-
-
-
-
-
-
-
- R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process
- is relational form of process class
- http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
-
-
-
-
-
-
-
-
- relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
- The general property hierarchy is:
-
- "directly P" SubPropertyOf "P"
- Transitive(P)
-
-Where we have an annotation assertion
-
- "directly P" "is direct form of" "P"
- If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
-
- is direct form of
-
-
-
-
-
-
-
-
-
- relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
-
- is indirect form of
-
-
-
-
-
-
-
-
-
- logical macro assertion on an axiom
-
-
-
-
-
-
-
-
- If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
- is a defining property chain axiom
-
-
-
-
-
-
-
-
- If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
- is a defining property chain axiom where second argument is reflexive
-
-
-
-
-
-
-
-
- An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.
- is relational form of a class
-
-
-
-
-
-
-
-
- A shortcut relationship that holds between two entities based on their identity criteria
- logical macro assertion involving identity
-
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- A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.
- in approximate one to one relationship with
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- x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y
- The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y"
- is approximately equivalent to
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- 'anterior end of organism' is-opposite-of 'posterior end of organism'
- 'increase in temperature' is-opposite-of 'decrease in temperature'
- x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
- is opposite of
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- x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
- is indistinguishable from
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- evidential logical macro assertion on an axiom
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- A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom
- This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
- axiom has evidence
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- A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom
- This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
- axiom contradicted by evidence
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- In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context.
- this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.
- If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion
- is representative IRI for equivalence set
- OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member
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- true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation.
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- nominally disjoint with
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- Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
-
- 2018-03-13T23:59:29Z
- is directional form of
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- 2018-03-14T00:03:16Z
- is positive form of
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- 2018-03-14T00:03:24Z
- is negative form of
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- part-of is homeomorphic for independent continuants.
- R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
-
- 2018-10-21T19:46:34Z
- R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
- is homeomorphic for
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- 2020-09-22T11:05:29Z
- valid_for_go_annotation_extension
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- 2020-09-22T11:05:18Z
- valid_for_go_gp2term
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- 2020-09-22T11:04:12Z
- valid_for_go_ontology
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- 2020-09-22T11:05:45Z
- valid_for_gocam
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- eco subset
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- subset_property
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- An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
-
- https://github.com/information-artifact-ontology/ontology-metadata/issues/18
- has broad synonym
- has_broad_synonym
- https://github.com/information-artifact-ontology/ontology-metadata/issues/18
-
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- disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
- An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
-
-
- 2024-03-18
- database_cross_reference
- has cross-reference
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- An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
-
- https://github.com/information-artifact-ontology/ontology-metadata/issues/20
- has exact synonym
- has_exact_synonym
- https://github.com/information-artifact-ontology/ontology-metadata/issues/20
-
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- An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
-
- https://github.com/information-artifact-ontology/ontology-metadata/issues/19
- has narrow synonym
- has_narrow_synonym
- https://github.com/information-artifact-ontology/ontology-metadata/issues/19
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- has_obo_format_version
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- An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
-
- https://github.com/information-artifact-ontology/ontology-metadata/issues/21
- has related synonym
- has_related_synonym
- https://github.com/information-artifact-ontology/ontology-metadata/issues/21
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- in_subset
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- is defined by
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- is defined by
- This is an experimental annotation
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- is part of
- my brain is part of my body (continuant parthood, two material entities)
- my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
- this day is part of this year (occurrent parthood)
- a core relation that holds between a part and its whole
- Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
- Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
- Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
-
-A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
- part_of
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- part of
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-
- http://www.obofoundry.org/ro/#OBO_REL:part_of
- https://wiki.geneontology.org/Part_of
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- has part
- my body has part my brain (continuant parthood, two material entities)
- my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
- this year has part this day (occurrent parthood)
- a core relation that holds between a whole and its part
- Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
- Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
- Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
-
-A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
- has_part
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- has part
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- realized in
- this disease is realized in this disease course
- this fragility is realized in this shattering
- this investigator role is realized in this investigation
- is realized by
- realized_in
- [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
- Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
-
- realized in
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- realizes
- this disease course realizes this disease
- this investigation realizes this investigator role
- this shattering realizes this fragility
- Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
- to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
- Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
-
- realizes
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- accidentally included in BFO 1.2 proposal
- - should have been BFO_0000062
- obsolete preceded by
- true
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- preceded by
- x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
- An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
- is preceded by
- preceded_by
- http://www.obofoundry.org/ro/#OBO_REL:preceded_by
-
- preceded by
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- precedes
- x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
-
- precedes
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- occurs in
- b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
- occurs_in
- unfolds in
- unfolds_in
-
-
-
- Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
-
- occurs in
- https://wiki.geneontology.org/Occurs_in
-
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- site of
- [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
- Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
-
- contains process
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- http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
- lacks_part
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- http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)
- lacks_plasma_membrane_part
-
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- A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity.
- derives from part of
-
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- A has part relationship between a whole and a part, where the number of parts present in the whole is higher than in comparable entities.
- This relation is present in ENVO to support compositional classes such as "X-enriched soil". These will later be formalized, and a different relation from RO may be chosen.
- has increased levels of
-
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- inheres in
- this fragility is a characteristic of this vase
- this red color is a characteristic of this apple
- a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
- inheres_in
-
- Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
- characteristic of
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- bearer of
- this apple is bearer of this red color
- this vase is bearer of this fragility
- Inverse of characteristic_of
- A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
- bearer_of
- is bearer of
-
- has characteristic
-
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- participates in
- this blood clot participates in this blood coagulation
- this input material (or this output material) participates in this process
- this investigator participates in this investigation
- a relation between a continuant and a process, in which the continuant is somehow involved in the process
- participates_in
- participates in
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- has participant
- this blood coagulation has participant this blood clot
- this investigation has participant this investigator
- this process has participant this input material (or this output material)
- a relation between a process and a continuant, in which the continuant is somehow involved in the process
- Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
- has_participant
- http://www.obofoundry.org/ro/#OBO_REL:has_participant
- has participant
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- A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
- An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
- A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.
- is concretized as
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- A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
- An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
- A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.
- concretizes
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- this catalysis function is a function of this enzyme
- a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
- A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
- function_of
- is function of
- This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
- function of
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- this red color is a quality of this apple
- a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
- A quality inheres in its bearer at all times for which the quality exists.
- is quality of
- quality_of
- This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
- quality of
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- this investigator role is a role of this person
- a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
- A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
- is role of
- role_of
- This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
- role of
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- this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
- a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
- A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
- has_function
- has function
-
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- this apple has quality this red color
- a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
- A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
- has_quality
- has quality
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-
-
-
-
-
-
- this person has role this investigator role (more colloquially: this person has this role of investigator)
- a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
- A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
- has_role
- has role
-
-
-
-
-
-
-
-
-
-
-
- a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
- has disposition
-
-
-
-
-
-
-
-
- inverse of has disposition
-
- This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
- disposition of
-
-
-
-
-
-
-
-
- OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.
-
-
-
- Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
- obsolete in neural circuit with
- true
-
-
-
-
-
-
-
-
- OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first.
-
-
-
- Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
- obsolete upstream in neural circuit with
- true
-
-
-
-
-
-
-
-
- OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first.
-
-
-
- Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).
- obsolete downstream in neural circuit with
- true
-
-
-
-
-
-
-
-
- this cell derives from this parent cell (cell division)
- this nucleus derives from this parent nucleus (nuclear division)
-
- a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
- This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
- derives_from
- This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
-
- derives from
-
-
-
-
-
-
-
- this parent cell derives into this cell (cell division)
- this parent nucleus derives into this nucleus (nuclear division)
-
- a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
- This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
- derives_into
-
- derives into
-
-
-
-
-
-
-
-
-
- is location of
- my head is the location of my brain
- this cage is the location of this rat
- a relation between two independent continuants, the location and the target, in which the target is entirely within the location
- Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
- location_of
-
- location of
-
-
-
-
-
-
-
- contained in
- Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
- Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
- contained_in
- obsolete contained in
-
- true
-
-
-
-
-
-
-
- contains
- obsolete contains
-
- true
-
-
-
-
-
-
-
-
-
-
- penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
- A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
- is allergic trigger for
-
-
-
-
-
-
-
-
-
-
- A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
- is autoimmune trigger for
-
-
-
-
-
-
-
-
-
- penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
- A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
- has allergic trigger
-
-
-
-
-
-
-
-
-
- A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
- has autoimmune trigger
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- located in
- my brain is located in my head
- this rat is located in this cage
- a relation between two independent continuants, the target and the location, in which the target is entirely within the location
- Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
- Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
- located_in
-
- http://www.obofoundry.org/ro/#OBO_REL:located_in
-
- located in
- https://wiki.geneontology.org/Located_in
-
-
-
-
-
- This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
-
-
-
-
-
- This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
-
-
-
-
-
-
-
-
-
- the surface of my skin is a 2D boundary of my body
- a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
- A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
- Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
- 2D_boundary_of
- boundary of
- is 2D boundary of
- is boundary of
- surface of
-
- 2D boundary of
-
-
-
-
-
-
-
-
-
- May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
-
-
- aligned with
-
-
-
-
-
-
-
-
-
-
- my body has 2D boundary the surface of my skin
- a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
- A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
- Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
-
- has boundary
- has_2D_boundary
-
- has 2D boundary
-
-
-
-
-
-
-
-
- A relation that holds between two neurons that are electrically coupled via gap junctions.
-
-
- electrically_synapsed_to
-
-
-
-
-
-
-
-
-
-
- The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
-
- tracheates
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- relation between an anatomical structure and a neuron projection bundle that has synaptic terminals in the structure.
-
- http://www.ncbi.nlm.nih.gov/pubmed/22402613
- innervated by
-
-
-
-
-
-
-
-
-
-
-
- has synaptic terminal of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- X outer_layer_of Y iff:
-. X :continuant that bearer_of some PATO:laminar
-. X part_of Y
-. exists Z :surface
-. X has_boundary Z
-. Z boundary_of Y
-
-has_boundary: http://purl.obolibrary.org/obo/RO_0002002
-boundary_of: http://purl.obolibrary.org/obo/RO_0002000
-
-
- A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
- bounding layer of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
- Note from NCEAS meeting: consider changing primary label
-
-
- Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
- coincident with
-
-
-
-
-
-
-
-
-
- A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.
-
- x 'cell expresses' y iff:
-cell(x)
-AND gene(y)
-AND exists some 'transcription, DNA templated (GO_0006351)'(t)
-AND t occurs_in x
-AND t has_input y
- cell expresses
-
-
-
-
-
-
-
-
-
-
- x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
-
- regulates in other organism
-
- regulates in another organism
-
-
-
-
-
-
-
-
-
-
-
- A relationship that holds between a process that regulates a transport process and the entity transported by that process.
-
-
- regulates transport of
-
-
-
-
-
-
-
-
-
-
-
- A part of relation that applies only between occurrents.
- occurrent part of
-
-
-
-
-
-
-
-
-
- A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
-
- 2017-05-24T09:30:46Z
- has regulatory component activity
-
-
-
-
-
-
-
-
-
- A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
-
- 2017-05-24T09:31:01Z
- By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
- has negative regulatory component activity
-
-
-
-
-
-
-
-
-
- A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
-
- 2017-05-24T09:31:17Z
- By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
- has positive regulatory component activity
-
-
-
-
-
-
-
-
-
-
- 2017-05-24T09:36:08Z
- A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.
- has necessary component activity
-
-
-
-
-
-
-
-
-
- 2017-05-24T09:44:33Z
- A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
- has component activity
-
-
-
-
-
-
-
-
-
-
- w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
-
- 2017-05-24T09:49:21Z
- has component process
-
-
-
-
-
-
-
-
- A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
-
- 2017-07-19T17:30:36Z
- has ligand
-
-
-
-
-
-
-
-
- Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.
-
- 2017-07-20T17:11:08Z
- transports
-
-
-
-
-
-
-
-
- A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
-
- 2017-07-20T17:19:37Z
- occurs across
-
-
-
-
-
-
-
-
-
-
- 2017-09-17T13:52:24Z
- Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
- directly regulated by
-
-
-
-
- Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
-
-
-
-
-
-
-
-
-
-
- Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
-
- 2017-09-17T13:52:38Z
- directly negatively regulated by
-
-
-
-
- Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
-
-
-
-
-
-
-
-
-
-
- Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
-
- 2017-09-17T13:52:47Z
- directly positively regulated by
-
-
-
-
- Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
-
-
-
-
-
-
-
-
-
-
- A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
-
- 2017-09-22T14:14:36Z
- This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
- has effector activity
-
-
-
-
- A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
-
-
-
-
-
-
-
-
-
-
-
- A relationship that holds between two images, A and B, where:
-A depicts X;
-B depicts Y;
-X and Y are both of type T'
-C is a 2 layer image consiting of layers A and B;
-A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.
-Note: A and B may be 2D or 3D.
-Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
-
- 2017-12-07T12:58:06Z
- in register with
-
-
-
-
- A relationship that holds between two images, A and B, where:
-A depicts X;
-B depicts Y;
-X and Y are both of type T'
-C is a 2 layer image consiting of layers A and B;
-A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.
-Note: A and B may be 2D or 3D.
-Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
-
-
-
-
-
-
-
-
-
-
- <=
-
- Primitive instance level timing relation between events
- before or simultaneous with
-
-
-
-
-
-
-
-
-
-
- x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time.
-
-
- t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
- simultaneous with
-
-
-
-
-
-
-
-
-
-
-
- t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
- before
-
-
-
-
-
-
-
-
-
-
-
- Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
- during which ends
-
-
-
-
-
-
-
-
-
-
-
- di
- Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
- encompasses
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
- ends after
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- starts_at_end_of
- X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
- immediately preceded by
-
-
-
-
-
-
-
-
-
-
-
- Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
- during which starts
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- starts before
-
-
-
-
-
-
-
-
-
-
-
-
-
- ends_at_start_of
- meets
-
-
- X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
- immediately precedes
-
-
-
-
-
-
-
-
-
-
-
- io
-
- X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
- starts during
-
-
-
-
-
-
-
-
-
-
-
- d
- during
-
-
-
-
- X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
- happens during
- https://wiki.geneontology.org/Happens_during
-
-
-
-
-
-
-
-
-
- o
- overlaps
-
- X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
- ends during
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Relation between a neuron and a material anatomical entity that its soma is part of.
-
- <http://purl.obolibrary.org/obo/BFO_0000051> some (
- <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
-
- has soma location
-
-
-
-
-
-
-
-
-
-
-
-
- relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
-
-
- fasciculates with
- (forall (?x ?y)
- (iff
- (fasciculates_with ?x ?y)
- (exists (?nps ?npbs)
- (and
- ("neuron ; CL_0000540" ?x)
- ("neuron projection bundle ; CARO_0001001" ?y)
- ("neuron projection segment ; CARO_0001502" ?nps)
- ("neuron projection bundle segment ; CARO_0001500' " ?npbs)
- (part_of ?npbs ?y)
- (part_of ?nps ?x)
- (part_of ?nps ?npbs)
- (forall (?npbss)
- (if
- (and
- ("neuron projection bundle subsegment ; CARO_0001501" ?npbss)
- (part_of ?npbss ?npbs)
- )
- (overlaps ?nps ?npbss)
- ))))))
-
-
- fasciculates with
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Relation between a neuron and some structure its axon forms (chemical) synapses in.
-
-
- <http://purl.obolibrary.org/obo/BFO_0000051> some (
- <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some (
- <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some (
- <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
-
-
- axon synapses in
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
-
-
- <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
-
-
- synapsed by
-
-
-
-
-
-
-
-
-
-
- Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
-
- Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
-
-
-
-
- <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
-
- has plasma membrane part
-
-
-
-
-
-
-
-
-
-
- A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.
-
-
- BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
-
-
- Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
- synapsed_via_type_Ib_bouton_to
-
-
-
-
-
-
-
-
-
-
- A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.
-
-
- BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
-
-
- Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
- synapsed_via_type_Is_bouton_to
-
-
-
-
-
-
-
-
-
-
- A relation between a motor neuron and a muscle that it synapses to via a type II bouton.
-
-
- BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
-
- Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
- synapsed_via_type_II_bouton_to
-
-
-
-
-
-
-
-
-
- Relation between a muscle and a motor neuron that synapses to it via a type II bouton.
-
-
- BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
-
-
-
- Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
- synapsed_by_via_type_II_bouton
-
-
-
-
-
-
-
-
-
- Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.
-
-
- BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
-
-
- Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
- synapsed_by_via_type_Ib_bouton
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
-
-
- synapsed in
- http://purl.obolibrary.org/obo/BFO_0000051 some (
- http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (
- http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
-
-
- has postsynaptic terminal in
-
-
-
-
-
-
-
-
-
-
- has neurotransmitter
- releases neurotransmitter
-
-
-
-
-
-
-
-
-
- Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.
-
-
- BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
-
-
- Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
- synapsed_by_via_type_Is_bouton
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
- synapses in
- <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
-
-
- has presynaptic terminal in
-
-
-
-
-
-
-
-
-
- A relation between a motor neuron and a muscle that it synapses to via a type III bouton.
- BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))
-
-
- Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))
- synapsed_via_type_III_bouton_to
-
-
-
-
-
-
-
-
- Relation between a muscle and a motor neuron that synapses to it via a type III bouton.
-
- BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))
-
-
- Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))
- synapsed_by_via_type_III_bouton
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
-
-
-
- <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
-
-
- N1 synapsed_to some N2
-Expands to:
-N1 SubclassOf (
- has_part some (
- ‘pre-synaptic membrane ; GO:0042734’ that part_of some (
- ‘synapse ; GO:0045202’ that has_part some (
- ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))
- synapsed to
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
-
-
-
-
- <http://purl.obolibrary.org/obo/BFO_0000051> some (
- <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some (
- http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some (
- <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
-
-
- dendrite synapsed in
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
-
- has synapse in
- <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
-
-
- has synaptic terminal in
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- x overlaps y if and only if there exists some z such that x has part z and z part of y
- http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
-
-
-
-
- overlaps
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
-
- has fasciculating component
- (forall (?x ?y)
- (iff
- (has_fasciculating_neuron_projection ?x ?y)
- (exists (?nps ?npbs)
- (and
- ("neuron projection bundle ; CARO_0001001" ?x)
- ("neuron projection ; GO0043005" ?y)
- ("neuron projection segment ; CARO_0001502" ?nps)
- ("neuron projection bundle segment ; CARO_0001500" ?npbs)
- (part_of ?nps ?y)
- (part_of ?npbs ?x)
- (part_of ?nps ?npbs)
- (forall (?npbss)
- (if
- (and
- ("neuron projection bundle subsegment ; CARO_0001501" ?npbss)
- (part_of ?npbss ?npbs)
- )
- (overlaps ?nps ?npbss)
- ))))))
-
-
-
-
-
- has fasciculating neuron projection
-
-
-
-
-
-
-
-
-
-
-
-
-
- Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.
-T innervates some R
-Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
-
- <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
-
-
- innervates
-
-
-
-
-
-
-
-
-
-
-
-
- X continuous_with Y if and only if X and Y share a fiat boundary.
-
- connected to
- The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
-
- continuous with
- FMA:85972
-
-
-
-
-
-
-
-
-
- x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
- We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
- proper overlaps
- (forall (?x ?y)
- (iff
- (proper_overlaps ?x ?y)
- (and
- (overlaps ?x ?y)
- (not (part_of ?x ?y))
- (not (part_of ?y ?x)))))
-
-
- partially overlaps
-
-
-
-
-
-
-
-
-
-
-
- d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.
- ancestral_stucture_of
- evolutionarily_descended_from
- derived by descent from
-
-
-
-
-
-
-
-
-
-
- inverse of derived by descent from
-
- has derived by descendant
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.
- Consider obsoleting and merging with child relation, 'in homology relationship with'
- VBO calls this homologous_to
- shares ancestor with
-
-
-
-
-
-
-
-
-
-
-
- serially homologous to
-
-
-
-
-
-
-
-
- lactation SubClassOf 'only in taxon' some 'Mammalia'
-
- x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
- The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.
-
- 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
-
-
-
- only in taxon
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
-
-
-
-
- life cycle stage of
-
- Connects a biological entity to its taxon of origin.
- in taxon
-
-
-
-
-
-
-
-
-
-
- A is spatially_disjoint_from B if and only if they have no parts in common
- There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
-
-
- Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
- BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
-
-
- spatially disjoint from
- https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
- a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
-
- connected to
- https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
- https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- The M8 connects Glasgow and Edinburgh
- a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
- c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
-
- connects
- https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
- https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
- attached to part of (anatomical structure to anatomical structure)
- attached to part of
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
-
-
-
- Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
- Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
-
- supplies
-
-
-
-
-
-
-
-
- Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
- Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
-
- drains
-
-
-
-
-
-
-
-
-
- w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
- The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
- For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
-
-
- has component
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
-
-
- has phenotype
-
-
-
-
-
-
-
-
-
- inverse of has phenotype
-
-
-
- phenotype of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
-
-
-
-
- This is the transitive form of the develops from relation
- develops from
-
-
-
-
-
-
-
-
-
-
-
-
- inverse of develops from
-
-
-
-
- develops into
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
- We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
-
- gene product of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- every HOTAIR lncRNA is the gene product of some HOXC gene
- every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
-
- x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
-
- has gene product
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
-
- x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
-
- expressed in
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
-
-
- FBbt
-
- has developmental precursor
- TODO - add child relations from DOS
- directly develops from
-
-
-
-
-
-
-
-
-
- A parasite that kills or sterilizes its host
- parasitoid of
-
-
-
-
-
-
-
-
- inverse of parasitoid of
-
- has parasitoid
-
-
-
-
-
-
-
-
-
- inverse of directly develops from
- developmental precursor of
-
- directly develops into
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
-
-
-
-
- GO
- Regulation precludes parthood; the regulatory process may not be within the regulated process.
- regulates (processual)
- false
-
-
-
- regulates
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
-
-
- negatively regulates (process to process)
-
-
-
-
- negatively regulates
-
-
-
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-
-
-
-
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-
-
-
-
-
-
-
-
- p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
-
-
- positively regulates (process to process)
-
-
-
-
- positively regulates
-
-
-
-
-
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-
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-
-
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-
-
-
- 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
- heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
-
- x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
- Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
- TODO: add homeomorphy axiom
- This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
-
- has prototype
-
-
-
-
-
-
-
-
-
-
- mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
- osteoclast SubClassOf 'capable of' some 'bone resorption'
- A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
-
- has function realized in
-
-
- For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
-
- capable of
-
-
-
-
-
-
-
-
-
-
-
-
-
- c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
-
- has function in
- capable of part of
-
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
-
-
- OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role
-
- agent in
-
- Obsoleted as the inverse property was obsoleted.
- obsolete actively participates in
- true
-
-
-
-
-
-
-
- OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
-
- has agent
-
- obsolete has active participant
- true
-
-
-
-
-
-
-
-
-
-
- x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
-
-
- surrounded by
-
-
-
-
-
-
-
-
-
-
- A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
- The epidermis layer of a vertebrate is adjacent to the dermis.
- The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
- The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
-
- x adjacent to y if and only if x and y share a boundary.
- This relation acts as a join point with BSPO
-
-
-
-
-
- adjacent to
-
-
-
-
- A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
-
-
-
-
-
-
-
-
-
-
- inverse of surrounded by
-
-
-
- surrounds
-
-
-
-
-
-
-
-
-
-
-
-
- Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
- https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
-
- A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
- temporally related to
-
-
-
-
-
-
-
-
-
-
-
- inverse of starts with
-
- Allen
-
- starts
-
-
-
-
-
-
-
-
-
-
- Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
-
- x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
-
- started by
-
- starts with
-
-
-
-
-
-
-
-
-
-
-
-
-
- x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
-
- develops from part of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- x develops_in y if x is located in y whilst x is developing
-
- EHDAA2
- Jonathan Bard, EHDAA2
- develops in
-
-
-
-
-
-
-
-
- A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.
- obligate parasite of
-
-
-
-
-
-
-
-
- A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.
- facultative parasite of
-
-
-
-
-
-
-
-
-
-
-
- inverse of ends with
-
-
- ends
-
-
-
-
-
-
-
-
-
-
-
- x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
-
- finished by
-
- ends with
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
-
- starts with process that occurs in
-
- has start location
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
-
- ends with process that occurs in
-
- has end location
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
-
- consumes
-
-
-
-
- has input
- https://wiki.geneontology.org/Has_input
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
-
- produces
-
-
-
-
- has output
- https://wiki.geneontology.org/Has_output
-
-
-
-
-
-
-
-
- A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)
- stem parasite of
-
-
-
-
-
-
-
-
- A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)
- root parasite of
-
-
-
-
-
-
-
-
- A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well.
- hemiparasite of
-
-
-
-
-
-
-
-
- X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys.
- This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).
-
-If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'.
-
- has component participant
-
-
-
-
-
-
-
-
- A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.
- ExO:0000001
- has exposure receptor
-
-
-
-
-
-
-
-
- A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
- ExO:0000000
- has exposure stressor
-
-
-
-
-
-
-
-
- A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
- ExO:0000055
- has exposure route
-
-
-
-
-
-
-
-
- A broad relationship between an exposure event or process and the course takes from the source to the target.
- http://purl.obolibrary.org/obo/ExO_0000004
- has exposure transport path
-
-
-
-
-
-
-
-
-
- Any relationship between an exposure event or process and any other entity.
- Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.
- related via exposure to
-
-
-
-
-
-
-
-
- g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.
- over-expressed in
-
-
-
-
-
-
-
-
- g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.
- under-expressed in
-
-
-
-
-
-
-
-
-
-
-
- Any portion of roundup 'has active ingredient' some glyphosate
- A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
- has active substance
- has active pharmaceutical ingredient
- has active ingredient
-
-
-
-
-
-
-
-
- inverse of has active ingredient
-
- active ingredient in
-
-
-
-
-
-
-
-
-
-
- In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1.
- b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.
-
- connecting branch of
-
-
-
-
-
-
-
-
-
- inverse of connecting branch of
-
-
- has connecting branch
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
-
- x has developmental contribution from y iff x has some part z such that z develops from y
-
- has developmental contribution from
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- inverse of has developmental contribution from
-
-
- developmentally contributes to
-
-
-
-
-
-
-
-
-
-
-
-
- t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T
-
-
-
- induced by
-
- Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
- GO:0001759
- We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
- developmentally induced by
-
-
-
-
-
-
-
-
-
-
- Inverse of developmentally induced by
-
- developmentally induces
-
-
-
-
-
-
-
-
-
-
-
-
- Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
- false
-
- In general you should not use this relation to make assertions - use one of the more specific relations below this one
- This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
- developmentally preceded by
-
-
-
-
-
-
-
-
- c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)
- has biological role
-
-
-
-
-
-
-
-
- c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)
- has application role
-
-
-
-
-
-
-
-
- c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)
- has chemical role
-
-
-
-
-
-
-
-
-
-
-
-
- A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
- c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
-
- acts upstream of
-
-
-
-
-
-
-
-
-
-
-
-
-
- A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
- c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
- affects
-
- acts upstream of or within
- https://wiki.geneontology.org/Acts_upstream_of_or_within
-
-
-
-
-
-
-
-
-
- x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
- This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
-
- replaces
- developmentally replaces
-
-
-
-
-
-
-
-
-
- Inverse of developmentally preceded by
-
- developmentally succeeded by
-
-
-
-
-
-
-
-
-
-
-
-
- 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
-
-
- part of developmental precursor of
-
-
-
-
-
-
-
-
-
-
- x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
- Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
-
- ubiquitously expressed in
-
-
-
-
-
-
-
-
-
- y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.
-
- expresses
-
-
-
-
-
-
-
-
-
- inverse of ubiquiotously expressed in
-
-
- ubiquitously expresses
-
-
-
-
-
-
-
-
-
-
-
- p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
- This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
-
- results in developmental progression of
-
-
-
-
-
-
-
-
-
-
- every flower development (GO:0009908) results in development of some flower (PO:0009046)
-
- p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
-
- http://www.geneontology.org/GO.doc.development.shtml
-
-
-
- results in development of
-
-
-
-
-
-
-
-
-
-
- an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
- every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
-
-
- GOC:mtg_berkeley_2013
-
-
-
- results in formation of anatomical entity
-
-
-
-
-
-
-
-
-
- an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
- tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
-
- The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
-
- GOC:mtg_berkeley_2013
-
-
-
- results in morphogenesis of
-
-
-
-
-
-
-
-
-
- an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
- bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
-
- The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
-
- GOC:mtg_berkeley_2013
-
-
-
- results in maturation of
-
-
-
-
-
-
-
-
- foramen ovale closure SubClassOf results in disappearance of foramen ovale
-
-
- May be merged into parent relation
- results in disappearance of
-
-
-
-
-
-
-
-
- every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
-
-
- May be merged into parent relation
- results in developmental regression of
-
-
-
-
-
-
-
-
-
- Inverse of 'is substance that treats'
-
-
- is treated by substance
-
-
-
-
-
-
-
-
-
-
- Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'
-where
-'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
-
- x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
-
- adapted for living in
-
- A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.
- has habitat
-
-
-
-
-
-
-
-
-
- p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
-
-
-
-
- holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
- causally upstream of, positive effect
-
-
-
-
-
-
-
-
-
-
- p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
-
-
-
-
- causally upstream of, negative effect
-
-
-
-
-
-
-
-
-
- A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.
-
-
-
-
- 2017-06-05T17:35:04Z
- has exposure stimulus
-
-
-
-
-
-
-
-
-
- evolutionary variant of
-
-
-
-
-
-
-
-
-
- Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
-
- regulates localization of
-
-
-
- transports or maintains localization of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
- Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
-
- inheres in part of
-
-
- characteristic of part of
-
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
-
-
-
-
-
- an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
- The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
-
- GOC:mtg_berkeley_2013
-
-
-
- results in acquisition of features of
-
-
-
-
-
-
-
- A relationship that holds via some environmental process
-
- Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
- evolutionarily related to
-
-
-
-
-
-
-
- A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
- Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
-
- Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
-
- ecologically related to
-
-
-
-
-
-
-
-
-
- An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial.
-
- adapted for
-
- confers advantage in
-
-
-
-
-
-
-
- A mereological relationship or a topological relationship
-
- Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
-
- mereotopologically related to
-
-
-
-
-
-
-
- A relationship that holds between entities participating in some developmental process (GO:0032502)
-
- Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
- developmentally related to
-
-
-
-
-
-
-
-
-
-
- Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
- a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
-
- In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
-
- colocalizes with
-
-
-
-
-
-
-
-
-
- ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
- Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
- eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
- We would like to say
-
-if and only if
- exists c', p'
- c part_of c' and c' capable_of p
- and
- c capable_of p' and p' part_of p
-then
- c contributes_to p
-
-However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
-
- In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
-
- contributes to
- https://wiki.geneontology.org/Contributes_to
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- a particular instances of akt-2 enables some instance of protein kinase activity
- c enables p iff c is capable of p and c acts to execute p.
-
- catalyzes
- executes
- has
- is catalyzing
- is executing
- This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
-
- enables
- https://wiki.geneontology.org/Enables
-
-
-
-
-
-
-
- A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
-
- This is a grouping relation that collects relations used for the purpose of connecting structure and function
- functionally related to
-
-
-
-
-
-
-
-
-
-
-
-
- this relation holds between c and p when c is part of some c', and c' is capable of p.
-
- false
- part of structure that is capable of
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
-
-
-
-
- holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
-
- Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
- genomically related to
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- c involved_in p if and only if c enables some process p', and p' is part of p
-
- actively involved in
- enables part of
- involved in
- https://wiki.geneontology.org/Involved_in
-
-
-
-
-
-
-
-
-
-
- every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
- p regulates levels of c if p regulates some amount (PATO:0000070) of c
-
-
- regulates levels of (process to entity)
- regulates levels of
-
-
-
-
-
-
-
-
-
- inverse of enables
-
-
- enabled by
- https://wiki.geneontology.org/Enabled_by
-
-
-
-
-
-
-
-
-
-
-
- inverse of regulates
-
- regulated by (processual)
-
- regulated by
-
-
-
-
-
-
-
-
- inverse of negatively regulates
-
-
- negatively regulated by
-
-
-
-
-
-
-
-
- inverse of positively regulates
-
-
- positively regulated by
-
-
-
-
-
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-
-
-
- A relationship that holds via some process of localization
-
- Do not use this relation directly. It is a grouping relation.
- related via localization to
-
-
-
-
-
-
-
-
-
-
-
-
- This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
-
-
-
-
- has target start location
-
-
-
-
-
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-
-
-
-
-
-
- This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
-
-
-
-
- has target end location
-
-
-
-
-
-
-
-
- Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
-
-
- imports
-
-
-
-
-
-
-
-
- Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
-
- results in transport along
-
-
-
-
-
-
-
-
-
- Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
-
-
- results in transport across
-
-
-
-
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-
-
-
- 'pollen tube growth' results_in growth_of some 'pollen tube'
-
- results in growth of
-
-
-
-
-
-
-
-
- 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
-
- results in transport to from or in
-
-
-
-
-
-
-
-
- Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.
-
-
- exports
-
-
-
-
-
-
-
-
-
- an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
- p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
-
-
-
-
- results in commitment to
-
-
-
-
-
-
-
-
-
- p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
-
-
-
-
- results in determination of
-
-
-
-
-
-
-
-
-
- An organism that is a member of a population of organisms
- is member of is a mereological relation between a item and a collection.
- is member of
- member part of
- SIO
-
- member of
-
-
-
-
-
-
-
-
-
- has member is a mereological relation between a collection and an item.
- SIO
-
- has member
-
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-
- inverse of has input
-
-
-
- input of
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- inverse of has output
-
-
-
- output of
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-
- formed as result of
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-
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- A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.
-
- results in structural organization of
-
-
-
-
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-
-
- The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
-
-
-
-
- results in specification of
-
-
-
-
-
-
-
-
- p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c.
-
- results in developmental induction of
-
-
-
-
-
-
-
-
-
- http://neurolex.org/wiki/Property:DendriteLocation
- has dendrite location
-
-
-
-
-
-
-
-
-
-
- a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
-
- attached to (anatomical structure to anatomical structure)
-
- attached to
-
-
-
-
-
-
-
-
-
-
- m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
-
- Wikipedia:Insertion_(anatomy)
- has muscle origin
-
-
-
-
-
-
- We need to import uberon muscle to create a stricter domain constraint
-
-
-
-
-
-
-
-
-
-
- m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
-
- Wikipedia:Insertion_(anatomy)
- has muscle insertion
-
-
-
-
-
-
- We need to import uberon muscle into RO to use as a stricter domain constraint
-
-
-
-
-
-
-
-
- false
-
- x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat
-
-
- has fused element
- A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B.
- derived from ancestral fusion of
-
-
-
-
-
-
-
-
-
-
-
- A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
-
- Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
- This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
-
- in branching relationship with
-
- https://github.com/obophenotype/uberon/issues/170
-
-
-
-
-
-
-
-
-
- Deschutes River tributary_of Columbia River
- inferior epigastric vein tributary_of external iliac vein
-
- x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
-
- drains into
- drains to
- tributary channel of
- http://en.wikipedia.org/wiki/Tributary
- http://www.medindia.net/glossary/venous_tributary.htm
- This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
-
- tributary of
-
- http://en.wikipedia.org/wiki/Tributary
-
-
-
-
-
-
-
-
-
- Deschutes River distributary_of Little Lava Lake
-
- x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
-
- branch of
- distributary channel of
- http://en.wikipedia.org/wiki/Distributary
-
- This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes
- distributary of
-
-
-
-
-
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-
-
-
-
-
-
-
-
- x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
-
- anastomoses with
-
- anabranch of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- A lump of clay and a statue
- x spatially_coextensive_with y if and inly if x and y have the same location
-
- This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
- spatially coextensive with
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S
- x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
-
-
- branching part of
-
- FMA:85994
-
-
-
-
-
-
-
-
-
- In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'.
-
- x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
-
-
- main stem of
-
-
-
-
-
-
-
-
-
-
- x proper_distributary_of y iff x distributary_of y and x does not flow back into y
-
-
- proper distributary of
-
-
-
-
-
-
-
-
-
- x proper_tributary_of y iff x tributary_of y and x does not originate from y
-
-
- proper tributary of
-
-
-
-
-
-
-
-
-
-
-
- x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
-
- has developmental potential involving
-
-
-
-
-
-
-
-
-
- x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
-
- has potential to developmentally contribute to
-
-
-
-
-
-
-
-
-
- x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
-
- has potential to developmentally induce
-
-
-
-
-
-
-
-
-
- x has the potential to develop into y iff x develops into y or if x is capable of developing into y
-
- This relation has a stronger meaning than merely indicating that X may develop into Y, in that the capability of developing into Y is always present, even if X does not always actually develop into Y. In particular, this means that if Y is restricted to a given taxon T, X is necessarily likewise restricted.
- has potential to develop into
-
-
-
-
-
-
-
-
-
-
- x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
-
- has potential to directly develop into
-
-
-
-
-
-
-
-
-
-
-
-
- 'protein catabolic process' SubClassOf has_direct_input some protein
-
- p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
-
- directly consumes
- This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
- has direct input
-
-
-
-
-
-
-
-
-
- Likely to be obsoleted. See:
-https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
- obsolete has indirect input
- true
-
-
-
-
-
-
-
- translation SubClassOf has_direct_output some protein
-
- p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
-
- directly produces
- obsolete has direct output
- true
-
-
-
-
-
-
-
-
-
-
-
-
-
- Likely to be obsoleted. See:
-https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
- obsolete has indirect output
- true
-
-
-
-
-
-
-
-
-
-
-
- inverse of upstream of
-
- causally downstream of
-
-
-
-
-
-
-
-
-
-
-
-
- immediately causally downstream of
-
-
-
-
-
-
-
-
- This term was obsoleted because it has the same meaning as 'directly positively regulates'.
- obsolete directly activates
- true
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
-
- indirectly activates
-
- indirectly positively regulates
- https://wiki.geneontology.org/Indirectly_positively_regulates
-
-
-
-
-
-
-
-
- This term was obsoleted because it has the same meaning as 'directly negatively regulates'.
- obsolete directly inhibits
- true
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
-
- indirectly inhibits
-
- indirectly negatively regulates
- https://wiki.geneontology.org/Indirectly_negatively_regulates
-
-
-
-
-
-
-
- relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
- This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
-
-To define causal relations in an activity-flow type network, we make use of 3 primitives:
-
- * Temporal: how do the intervals of the two occurrents relate?
- * Is the causal relation regulatory?
- * Is the influence positive or negative?
-
-The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
-
-For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
-
-For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
-
-Each of these 3 primitives can be composed to yield a cross-product of different relation types.
-
- Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
- causally related to
-
-
-
-
- relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
- https://en.wikipedia.org/wiki/Causality
-
-
-
-
-
-
-
-
-
-
- p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
-
-
-
- causally upstream of
-
-
-
-
-
-
-
-
-
- p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
-
-
- immediately causally upstream of
-
-
-
-
-
-
-
-
-
-
-
-
-
- p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.
-
- directly provides input for
-
- directly provides input for (process to process)
- provides input for
- https://wiki.geneontology.org/Provides_input_for
-
-
-
-
-
-
-
-
-
-
-
-
- transitive form of directly_provides_input_for
-
- This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'.
- transitively provides input for (process to process)
- transitively provides input for
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
- We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
-
- influences (processual)
- affects
- causally upstream of or within
-
-
-
-
-
-
-
- false
-
- This is an exploratory relation
- differs in
- https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions
-
-
-
-
-
-
-
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- differs in attribute of
-
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- differs in attribute
-
-
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- inverse of causally upstream of or within
-
-
-
- causally downstream of or within
-
-
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-
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-
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- c involved in regulation of p if c is involved in some p' and p' regulates some p
-
- involved in regulation of
-
-
-
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-
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-
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-
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-
- c involved in regulation of p if c is involved in some p' and p' positively regulates some p
-
-
- involved in positive regulation of
-
-
-
-
-
-
-
-
-
-
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-
- c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
-
-
- involved in negative regulation of
-
-
-
-
-
-
-
-
-
-
- c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
- OWL does not allow defining object properties via a Union
-
- involved in or reguates
- involved in or involved in regulation of
-
-
-
-
-
-
-
-
-
-
-
-
-
- A protein that enables activity in a cytosol.
- c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
-
- executes activity in
- enables activity in
- is active in
- https://wiki.geneontology.org/Is_active_in
-
-
-
-
-
-
-
-
- true
-
-
-
-
- c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
-
-
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- p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
-
- contributes to morphology of
-
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-
- A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
- This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
- Considering relabeling as 'pairwise interacts with'
-
- Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
- in pairwise interaction with
-
- interacts with
- http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
- http://purl.obolibrary.org/obo/MI_0914
-
-
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-
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-
- An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
-
- genetically interacts with
-
- http://purl.obolibrary.org/obo/MI_0208
-
-
-
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-
- An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
-
- binds
- molecularly binds with
- molecularly interacts with
-
- http://purl.obolibrary.org/obo/MI_0915
-
-
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-
-
- An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
-
- interacts with on organism level
-
- biotically interacts with
-
- http://eol.org/schema/terms/interactsWith
-
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- lions trophically interact with the zebras that they eat
- An interaction relationship in which the partners are related via a feeding relationship.
-
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- trophically interacts with
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- A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]
- Baleen whale preys on krill
- An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members
-
-
-
- is subject of predation interaction with
- preys upon
-
- preys on
- http://eol.org/schema/terms/preysUpon
- http://www.inaturalist.org/observations/2942824
-
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- whales symbiotically interact with the barnacles that attach to them
- A biotic interaction in which the two organisms live together in more or less intimate association.
-
- http://www.ncbi.nlm.nih.gov/pubmed/19278549
- We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
-
- symbiotically interacts with
-
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- An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).
-
- http://www.ncbi.nlm.nih.gov/pubmed/19278549
-
- commensually interacts with
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- An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).
-
- http://www.ncbi.nlm.nih.gov/pubmed/19278549
-
- mutualistically interacts with
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- An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
-
- http://www.ncbi.nlm.nih.gov/pubmed/19278549
- This relation groups a pair of inverse relations, parasite of and parasitized by
-
- interacts with via parasite-host interaction
-
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- Pediculus humanus capitis parasite of human
- A parasite-host relationship where an organism benefits at the expense of another.
-
- parasitizes
- direct parasite of
-
- parasite of
- http://eol.org/schema/terms/parasitizes
-
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- Inverse of parasite of
-
- has parasite
- parasitised by
- directly parasitized by
-
- parasitized by
- http://eol.org/schema/terms/hasParasite
-
-
-
-
-
-
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-
- Porifiera attaches to substrate
- A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
-
- semibiotically interacts with
-
- participates in a abiotic-biotic interaction with
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- Axiomatization to GO to be added later
-
- An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
- phosphorylates
-
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- The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
-
-A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
-
-
- molecularly controls
- directly regulates activity of
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- The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
-For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
-
-
- directly inhibits
- molecularly decreases activity of
- directly negatively regulates activity of
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- The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
-For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
-
-
- directly activates
- molecularly increases activity of
- directly positively regulates activity of
-
-
-
-
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-
- all dengue disease transmitted by some mosquito
- A relationship that holds between a disease and organism
- Add domain and range constraints
-
- transmitted by
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-
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-
- A relation that holds between a disease or an organism and a phenotype
-
- has symptom
-
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-
- The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
-
- host of
-
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-
-
- X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
-
-
- has host
- http://eol.org/schema/terms/hasHost
-
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- Bees pollinate Flowers
- This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this.
-
- is subject of pollination interaction with
-
- pollinates
- http://eol.org/schema/terms/pollinates
-
-
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- has polinator
- is target of pollination interaction with
-
- pollinated by
- http://eol.org/schema/terms/hasPollinator
-
-
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-
- Inverse of provides nutrients for
-
- Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion.
-
- acquires nutrients from
-
-
-
-
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-
- inverse of preys on
-
- has predator
- is target of predation interaction with
-
-
- preyed upon by
- http://eol.org/schema/terms/HasPredator
- http://polytraits.lifewatchgreece.eu/terms/PRED
-
-
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- Anopheles is a vector for Plasmodium
-
- a is a vector for b if a carries and transmits an infectious pathogen b into another living organism
-
- is vector for
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- has vector
-
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- Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target
- partner in
-
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-
- Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed.
- subject participant in
-
-
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-
- Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed.
- target participant in
-
-
-
-
-
-
-
-
- This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
- helper property (not for use in curation)
-
-
-
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-
- is symbiosis
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- is commensalism
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- is mutualism
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- is parasitism
-
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-
- A biotic interaction where a material entity provides nutrition for an organism.
-
-
- provides nutrients for
-
-
-
-
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-
-
-
- A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening.
-
- is subject of eating interaction with
-
- eats
-
-
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-
- Inverse of eats
-
- eaten by
- is target of eating interaction with
-
- is eaten by
-
-
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-
-
- A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and
-the a supports either the existence of b, or the truth value of b.
-
-
- is evidence for
-
-
-
-
-
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-
-
-
- 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
- x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
-
-
-
-
- composed primarily of
-
-
-
-
-
-
-
-
-
-
- ABal nucleus child nucleus of ABa nucleus (in C elegans)
- c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d
-
- This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage.
- child nucleus of
-
-
-
-
-
-
-
-
- A child nucleus relationship in which the cells are part of a hermaphroditic organism
-
- child nucleus of in hermaphrodite
-
-
-
-
-
-
-
-
- A child nucleus relationship in which the cells are part of a male organism
-
- child nucleus of in male
-
-
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-
-
-
-
- p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
-
-
- has part that occurs in
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
-
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-
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-
-
- An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y
- Axiomatization to GO to be added later
-
- ubiquitinates
-
-
-
-
-
-
-
-
-
- is kinase activity
-
-
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-
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-
-
- is ubiquitination
-
-
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-
-
-
-
- See notes for inverse relation
-
- receives input from
-
-
-
-
-
-
-
-
- This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
-
- sends output to
-
-
-
-
-
-
-
-
-
-
- Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
- relation between physical entity and a process or stage
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
-
- existence starts during
-
-
-
-
-
-
-
-
- x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
-
- existence starts with
-
-
-
-
-
-
-
-
- x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
-
- The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
- existence overlaps
-
-
-
-
-
-
-
-
-
- x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
-
- exists during
- The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
- existence starts and ends during
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
-
- The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
- existence ends during
-
-
-
-
-
-
-
-
- x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
-
- The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
- existence ends with
-
-
-
-
-
-
-
-
-
- x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
-
- transformation of
-
-
-
-
-
-
-
-
-
- x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
-
-
- immediate transformation of
-
-
-
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-
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-
-
-
-
-
-
- x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
-
- The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
- existence starts during or after
-
-
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-
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-
-
-
-
-
-
- x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
-
- The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
- existence ends during or before
-
-
-
-
-
-
-
-
-
- A relationship between a material entity and a process where the material entity has some causal role that influences the process
-
- causal agent in process
-
-
-
-
-
-
-
-
-
-
- p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
-
-
- Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
- causal relation between processes
-
-
-
-
-
-
-
-
- depends on
-
-
-
-
-
-
-
-
-
- q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
- This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
-
-
- towards
-
-
-
-
-
-
-
-
- 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
- p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
-
- has intermediate product
-
- has intermediate
-
-
-
-
-
-
-
-
-
-
- The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
-
-
- Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
- causal relation between entities
-
-
-
-
-
-
-
-
-
-
-
-
-
- A coral reef environment is determined by a particular coral reef
- s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
- The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
-
-
- determined by (system to material entity)
-
-
-
- determined by
-
-
-
-
-
-
-
-
- inverse of determined by
-
- determines (material entity to system)
-
-
- determines
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
-
-
- determined by part of
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- x is transcribed from y if and only if x is synthesized from template y
-
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
- transcribed from
-
-
-
-
-
-
-
-
- inverse of transcribed from
-
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
-
- transcribed to
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y
-
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
- ribosomal translation of
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- inverse of ribosomal translation of
-
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
- ribosomally translates to
-
-
-
-
-
-
-
-
-
- A relation that holds between two entities that have the property of being sequences or having sequences.
-
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
- Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
- The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
-
- sequentially related to
-
-
-
-
-
-
-
-
- Every UTR is adjacent to a CDS of the same transcript
- Two consecutive DNA residues are sequentially adjacent
- Two exons on a processed transcript that were previously connected by an intron are adjacent
- x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
-
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
-
- sequentially adjacent to
-
-
-
-
-
-
-
-
-
-
- Every CDS has as a start sequence the start codon for that transcript
- x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
-
- started by
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
-
- has start sequence
-
-
-
-
-
-
-
-
-
- inverse of has start sequence
-
- starts
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
-
-
- is start sequence of
-
-
-
-
-
-
-
-
-
-
- Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
- x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
-
- ended by
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
-
- has end sequence
-
-
-
-
-
-
-
-
-
- inverse of has end sequence
-
- ends
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
-
-
- is end sequence of
-
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- x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
- In the SO paper, this was defined as an instance-type relation
-
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
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- is consecutive sequence of
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- Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
- x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
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- is sequentially aligned with
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- The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
- x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
-
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- bounds sequence of
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- inverse of bounds sequence of
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- is bound by sequence of
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- x has subsequence y iff all of the sequence parts of y are sequence parts of x
-
- contains
- http://www.ncbi.nlm.nih.gov/pubmed/20226267
-
- has subsequence
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- inverse of has subsequence
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- contained by
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- is subsequence of
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- x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y.
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- overlaps sequence of
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- x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
-
- disconnected from
-
- does not overlap sequence of
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- inverse of downstream of sequence of
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- is upstream of sequence of
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- x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
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- is downstream of sequence of
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- A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
- x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
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- is immediately downstream of sequence of
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- A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
- inverse of immediately downstream of
-
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- is immediately upstream of sequence of
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- Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
- A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
-
- has supporting framework
- The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
- has skeleton
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- This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.
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- p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
-
- results in ending of
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- x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
- Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
-
- http://eol.org/schema/terms/hyperparasitoidOf
- https://en.wikipedia.org/wiki/Hyperparasite
- hyperparasitoid of
- epiparasite of
-
- hyperparasite of
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- inverse of hyperparasite of
-
- has epiparasite
- has hyperparasite
- hyperparasitoidized by
-
-
- hyperparasitized by
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- A relationship between organisms where one organism is influenced by the biochemicals produced by another.
-
- http://en.wikipedia.org/wiki/Allelopathy
-
- Allelopathy is a phenomenon in which one organism releases chemicals to positively or negatively influence the growth, survival or reproduction of other organisms in its vicinity.
- allelopath of
- http://eol.org/schema/terms/allelopathyYes
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172429/
- x is an allelopath of y if x produces one or more biochemicals that influence the growth, survival, and reproduction of y
-
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- Inverse of has pathogen
-
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- pathogen of
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- A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member
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- has pathogen
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- inverse of is evidence for
-
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- x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.
- has evidence
-
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- causally influenced by (entity-centric)
- causally influenced by
-
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- interaction relation helper property
-
- http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
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- molecular interaction relation helper property
-
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- Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
-
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- results in movement of
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- The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
-
-
-
- causally influences (entity-centric)
- causally influences
-
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- A relation that holds between elements of a musculoskeletal system or its analogs.
-
- Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
- biomechanically related to
-
-
-
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- m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
-
- Wikipedia:Antagonist_(muscle)
- has muscle antagonist
-
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- inverse of branching part of
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- has branching part
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- x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
-
- UBERON:cjm
- This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
-
- conduit for
-
-
-
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-
- x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
-
-
-
- lumen of
-
-
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- s is luminal space of x iff s is lumen_of x and s is an immaterial entity
-
-
- luminal space of
-
-
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- A relation that holds between an attribute or a qualifier and another attribute.
-
-
- This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
-
- has modifier
-
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- participates in a biotic-biotic interaction with
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- inverse of has skeleton
-
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- skeleton of
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- p directly regulates q iff p is immediately causally upstream of q and p regulates q.
-
-
- directly regulates (processual)
-
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-
- directly regulates
-
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-
- holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y).
- existence starts at end of
-
-
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-
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- gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
- s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
-
- has part structure that is capable of
-
-
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- p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed.
- results in closure of
-
-
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- p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
- results in breakdown of
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-
- results in synthesis of
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-
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- results in assembly of
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- p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.
- results in catabolism of
-
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- results in disassembly of
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- results in remodeling of
-
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-
- p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
- results in organization of
-
-
-
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-
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-
-
- holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y).
- existence ends at start of
-
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-
- A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
- Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
-
-
- causal relation between material entity and a process
-
-
-
-
-
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-
-
-
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-
-
- pyrethroid -> growth
- Holds between c and p if and only if c is capable of some activity a, and a regulates p.
-
- capable of regulating
-
-
-
-
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-
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-
- Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
-
- capable of negatively regulating
-
-
-
-
-
-
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-
- renin -> arteriolar smooth muscle contraction
- Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
-
- capable of positively regulating
-
-
-
-
-
-
-
-
- pazopanib -> pathological angiogenesis
- Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
- treats
-
- The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber.
- capable of inhibiting or preventing pathological process
-
-
-
-
- treats
- Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship
-
-
-
-
-
-
-
-
- benzene -> cancer [CHEBI]
- Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
- causes disease
-
- capable of upregulating or causing pathological process
-
-
-
-
-
-
-
-
- c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
- treats
-
- is substance that treats
-
-
-
-
-
-
-
-
-
-
- c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
- May be ceded to OBI
- indicates
- is marker for
-
-
-
-
-
-
-
-
- Inverse of 'causal agent in process'
-
- process has causal agent
-
-
-
-
-
-
-
- A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
- Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
- obsolete related via dependence to
- true
-
-
-
-
-
-
-
- A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
- Groups both positive and negative correlation
- correlated with
-
-
-
-
-
-
-
-
- An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
- A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
- In the Gene Ontology association model, this corresponds to the With/From field
- is evidence with support from
-
-
-
-
-
-
-
-
- Inverse of is-model-of
- has model
-
-
-
-
-
-
-
- Do not use this relation directly. It is a grouping relation.
- related via evidence or inference to
-
-
-
-
-
-
-
-
-
- visits
- https://github.com/oborel/obo-relations/issues/74
-
-
-
-
-
-
-
-
- visited by
-
-
-
-
-
-
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-
-
- visits flowers of
-
-
-
-
-
-
-
-
- has flowers visited by
-
-
-
-
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-
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-
-
-
- lays eggs in
-
-
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-
-
- has eggs laid in by
-
-
-
-
-
-
-
-
-
- https://github.com/jhpoelen/eol-globi-data/issues/143
- kills
-
-
-
-
-
-
-
-
- is killed by
-
-
-
-
-
-
-
-
-
- p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
-
- directly positively regulates (process to process)
-
-
-
-
- directly positively regulates
- https://wiki.geneontology.org/Directly_positively_regulates
-
-
-
-
-
-
-
-
-
- p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
-
- directly negatively regulates (process to process)
-
-
-
-
- directly negatively regulates
- https://wiki.geneontology.org/Directly_negatively_regulates
-
-
-
-
-
-
-
-
-
- A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host
-
- ectoparasite of
-
-
-
-
-
-
-
-
- inverse of ectoparasite of
-
- has ectoparasite
-
-
-
-
-
-
-
-
-
-
- A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system
- lives inside of
- endoparasite of
-
-
-
-
-
-
-
-
- has endoparasite
-
-
-
-
-
-
-
-
-
- A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite
- mesoparasite of
-
-
-
-
-
-
-
-
- inverse of mesoparasite of
-
- has mesoparasite
-
-
-
-
-
-
-
-
-
- A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.
-
- intercellular endoparasite of
-
-
-
-
-
-
-
-
- inverse of intercellular endoparasite of
-
- has intercellular endoparasite
-
-
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-
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-
-
- A sub-relation of endoparasite-of in which the parasite inhabits host cells.
-
- intracellular endoparasite of
-
-
-
-
-
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-
-
- inverse of intracellular endoparasite of
-
- has intracellular endoparasite
-
-
-
-
-
-
-
-
-
- Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting.
-
- co-roosts with
-
-
-
-
-
-
-
-
-
- An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s.
- A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host.
-
-
-
- A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts.
- reservoir host of
-
-
-
-
-
-
-
-
- An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s.
- inverse of reservoir host of
-
- has reservoir host
-
-
-
-
-
-
-
-
-
-
-
- According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle).
- x is an ectomycorrhizal host of y if and only if x is a plant (Plantae) whose roots form an intercellular interface (aka Hartig net) with fungus (Fungi) y. This interface consists of highly branched hyphae forming a latticework between epidermal and cortical root cells.
-
-
-
- An ectomycorrhiza is a form of symbiotic relationship that occurs between a fungal symbiont, or mycobiont, and the roots of various plant species. The mycobiont is often from the phyla Basidiomycota and Ascomycota, and more rarely from the Zygomycota. Ectomycorrhizae form on the roots of around 2% of plant species, usually woody plants, including species from the birch, dipterocarp, myrtle, beech, willow, pine and rose families. Research on ectomycorrhizae is increasingly important in areas such as ecosystem management and restoration, forestry, and agriculture. Unlike other mycorrhizal relationships, such as arbuscular mycorrhiza and ericoid mycorrhiza, ectomycorrhizal fungi do not penetrate their host's cell wall. Instead they form an entirely intercellular interfaces known as the Hartig net, consisting of highly branched hyphae forming a latticework between epidermal and cortical root cells.
- ectomycorrhizal host of
-
-
-
-
-
-
-
-
- According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle).
- inverse of ectomycorrhizal host of
-
- has ectomycorrhizal host
-
-
-
-
-
-
-
-
-
-
-
- According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae).
- x is an arbuscular mycorrhizal host of y if and only if x is a vascular plant (Plantae) whose cortical cells of the roots are penetrated by fungus (Fungi) y and form arbuscules.
-
-
-
- An arbuscular mycorrhiza (AM) (plural mycorrhizae) is a type of mycorrhiza in which the symbiont fungus (Arbuscular mycorrhizal fungi, or AMF) penetrates the cortical cells of the roots of a vascular plant forming arbuscules. Arbuscular mycorrhiza is a type of endomycorrhiza along with ericoid mycorrhiza and orchid mycorrhiza (not to be confused with ectomycorrhiza). They are characterized by the formation of unique tree-like structures, the arbuscules. In addition, globular storage structures called vesicles are often encountered. Arbuscular mycorrhizae are formed by fungi in the subphylum Glomeromycotina and some fungi from the Mucoromycotina. These subphyla, along with the Mortierellomycotina, form the phylum Mucoromycota, a sister clade of the more well-known and diverse dikaryan fungi. AM fungi help plants to capture nutrients such as phosphorus, sulfur, nitrogen and micronutrients from the soil. It is believed that the development of the arbuscular mycorrhizal symbiosis played a crucial role in the initial colonisation of land by plants and in the evolution of the vascular plants. It has been said that it is quicker to list the plants that do not form endomycorrhizae than those that do. This symbiosis is a highly evolved mutualistic relationship found between fungi and plants, the most prevalent plant symbiosis known, and AMF is found in 80% of vascular plant families in existence today.
- arbuscular mycorrhizal host of
-
-
-
-
-
-
-
-
- According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae).
- inverse of arbuscular mycorrhizal host of
-
-
- has arbuscular mycorrhizal host
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
-
-
- Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
- produces
-
-
-
-
-
-
-
-
-
-
- a produced_by b iff some process that occurs_in b has_output a.
-
-
- produced by
-
-
-
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-
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-
-
- Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA.
-
- represses expression of
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-
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- Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA.
-
- increases expression of
-
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-
-
- A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
-
- is used to study
- The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate.
- has role in modeling
-
-
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-
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-
- The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.
-
-An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
- A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
- Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
- Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.
-
-Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
- causes or contributes to condition
-
-
-
-
-
-
-
-
- A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.
- causes condition
-
-
-
-
-
-
-
-
- A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.
- contributes to condition
-
-
-
-
-
-
-
-
- A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
- contributes to expressivity of condition
- contributes to severity of condition
-
-
-
-
-
-
-
-
- A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
- contributes to penetrance of condition
- contributes to frequency of condition
-
-
-
-
-
-
-
-
- A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
- is preventative for condition
- Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.
-
-Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
- ameliorates condition
-
-
-
-
-
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-
-
- A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.
- correlated with condition
-
-
-
-
-
-
-
-
- A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.
- exacerbates condition
-
-
-
-
-
-
-
-
- A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.
- condition ameliorated by
-
-
-
-
-
-
-
-
- A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.
- condition exacerbated by
-
-
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-
- Do not use this relation directly. It is intended as a grouping for a more specific relations
-
- 2017-11-05T02:38:20Z
- condition has genetic basis in
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- 2017-11-05T02:45:20Z
- has material basis in gain of function germline mutation in
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- 2017-11-05T02:45:37Z
- has material basis in loss of function germline mutation in
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- 2017-11-05T02:45:54Z
- has material basis in germline mutation in
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- 2017-11-05T02:46:07Z
- has material basis in somatic mutation in
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- 2017-11-05T02:46:26Z
- has major susceptibility factor
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- 2017-11-05T02:46:57Z
- has partial material basis in germline mutation in
-
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- p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
-
- 2018-12-13T11:26:17Z
-
- has primary input or output
-
-
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- p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
-
- 2018-12-13T11:26:32Z
-
- has primary output
-
-
-
-
- p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
-
- GOC:dph
- GOC:kva
- GOC:pt
- PMID:27812932
-
-
-
-
-
-
-
-
-
- p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
-
- 2018-12-13T11:26:56Z
-
- has primary input
-
-
-
-
- p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
-
- GOC:dph
- GOC:kva
- GOC:pt
- PMID:27812932
-
-
-
-
-
-
-
-
-
- Do not use this relation directly. It is intended as a grouping for a more specific relations
-
- 2017-11-05T02:53:08Z
- is genetic basis for condition
-
-
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- Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
-
- 2017-11-05T02:55:51Z
- is causal gain of function germline mutation of in
-
-
-
-
-
-
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- Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
-
- 2017-11-05T02:56:06Z
- is causal loss of function germline mutation of in
-
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- Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
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- 2017-11-05T02:56:40Z
- is causal germline mutation in
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- Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet].
-
- 2017-11-05T02:57:07Z
- is causal somatic mutation in
-
-
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-
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-
- Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet].
-
- 2017-11-05T02:57:43Z
- is causal susceptibility factor for
-
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-
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-
-
- Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet].
-
- 2017-11-05T02:58:43Z
- is causal germline mutation partially giving rise to
-
-
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- 2017-11-05T03:20:01Z
- realizable has basis in
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- 2017-11-05T03:20:29Z
- is basis for realizable
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- 2017-11-05T03:26:47Z
- disease has basis in
-
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-
-
- A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.
- disease has basis in dysfunction of (disease to anatomical structure)
-
- 2017-11-05T03:29:32Z
- disease has basis in dysfunction of
-
-
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-
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-
- A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
- disease has basis in disruption of (disease to process)
-
- 2017-11-05T03:37:52Z
- disease has basis in disruption of
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-
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- A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
-
- 2017-11-05T03:46:07Z
- disease has basis in feature
-
-
-
-
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-
- Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.
-
- 2017-11-05T03:50:54Z
- causal relationship with disease as subject
-
-
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- A relationship between a disease and a process where the disease process disrupts the execution of the process.
- disease causes disruption of (disease to process)
-
- 2017-11-05T03:51:09Z
- disease causes disruption of
-
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- disease causes dysfunction of (disease to anatomical entity)
-
- 2017-11-05T03:58:20Z
- disease causes dysfunction of
-
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- A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
- TODO: complete range axiom once more of CARO has been mireoted in to this ontology
- This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here.
-
- 2017-11-05T04:06:02Z
- disease has location
-
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- A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity
-
- 2017-12-26T19:37:31Z
- disease has inflammation site
-
-
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-
- A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
-
- 2017-12-26T19:45:49Z
- realized in response to stimulus
-
-
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-
- A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
-
- 2017-12-26T19:50:53Z
- disease has feature
-
-
-
-
-
-
-
-
-
- A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.
-
- 2017-12-26T19:58:44Z
- disease arises from alteration in structure
-
-
-
-
-
-
-
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-
-
-
-
- Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
-
- 2018-01-25T23:20:13Z
- enables subfunction
-
-
-
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-
-
-
-
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-
- 2018-01-26T23:49:30Z
-
- acts upstream of or within, positive effect
- https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect
-
-
-
-
-
-
-
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- 2018-01-26T23:49:51Z
-
- acts upstream of or within, negative effect
- https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect
-
-
-
-
-
-
-
-
-
-
-
-
-
- c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
-
-
- 2018-01-26T23:53:14Z
-
- acts upstream of, positive effect
- https://wiki.geneontology.org/Acts_upstream_of,_positive_effect
-
-
-
-
-
-
-
-
-
-
-
-
-
- c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
-
-
- 2018-01-26T23:53:22Z
-
- acts upstream of, negative effect
- https://wiki.geneontology.org/Acts_upstream_of,_negative_effect
-
-
-
-
-
-
-
-
-
-
- 2018-03-13T23:55:05Z
- causally upstream of or within, negative effect
- https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect
-
-
-
-
-
-
-
-
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-
- 2018-03-13T23:55:19Z
- causally upstream of or within, positive effect
-
-
-
-
-
-
-
-
- DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
- DEPRECATED inheres in
- true
-
-
-
-
-
-
-
- DEPRECATED bearer of
- true
-
-
-
-
-
-
-
- A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity.
-
- has driver
-
-
-
-
-
-
-
-
-
- A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes.
-
- has disease driver
-
-
-
-
-
-
-
-
-
-
- An interaction relationship wherein a plant or algae is living on the outside surface of another plant.
- https://en.wikipedia.org/wiki/Epiphyte
- epiphyte of
-
-
-
-
-
-
-
-
- inverse of epiphyte of
-
- has epiphyte
-
-
-
-
-
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-
-
-
- A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material
- https://en.wikipedia.org/wiki/Kleptoparasitism
- kleptoparasite of
-
-
-
-
-
-
-
-
- inverse of kleptoparasite of
-
- kleptoparasitized by
-
-
-
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-
- An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.
- creates habitat for
-
-
-
-
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-
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-
-
- An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.
- ecologically co-occurs with
-
-
-
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-
- An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.
- lays eggs on
-
-
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-
-
- inverse of lays eggs on
- has eggs laid on by
-
-
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-
- Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)
- x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x.
-
- 2023-01-18T14:28:21Z
-
- A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y.
- has roost
-
-
-
-
-
-
-
-
- frog symbiotrophically interacts with the pitcher plant it lives inside of
- A trophic interaction in which one organism acquires nutrients through a symbiotic relationship with another organism
-
- 2023-07-17T14:39:56Z
-
- symbiotrophically interacts with
-
-
-
-
-
-
-
-
- tapeworm is trophic parasite of the cow it lives inside of
- A symbiotrophic interaction in which one organism acquires nutrients through a parasitic relationship with another organism
-
- 2023-07-17T14:41:07Z
-
- trophic parasite of
-
-
-
-
-
-
-
-
-
-
- muffin 'has substance added' some 'baking soda'
-
- "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.
- The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients.
-
- has substance added
-
-
-
-
-
-
-
-
-
-
- 'egg white' 'has substance removed' some 'egg yolk'
-
- "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time.
-
- has substance removed
-
-
-
-
-
-
-
-
-
-
- sardines 'immersed in' some 'oil and mustard'
-
- "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance.
-
- immersed in
-
-
-
-
-
-
-
-
-
- sardine has consumer some homo sapiens
-
- 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect.
-
- has consumer
-
-
-
-
-
-
-
-
-
- bread 'has primary substance added' some 'flour'
-
- 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance.
-
- has primary substance added
-
-
-
-
-
-
-
-
-
-
- A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material.
- A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic.
-
- 2023-05-23T15:24:15Z
- assay measures characteristic
-
-
-
-
-
-
-
-
-
- Inverse of 'assay measures characteristic'
-
- 2023-05-23T15:29:50Z
- characteristic measured by assay
-
-
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-
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-
-
- A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
- An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
- Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
- r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
-
-
-
-
- triggered by process
- realized in response to
- https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit
-
-
-
-
- triggered by process
-
-
-
-
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-
-
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-
-
- Genetic information generically depend on molecules of DNA.
- The novel *War and Peace* generically depends on this copy of the novel.
- The pattern shared by chess boards generically depends on any chess board.
- The score of a symphony g-depends on a copy of the score.
- This pdf file generically depends on this server.
- A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
- [072-ISO]
- g-depends on
- generically depends on
-
-
-
-
-
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-
-
-
-
-
-
- Molecules of DNA are carriers of genetic information.
- This copy of *War and Peace* is carrier of the novel written by Tolstoy.
- This hard drive is carrier of these data items.
- *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
- [072-ISO]
- is carrier of
-
-
-
-
-
-
-
-
-
-
- The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
-
- regulates activity of
-
-
-
-
-
-
-
-
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-
- The entity A has an activity that regulates the quantity or abundance or concentration of the entity B.
-
- regulates quantity of
-
-
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-
- The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B.
-
- indirectly regulates activity of
-
-
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-
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-
-
- The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.
-
-For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B.
-
- decreases by repression quantity of
-
-
-
-
-
-
-
-
-
-
- The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.
-
-For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B.
-
- increases by expression quantity of
-
-
-
-
-
-
-
-
-
-
- The entity A has an activity that directly positively regulates the quantity of B.
-
- directly positively regulates quantity of
-
-
-
-
-
-
-
-
-
-
- The entity A has an activity that directly negatively regulates the quantity of B.
-
- directly negatively regulates quantity of
-
-
-
-
-
-
-
-
-
-
- The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B.
-
- indirectly activates
- indirectly positively regulates activity of
-
-
-
-
-
-
-
-
-
-
- AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)
- An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it.
-
- destabilizes quantity of
-
-
-
-
-
-
-
-
-
-
- AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)
- An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it.
-
- stabilizes quantity of
-
-
-
-
-
-
-
-
- The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B.
-
- indirectly inhibits
- indirectly negatively regulates activity of
-
-
-
-
-
-
-
-
- The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B.
-
- directly regulates quantity of
-
-
-
-
-
-
-
-
- The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B.
-
- indirectly regulates quantity of
-
-
-
-
-
-
-
-
- The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B.
-
- indirectly negatively regulates quantity of
-
-
-
-
-
-
-
-
- The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B.
-
- indirectly positively regulates quantity of
-
-
-
-
-
-
-
-
-
- a relation between a process and a continuant, in which the process is regulated by the small molecule continuant
-
- 2020-04-22T20:27:26Z
- has small molecule regulator
-
-
-
-
-
-
-
-
-
- a relation between a process and a continuant, in which the process is activated by the small molecule continuant
-
- 2020-04-22T20:28:37Z
- has small molecule activator
-
-
-
-
-
-
-
-
-
- a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant
-
- 2020-04-22T20:28:54Z
- has small molecule inhibitor
-
-
-
-
-
-
-
-
- p acts on population of c iff c' is a collection, has members of type c, and p has participant c
-
- 2020-06-08T17:21:33Z
-
-
-
- acts on population of
-
-
-
-
-
-
-
-
- a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process
-
- 2020-06-24T13:15:17Z
- is small molecule regulator of
-
-
-
-
-
-
-
-
-
- a relation between a continuant and a process, in which the continuant is a small molecule that activates the process
-
- 2020-06-24T13:15:26Z
- is small molecule activator of
- https://wiki.geneontology.org/Is_small_molecule_activator_of
-
-
-
-
-
-
-
-
-
- a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process
-
- 2020-06-24T13:15:35Z
- is small molecule inhibitor of
- https://wiki.geneontology.org/Is_small_molecule_inhibitor_of
-
-
-
-
-
-
-
-
- The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities.
-
- 2020-08-27T08:13:59Z
- results in adhesion of
-
-
-
-
-
-
-
-
-
- 2021-02-26T07:28:29Z
-
-
-
- results in fusion of
-
-
-
-
-
-
-
-
- p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.
-
- 2022-09-26T06:01:01Z
-
-
- constitutively upstream of
- https://wiki.geneontology.org/Constitutively_upstream_of
-
-
-
-
-
-
-
-
- p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.
-
- 2022-09-26T06:06:20Z
-
-
- removes input for
- https://wiki.geneontology.org/Removes_input_for
-
-
-
-
-
-
-
-
- p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
-
- 2022-09-26T06:07:17Z
- indirectly causally upstream of
-
-
-
-
-
-
-
-
-
- p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
-
- 2022-09-26T06:08:01Z
- indirectly regulates
-
-
-
-
-
-
-
-
- x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
-
-
- 2023-10-12T10:02:28Z
- positively regulates in other organism
-
- positively regulates in another organism
-
-
-
-
-
-
-
-
- x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
-
-
- 2023-10-12T10:02:42Z
- negatively regulates in other organism
-
- negatively regulates in another organism
-
-
-
-
-
-
-
-
-
-
-
-
- A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
-
- 2020-07-17T09:26:52Z
- has synaptic input or output in
- has synaptic IO in region
-
-
-
-
-
-
-
-
-
-
-
-
-
- A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.
-
- 2020-07-17T09:42:23Z
- receives synaptic input in region
-
-
-
-
-
-
-
-
-
-
-
-
-
- A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.
-
- 2020-07-17T09:45:06Z
- sends synaptic output to region
-
-
-
-
-
-
-
-
- A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion).
-
- 2020-07-17T09:52:19Z
- has synaptic IO throughout
-
-
-
-
-
-
-
-
-
- A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion).
-
- 2020-07-17T09:55:36Z
- receives synaptic input throughout
-
-
-
-
-
-
-
-
-
- A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion).
-
- 2020-07-17T09:57:27Z
- sends synaptic output throughout
-
-
-
-
-
-
-
-
-
-
-
-
-
- Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.
-
- 2020-07-20T12:10:09Z
- has sensory dendrite location
- has sensory terminal in
- has sensory terminal location
- has sensory dendrite in
-
-
-
-
-
-
-
-
-
- A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it.
-
- 2021-05-26T08:40:18Z
- receives synaptic input from neuron
-
-
-
-
-
-
-
-
- A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to.
-
- 2021-05-26T08:41:07Z
- Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron.
- sends synaptic output to cell
-
-
-
-
-
-
-
-
-
-
-
-
- An optic lobe intrinsic neuron has its synapses restricted to optic lobe neuropil.
- A relationship between a neuron and a region, where all of the functionally relevant input and output synapses are in that region.
-
- 2023-08-17T12:17:24Z
- intrinsic to
- This relation may still be used if a very small number of synapses fall slightly outside the boundaries of the region, but any class using this relation should not have another restriction using this relation to another non-overlapping region.
- synapses restricted to region
-
-
-
-
-
-
-
-
- A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent.
-
- disease has infectious agent
-
-
-
-
-
-
-
-
-
-
-
-
-
- transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])
- A relation between a material entity and some data in which the data is taken as exemplifying the material entity.
- C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C.
-
- This relation is not meant to capture the relation between occurrents and data.
- has exemplar data
-
-
-
-
-
-
-
-
-
- exemplar data of
-
-
-
-
-
-
-
-
-
- A relation between a group and another group it is part of but does not fully constitute.
- X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y.
-
- This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics.
- subcluster of
-
-
-
-
-
-
-
-
- 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1').
- transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3.
- A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type.
- C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types.
- This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context.
-
- has marker gene combination
- has marker signature set
- has characterizing marker set
-
-
-
-
-
-
-
-
-
- q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
- different in magnitude relative to
-
-
-
-
- q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
- https://orcid.org/0000-0002-6601-2165
-
-
-
-
-
-
-
-
-
-
- q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
- This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
- increased in magnitude relative to
-
-
-
-
- q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
- https://orcid.org/0000-0002-6601-2165
-
-
-
-
-
-
-
-
-
-
- q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
- This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
- decreased in magnitude relative to
-
-
-
-
- q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
- https://orcid.org/0000-0002-6601-2165
-
-
-
-
-
-
-
- q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
- similar in magnitude relative to
-
-
-
-
- q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
- https://orcid.org/0000-0002-6601-2165
-
-
-
-
-
-
-
- has relative magnitude
-
-
-
-
-
-
-
- s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
- Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
- has cross section
-
-
-
-
- s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
- https://orcid.org/0000-0002-6601-2165
-
-
-
-
-
-
-
- q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
- There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.
- reciprocal of
-
-
-
-
- q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
- https://orcid.org/0000-0002-6601-2165
-
-
-
-
-
-
-
-
-
- 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')
- A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
-
-
- has high plasma membrane amount
-
-
-
-
- A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
- PMID:19243617
-
-
-
-
-
-
-
-
-
- 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')
- A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
-
-
- has low plasma membrane amount
-
-
-
-
- A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
- PMID:19243617
-
-
-
-
-
-
-
- Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease.
-
- 2021-11-05T17:30:14Z
- has phenotype or disease
- https://github.com/oborel/obo-relations/issues/478
-
-
-
-
-
-
-
-
- A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
-
- 2021-11-05T17:30:44Z
- has disease
- https://github.com/oborel/obo-relations/issues/478
-
-
-
-
-
-
-
-
- X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y.
- ExO:0000083
-
- 2021-12-14T20:41:45Z
- has exposure medium
-
-
-
-
-
-
-
-
-
-
-
- A diagnostic testing device utilizes a specimen.
- X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
- A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
- See github ticket https://github.com/oborel/obo-relations/issues/497
-
-
- 2021-11-08T12:00:00Z
- utilizes
- device utilizes material
-
-
-
-
-
-
-
-
- The information in a blueprint specifies the dimensions of a building.
- The information in a recipe specifies what interredients to use and the steps needed to prepare a meal.
- The information in a software program specifies the order of computations.
- A relation between information and an entity such that the information serves as a rule or guide if the entity is an occurrent, or the information serves as a model if the entity is a continuant.
-
- 2025-06-16T17:08:04Z
- prescribes
- specifies
- information specifies
- https://www.ontologyrepository.com/CommonCoreOntologies/prescribes
-
-
-
-
-
-
-
-
-
- A relation between entities in which one increases or decreases as the other does the same.
- directly correlated with
-
- positively correlated with
-
-
-
-
-
-
-
-
-
-
- A relation between entities in which one increases as the other decreases.
- inversely correlated with
-
- negatively correlated with
-
-
-
-
-
-
-
-
-
- anticoagulant-containing test tube contains measured amount 5 ml of blood specimen.
- A relation between a container and measurement datum that specifies the actual amount of material in the container.
-
-
- contains measured amount
-
-
-
-
-
-
-
-
-
- anticoagulant-containing test tube has maximum capacity 10 ml.
- A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume.
-
-
- has maximum capacity
-
-
-
-
-
-
-
- inverse of 'has symptom'
-
- 2025-06-16T17:42:05Z
- symptom of
-
-
-
-
-
-
-
-
- biobank organization owns a specimen
- hospital owns a laboratory facility
- A primitive relation that holds between entities x and y in which y is at x's full disposal.
-
-
-
- This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal.
- 2023-03-29T16:57:03Z
- owns
-
-
-
-
-
-
-
- freezer is owned by a biobank organization
- Inverse of the owns relation.
-
-
-
- 2023-03-29T17:06:06Z
-
- is owned by
-
-
-
-
-
-
-
- Inverse of information specifies.
-
- 2025-06-16T17:13:17Z
- specified by information
-
-
-
-
-
-
-
-
- Inverse relation of 'is marker for'.
-
- 2025-07-14T20:57:25Z
- has marker
-
-
-
-
-
-
-
-
-
- A thorax specimen was collected during the larval stage.
- An oyster was collected during low tide.
- A relation between a material entity and an occurrent in which the material entity is collected during the existence of the occurrent.
-
- 2023-09-13T04:12:32Z
- collected during
-
-
-
-
-
-
-
-
- Helper relation for OWL definition of RO:0018002 myristoylates
-
- is myristoyltransferase activity
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input
-
-
- myristoylates
-
-
-
-
-
-
-
- inverse of myristoylates
-
- myristoylated by
-
-
-
-
-
-
-
-
- mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)
- a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor
-
- is agonist of
-
-
-
-
-
-
-
-
-
- pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)
- a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level
-
- is inverse agonist of
-
-
-
-
-
-
-
-
-
- tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)
- a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level
-
- is antagonist of
-
-
-
-
-
-
-
-
- Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical.
-
- chemical relationship
-
-
-
-
-
-
-
-
-
- pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816)
- A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B.
-
-
- is direct conjugate base of
-
-
-
-
-
-
-
-
-
- neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361)
- A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B.
-
-
- is direct conjugate acid of
-
-
-
-
-
-
-
-
-
-
-
- (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons.
- A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B.
-
-This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.
-
- obo:chebi#is_conjugate_base_of
- is deprotonated form of
-
-
-
-
-
-
-
-
-
-
- (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons.
- A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B.
-
-This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.
-
- obo:chebi#is_conjugate_acid_of
- is protonated form of
-
-
-
-
-
-
-
-
-
-
- phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol.
- A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification.
-
-While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts.
-
-This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A.
-
-This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C.
-
- 2023-02-28T18:53:32Z
- is MMP with
- is matched molecular pair with
- is matched small molecular pair with
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- A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification.
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-While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts.
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-This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A.
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-This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C.
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- 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol.
- Two chemicals are tautomers if they can be readily interconverted.
-
-This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms.
-
- 2023-03-18T23:49:31Z
- obo:chebi#is_tautomer_of
- is desmotrope of
- is tautomer of
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- 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol.
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- carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)
- Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization.
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- 2023-03-18T23:49:31Z
- obo:chebi#is_substituent_group_from
- is substitutent group from
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- carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)
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- hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)
- Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A.
-
-For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship.
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- 2023-03-18T23:49:31Z
- obo:chebi#has_functional_parent
- has functional parent
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- hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)
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- dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped.
- Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center.
-
-A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers).
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- 2023-03-18T23:49:31Z
- obo:chebi#is_enantiomer_of
- is optical isomer of
- is enantiomer of
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- dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped.
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- pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates.
- Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B.
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- 2023-03-18T23:49:31Z
- obo:chebi#has_parent_hydride
- has parent hydride
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- pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates.
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- A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
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- regulates characteristic
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- A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
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- positively regulates characteristic
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- A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
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- negatively regulates characteristic
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- Given individuals f, i, x, and y, where f is a 'molecular function', i is an 'information biomacromolecule', and x and y are instances of different types of gene products, if f 'enabled by' i within an OWL model of a biological pathway, and i 'has substitutable entity' both x and y, then either x or y are valid enablers of function f within the modeled biological context.
- Relates one individual to another which is capable of standing in for the first individual in its other relations to other individuals.
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- has substitutable entity
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- Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition.
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- confers susceptibility to condition
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- brachial artery vessel supplies blood to brachialis muscle
- x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y.
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- 2024-02-01T10:09:22Z
- vessel supplies blood to
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- cystic vein vessel drains blood from gallbladder
- x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y.
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- 2024-02-01T10:09:41Z
- vessel drains blood from
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- alveolar capillary directly supplies and drains some alveolus
- x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y.
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- 2024-02-01T10:09:59Z
- directly supplies and drains
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- This property only applies to neurons
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- 2024-10-23T14:34:52Z
- is neuron
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- This property only applies to anatomical entities.
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- 2024-10-29T09:55:07Z
- is anatomical entity
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- A relationship between a ratio or proportion and its dividend.
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- has dividend
- has numerator
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- A relationship between a ratio or proportion and its divisor.
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- has divisor
- has denominator
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- inverse of allelopath of
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- has allelopath
- https://en.wikipedia.org/wiki/Allelopathy
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- A cancer biomarker provides_clinical_information_for some cancer, which is to say that the presence of or features of the biomarker is clinically informative for the presence of or features of the cancer.
- A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' provides clinical information about 'd'.
- https://orcid.org/0000-0001-5809-9523
-
- Usage note: This does not imply that 'b' and 'd' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and 'd'.
-
-Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
- provides clinical information for
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- A below-normal level of creatine in cerebrospinal fluid is diagnostic_for guanidinoacetate methyltransferase deficiency, which is to say that such levels indicate that the patient has the indicated clinical issue.
- An above-normal level of succinylacetone in urine is diagnostic_for type 1 tyrosinemia, while an above-normal level of 4-hydroxyphenylpyruvate is diagnostic_for either type 2 or type 3 tyrosinemia.
- A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the presence or occurrence of 'd' or determine its subtype.
- https://orcid.org/0000-0001-5809-9523
-
- Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
- diagnostic for
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- Hemoglobin A1c (HbA1c) level in blood monitors_status_of diabetes since HbA1c levels reflect a three-month average of blood glucose levels, and can thus be used to monitor the disease progression.
- A relationship between a serially-measured biomarker 'b' and a disease or condition of clinical interest 'd', where 'b' is used to infer the status of 'd'.
- https://orcid.org/0000-0001-5809-9523
-
- Usage note: The status of 'd' refers to disease progression/remission or treatment response.
-
-Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
- monitors status of
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- The level of urinary glycosaminoglycans indicates_response_to enzyme replacement therapy for patients with mucopolysaccharidosis type 1.
- A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to show that a biological response to 'e' has occurred.
- https://orcid.org/0000-0001-5809-9523
-
- Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment.
-
-Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
- indicates response to
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- The incidence of squamous cell differentiation (indicated, for example, by keratinization) in non-small cell lung cancer patients predicts_effect_of the drug pemetrexed, where the prediction is that such patients will have a poor outcome with use of the drug.
- A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to identify individuals who are likely to experience a favorable or unfavorable effect from exposure to 'e'.
- https://orcid.org/0000-0001-5809-9523
-
- Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. In the context of predictive biomarkers, 'e' is typically a medical product such as a drug.
-
-Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (RO:0020331), and 'predicts effect of' (this relation) are each used to relate biomarkers to possible future clinical outcomes:
- - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue;
- - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest;
- - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment.
-
-Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
- predicts effect of
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- A high number of tumor cells expressing the nuclear protein Ki-67 is prognostic_for an aggressive cancer.
- A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the likelihood of a clinical event, disease recurrence or progression in patients who have 'd'.
- https://orcid.org/0000-0001-5809-9523
-
- Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (this relation), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes:
- - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue;
- - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest;
- - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment.
-
-Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
- prognostic for
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-
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- As an indicator of kidney issues, reduced creatinine clearance capability assesses_toxicity_of certain drugs (such as antibiotics or chemotherapy agents) to the kidneys.
- A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to indicate the likelihood, presence, or extent of toxicity as an adverse effect of exposure to 'e'.
- https://orcid.org/0000-0001-5809-9523
-
- Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment.
-
-Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
- assesses toxicity of
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-
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- The presence of a certain BRCA1 mutation indicates_risk_of_developing breast cancer in those who don't currently have the cancer.
- A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the potential for developing 'd' in an individual that currently does not have 'd'.
- https://orcid.org/0000-0001-5809-9523
-
- Usage note: The relations 'indicates risk of developing' (this relation), 'prognostic for' (RO:0020331), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes:
- - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue;
- - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest;
- - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment.
-
-Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
- indicates risk of developing
-
-
-
-
-
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-
- An image biomarker showing tumor size indicates_clinical_effect_of some radiotherapy.
- A relationship between a biomarker 'b' and an exposure agent 'e', where the effect of exposure to 'e' is correlated with the presence or occurrence of 'b', and the observation of 'b' is used to infer exposure to 'e'.
- https://orcid.org/0000-0001-5809-9523
-
- Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment.
-
-Usage note: This does not imply that 'b' and exposure to 'e' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and exposure to 'e'.
-
-Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
- indicates clinical effect of
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-
-
-
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-
- The level of prostate-specific antigen (PSA) monitors_effect_of therapies applied for the treatment of prostate cancers.
- A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of a biological effect of 'e'.
- https://orcid.org/0000-0001-5809-9523
-
- Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment.
-
-Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
- monitors effect of
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- The concentration of tobacco specific nitrosamines in urine monitors_exposure_to tobacco/tobacco smoke.
- A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of exposure to 'e'.
- https://orcid.org/0000-0001-5809-9523
-
- Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment.
-
-Usage note: The relations 'monitors status of' (RO:0020328), 'monitors exposure to' (this relation), and 'monitors effect of' (RO:0020335) are each used for serially-measured biomarkers:
- - 'monitors status of' pertains to cases where the biomarker is used to assess the progression/remission of a disease or condition of clinical interest;
- - 'monitors exposure to' pertains to cases where the biomarker is used to assess the occurrence of or amount of exposure to some exposure agent;
- - 'monitors effect of' pertains to cases where the biomarker is used to assess any possible biological effect arising from exposure to some exposure agent.
-
- Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
- monitors exposure to
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- A polyubiquitin has_constituent_monomer some ubiquitin.
- An amino acid chain has_constituent_monomer at least two amino acid residues.
- A relation that holds between a polymer and its constituent monomers. P has_constituent_monomer 'm' if and only if P has_component multiple instances of 'm' and each instance of 'm' is covalently attached to another instance of 'm'.
-
- Usage note: The constituent monomers need not be covalently attached in an end-to-end manner; that is, polymers with internal connections (e.g., polyubiquitin) can use this relation, as can circular polymers (e.g., plasmids) and multi-branched polymers (e.g., glycans). This relation, as non-transitive, allows the number of instances of 'm' to be indicated.
- has constituent monomer
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- Charged tRNA (i.e., aminoacyl-tRNA) is a tRNA that is covalently_bound_to some amino acid.
- A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of covalent interactions.
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- Such entities will colocalize at all times of the interaction.
- covalently bound to
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- Holo-calmodulin is a calmodulin that is non-covalently_bound_to calcium.
- A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of non-covalent interactions.
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- Such entities will colocalize at all times of the interaction.
- non-covalently bound to
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- This relation groups relations between diseases and any other kind of entity.
- Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease.
-
- 2018-09-26T00:00:32Z
- disease relationship
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- p has anatomical participant c iff p has participant c, and c is an anatomical entity
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- 2018-09-26T01:08:58Z
- results in changes to anatomical or cellular structure
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- Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
- TODO: Add homeomorphy axiom
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- ECO:0000041
- SO:similar_to
- sameness
- similar to
- correspondence
- resemblance
- in similarity relationship with
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- Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
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- BGEE:curator
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- correspondence
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- Similarity that results from common evolutionary origin.
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- homologous to
- This broad definition encompasses all the working definitions proposed so far in the literature.
- in homology relationship with
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- Similarity that results from common evolutionary origin.
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- Similarity that results from independent evolution.
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- homoplasous to
- analogy
- in homoplasy relationship with
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- Similarity that results from independent evolution.
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- Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
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- ECO:0000075
- homocracous to
- Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.
- in homocracy relationship with
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- Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
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- Homoplasy that involves different underlying mechanisms or structures.
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- analogy
- Convergence usually implies a notion of adaptation.
- in convergence relationship with
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- Homoplasy that involves different underlying mechanisms or structures.
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- Homoplasy that involves homologous underlying mechanisms or structures.
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- parallel evolution
- Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.
- in parallelism relationship with
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- Homoplasy that involves homologous underlying mechanisms or structures.
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- Homology that is defined by similarity with regard to selected structural parameters.
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- ECO:0000071
- MI:2163
- structural homologous to
- idealistic homology
- in structural homology relationship with
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- Homology that is defined by similarity with regard to selected structural parameters.
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-
- ISBN:0123195837
-
-
-
-
-
-
-
-
-
- Homology that is defined by common descent.
-
-
- homology
- ECO:0000080
- RO_proposed_relation:homologous_to
- SO:0000330
- SO:0000853
- SO:0000857
- SO:homologous_to
- TAO:homologous_to
- cladistic homology
- historical homologous to
- phylogenetic homology
- taxic homology
- true homology
- in historical homology relationship with
-
-
-
-
-
- Homology that is defined by common descent.
-
-
- ISBN:0123195837
-
-
-
-
-
-
-
-
-
- Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
-
-
- ECO:0000067
- biological homologous to
- transformational homology
- Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.
- in biological homology relationship with
-
-
-
-
-
- Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
-
-
-
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-
-
-
-
-
-
-
-
- Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
-
-
- atavism
- rudiment
- reversion
- in reversal relationship with
-
-
-
-
-
- Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
-
-
-
-
-
-
-
-
-
-
-
- Structural homology that is detected by similarity in content and organization between chromosomes.
-
-
- MeSH:Synteny
- SO:0000860
- SO:0005858
- syntenic homologous to
- synteny
- in syntenic homology relationship with
-
-
-
-
-
- Structural homology that is detected by similarity in content and organization between chromosomes.
-
- MeSH:Synteny
-
-
-
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-
-
-
-
-
-
- Historical homology that involves genes that diverged after a duplication event.
-
-
- SO:0000854
- SO:0000859
- SO:paralogous_to
- paralogous to
- in paralogy relationship with
-
-
-
-
-
- Historical homology that involves genes that diverged after a duplication event.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Paralogy that involves sets of syntenic blocks.
-
-
- syntenic paralogous to
- duplicon
- paralogon
- in syntenic paralogy relationship with
-
-
-
-
-
- Paralogy that involves sets of syntenic blocks.
-
-
- DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y
-
-
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-
-
- Syntenic homology that involves chromosomes of different species.
-
-
- syntenic orthologous to
- in syntenic orthology relationship with
-
-
-
-
-
- Syntenic homology that involves chromosomes of different species.
-
-
-
-
-
-
-
-
-
-
-
- Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
-
-
- fractional homology
- partial homologous to
- segmental homology
- mixed homology
- modular homology
- partial correspondence
- percent homology
- in partial homology relationship with
-
-
-
-
-
- Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
-
- ISBN:0123195837
- ISBN:978-0471984931
-
-
-
-
-
-
-
-
-
- Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
-
-
- MeSH:Structural_Homology,_Protein
- protein structural homologous to
- in protein structural homology relationship with
-
-
-
-
-
- Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
-
-
-
-
-
-
-
-
-
-
-
-
- Structural homology that involves a pseudogenic feature and its functional ancestor.
-
-
- pseudogene
- SO:non_functional_homolog_of
- non functional homologous to
- in non functional homology relationship with
-
-
-
-
-
- Structural homology that involves a pseudogenic feature and its functional ancestor.
-
- SO:non_functional_homolog_of
-
-
-
-
-
-
-
-
-
- Historical homology that involves genes that diverged after a speciation event.
-
-
- ECO:00000060
- SO:0000855
- SO:0000858
- SO:orthologous_to
- orthologous to
- The term is sometimes also used for anatomical structures.
- in orthology relationship with
-
-
-
-
-
- Historical homology that involves genes that diverged after a speciation event.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
-
-
- xenologous to
- The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).
- in xenology relationship with
-
-
-
-
-
- Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
-
-
-
-
-
-
-
-
-
-
-
-
- Historical homology that involves two members sharing no other homologs in the lineages considered.
-
-
- 1 to 1 homologous to
- 1:1 homology
- one-to-one homology
- in 1 to 1 homology relationship with
-
-
-
-
-
- Historical homology that involves two members sharing no other homologs in the lineages considered.
-
- BGEE:curator
-
-
-
-
-
-
-
-
-
-
- Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
-
-
- 1 to 1 orthologous to
- 1:1 orthology
- one-to-one orthology
- in 1 to 1 orthology relationship with
-
-
-
-
-
- Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
-
-
-
-
-
-
-
-
-
-
-
-
- Paralogy that results from a whole genome duplication event.
-
-
- ohnologous to
- homoeology
- in ohnology relationship with
-
-
-
-
-
- Paralogy that results from a whole genome duplication event.
-
-
-
-
-
-
-
-
-
-
-
-
- Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
-
-
- in-paralogous to
- inparalogy
- symparalogy
- in in-paralogy relationship with
-
-
-
-
-
- Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
-
-
-
-
-
-
-
-
-
-
-
- Paralogy that results from a duplication preceding a given speciation event.
-
-
- alloparalogy
- out-paralogous to
- outparalogy
- in out-paralogy relationship with
-
-
-
-
-
- Paralogy that results from a duplication preceding a given speciation event.
-
-
-
-
-
-
-
-
-
-
-
- 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
-
-
- pro-orthologous to
- in pro-orthology relationship with
-
-
-
-
-
- 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
-
-
-
-
-
-
-
-
-
-
-
-
- 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
-
-
- semi-orthologous to
- The converse of pro-orthologous.
- in semi-orthology relationship with
-
-
-
-
-
- 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
-
-
-
-
-
-
-
-
-
-
-
-
- Iterative homology that involves structures arranged along the main body axis.
-
-
- serial homologous to
- homonomy
- in serial homology relationship with
-
-
-
-
-
- Iterative homology that involves structures arranged along the main body axis.
-
-
-
-
-
-
-
-
-
-
-
- Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
-
-
- heterochronous homologous to
- heterochrony
- in heterochronous homology relationship with
-
-
-
-
-
- Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
-
- ISBN:978-0674639416
-
-
-
-
-
-
-
-
-
-
- Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
-
-
- juvenification
- pedomorphosis
- in paedomorphorsis relationship with
-
-
-
-
-
- Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
-
-
- ISBN:978-0674639416
-
-
-
-
-
-
-
-
-
- Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
-
-
- in peramorphosis relationship with
-
-
-
-
-
- Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
-
-
-
-
-
-
-
-
-
-
-
- Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
-
-
- in progenesis relationship with
-
-
-
-
-
- Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
-
-
- ISBN:978-0674639416
-
-
-
-
-
-
-
-
-
- Paedomorphosis that is produced by a retardation of somatic development.
-
-
- juvenilization
- neotenous to
- in neoteny relationship with
-
-
-
-
-
- Paedomorphosis that is produced by a retardation of somatic development.
-
-
- ISBN:978-0674639416
-
-
-
-
-
-
-
-
-
- Convergence that results from co-evolution usually involving an evolutionary arms race.
-
-
- mimicrous to
- in mimicry relationship with
-
-
-
-
-
- Convergence that results from co-evolution usually involving an evolutionary arms race.
-
-
-
-
-
-
-
-
-
-
-
-
- Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
-
-
- 1 to many orthologous to
- 1:many orthology
- one-to-many orthology
- co-orthology
- many to 1 orthology
- in 1 to many orthology relationship with
-
-
-
-
-
- Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
-
-
-
-
-
-
-
-
-
-
-
-
- Historical homology that involves two members of a larger set of homologs.
-
-
- many to many homologous to
- many-to-many homology
- many:many homology
- in many to many homology relationship with
-
-
-
-
-
- Historical homology that involves two members of a larger set of homologs.
-
-
-
-
-
-
-
-
-
-
-
- Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
-
-
- 1 to many homologous to
- one-to-many homology
- 1:many homology
- in 1 to many homology relationship with
-
-
-
-
-
- Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
-
- BGEE:curator
-
-
-
-
-
-
-
-
-
-
- Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
-
-
- apomorphous to
- synapomorphy
- in apomorphy relationship with
-
-
-
-
-
- Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
-
- ISBN:978-0252068140
-
-
-
-
-
-
-
-
-
- Historical homology that is based on distant shared ancestry.
-
-
- plesiomorphous to
- symplesiomorphy
- This term is usually contrasted to apomorphy.
- in plesiomorphy relationship with
-
-
-
-
-
- Historical homology that is based on distant shared ancestry.
-
- ISBN:978-0252068140
-
-
-
-
-
-
-
-
-
-
- Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
-
-
- deep genetic homology
- deep homologous to
- generative homology
- homoiology
- Used for structures in distantly related taxa.
- in deep homology relationship with
-
-
-
-
-
- Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
-
-
-
-
-
-
-
-
-
-
-
-
- Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
-
-
- hemiplasous to
- in hemiplasy relationship with
-
-
-
-
-
- Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
-
-
-
-
-
-
-
-
-
-
-
- Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
-
-
- gametologous to
- in gametology relationship with
-
-
-
-
-
- Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
-
-
-
-
-
-
-
-
-
-
-
- Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
-
-
- MeSH:Chromosome_Pairing
- chromosomal homologous to
- in chromosomal homology relationship with
-
-
-
-
-
- Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
-
- ISBN:0195307615
-
-
-
-
-
-
-
-
-
-
- Orthology that involves two genes that experienced duplications more recent than the species split that created them.
-
-
- many to many orthologous to
- many-to-many orthology
- many:many orthology
- trans-orthology
- co-orthology
- trans-homology
- in many to many orthology relationship with
-
-
-
-
-
- Orthology that involves two genes that experienced duplications more recent than the species split that created them.
-
-
-
-
-
-
-
-
-
-
-
-
-
- Paralogy that involves genes from the same species.
-
-
- within-species paralogous to
- in within-species paralogy relationship with
-
-
-
-
-
- Paralogy that involves genes from the same species.
-
-
-
-
-
-
-
-
-
-
-
- Paralogy that involves genes from different species.
-
-
- between-species paralogous to
- The genes have diverged before a speciation event.
- in between-species paralogy relationship with
-
-
-
-
-
- Paralogy that involves genes from different species.
-
-
-
-
-
-
-
-
-
-
-
- Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
-
-
- post-displacement
- in postdisplacement relationship with
-
-
-
-
-
- Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
-
-
-
-
-
-
-
-
-
-
-
- Peramorphosis that is produced by a delay in the offset of development.
-
-
- in hypermorphosis relationship with
-
-
-
-
-
- Peramorphosis that is produced by a delay in the offset of development.
-
-
- ISBN:978-0674639416
-
-
-
-
-
-
-
-
-
- Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
-
-
- synologous to
- in synology relationship with
-
-
-
-
-
- Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
-
-
-
-
-
-
-
-
-
-
-
-
-
- Orthology that involves functional equivalent genes with retention of the ancestral function.
-
-
- ECO:0000080
- isoorthologous to
- in isoorthology relationship with
-
-
-
-
-
- Orthology that involves functional equivalent genes with retention of the ancestral function.
-
-
-
-
-
-
-
-
-
-
-
- Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
-
-
- tandem paralogous to
- iterative paralogy
- serial paralogy
- in tandem paralogy relationship with
-
-
-
-
-
- Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
-
-
- ISBN:978-0878932665
-
-
-
-
-
-
-
-
-
-
- Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
-
-
- apomorphic tendency
- cryptic homology
- latent homologous to
- underlying synapomorphy
- homoiology
- homoplastic tendency
- re-awakening
- Used for structures in closely related taxa.
- in latent homology relationship with
-
-
-
-
-
- Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
-
-
-
-
- ISBN:0199141118
-
-
-
-
-
-
-
-
-
- Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
-
-
- generative homology
- syngenous to
- Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.
- in syngeny relationship with
-
-
-
-
-
- Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
-
-
- DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R
-
-
-
-
-
-
-
-
-
-
- Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
-
-
- 1:1 paralogy
- apparent 1:1 orthology
- apparent orthologous to
- pseudoorthology
- The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.
- in apparent orthology relationship with
-
-
-
-
-
- Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
-
-
-
-
-
-
-
-
-
-
-
-
- Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
-
-
- pseudoparalogous to
- These genes may come out as paralogs in a single-genome analysis.
- in pseudoparalogy relationship with
-
-
-
-
-
- Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
-
-
-
-
-
-
-
-
-
-
-
-
- Historical homology that involves functional equivalent genes with retention of the ancestral function.
-
-
- equivalogous to
- This may include examples of orthology, paralogy and xenology.
- in equivalogy relationship with
-
-
-
-
-
- Historical homology that involves functional equivalent genes with retention of the ancestral function.
-
-
-
-
-
-
-
-
-
-
-
- Historical homology that involves orthologous pairs of interacting molecules in different organisms.
-
-
- interologous to
- in interology relationship with
-
-
-
-
-
- Historical homology that involves orthologous pairs of interacting molecules in different organisms.
-
-
-
-
-
-
-
-
-
-
-
-
- Similarity that is characterized by interchangeability in function.
-
-
- functional similarity
- in functional equivalence relationship with
-
-
-
-
-
- Similarity that is characterized by interchangeability in function.
-
-
-
-
-
-
-
-
-
-
-
-
- Biological homology that involves parts of the same organism.
-
-
- iterative homologous to
- in iterative homology relationship with
-
-
-
-
-
- Biological homology that involves parts of the same organism.
-
-
-
-
-
-
-
-
-
-
-
- Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
-
-
- duplicate xenology
- multiple xenology
- paraxenologous to
- in paraxenology relationship with
-
-
-
-
-
- Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
-
-
-
-
-
-
-
-
-
-
-
- Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
-
-
- plerologous to
- This phenomenon is usually due to gene conversion process.
- in plerology relationship with
-
-
-
-
-
- Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
-
-
-
-
-
-
-
-
-
-
-
-
- Structural homology that involves structures with the same or similar relative positions.
-
-
- homotopous to
- Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.
- in homotopy relationship with
-
-
-
-
-
- Structural homology that involves structures with the same or similar relative positions.
-
-
-
- ISBN:0123195837
-
-
-
-
-
-
-
-
-
- Biological homology that involves an ectopic structure and the normally positioned structure.
-
-
- heterotopy
- in homeosis relationship with
-
-
-
-
-
- Biological homology that involves an ectopic structure and the normally positioned structure.
-
-
-
-
-
-
-
-
-
-
-
-
-
- Synology that results from allopolyploidy.
-
-
- homoeologous to
- On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.
- in homoeology relationship with
-
-
-
-
-
- Synology that results from allopolyploidy.
-
-
-
-
-
-
-
-
-
-
-
-
- Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
-
-
- axis paramorphism
- in paramorphism relationship with
-
-
-
-
-
- Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
-
-
-
-
-
-
-
-
-
-
-
-
- Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
-
-
- regulogous to
- in regulogy relationship with
-
-
-
-
-
- Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 0
-
-
- 100
-
-
-
-
- Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
-
- 2018-05-22T16:43:28Z
- This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses.
- has increased age-specific mortality rate
-
-
-
-
- Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
- PMID:24138933
- Wikipedia:Infant_mortality
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- An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
- continuant
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- An entity that has temporal parts and that happens, unfolds or develops through time.
- occurrent
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- b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
- A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
- independent continuant
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- spatial region
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- p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
- An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
- process
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- disposition
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- A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
- realizable entity
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- quality
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- b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
- A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
- specifically dependent continuant
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- A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
- role
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- b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
- A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
- generically dependent continuant
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- function
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- An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
- Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
- material entity
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- immaterial entity
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- A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
- CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
- We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.
- CALOHA:TS-2035
- FMA:68646
- GO:0005623
- KUPO:0000002
- MESH:D002477
- VHOG:0001533
- WBbt:0004017
- XAO:0003012
- The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
- cell
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- A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
- CARO:mah
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- Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
-
- BTO:0001037
- FMA:84649
- MESH:D011984
- WBbt:0005759
- sensory neuron
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- Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
- ISBN:0721662544
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- true
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- The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
-
- BTO:0000938
- CALOHA:TS-0683
- FMA:54527
- VHOG:0001483
- WBbt:0003679
- nerve cell
- These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.
- neuron
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- The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
- MESH:D009474
- http://en.wikipedia.org/wiki/Neuron
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- A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome
- 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'.
- Includes virus - we will later have a class for cellular organisms.
- organism
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- A material entity processed by human activity with an intent to produce it.
- In the COB 2024 workshop there was much disagreement about this label.
- processed material entity
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- completely executed planned process
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- A process during which an organism comes into contact with another entity.
- exposure of organism
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- A processed material entity which is designed to be capable of a process.
- device
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- A system which has the disposition to environ one or more material entities.
- 2013-09-23T16:04:08Z
- EcoLexicon:environment
- environment
- In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
- environmental system
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- A system which has the disposition to environ one or more material entities.
- DOI:10.1186/2041-1480-4-43
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- An environmental system which can sustain and allow the growth of an ecological population.
- EcoLexicon:habitat
- LTER:238
- SWEETRealm:Habitat
- https://en.wikipedia.org/wiki/Habitat
- A habitat's specificity to an ecological population differentiates it from other environment classes.
- habitat
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- An environmental system which can sustain and allow the growth of an ecological population.
- EnvO:EnvO
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- A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
- This is the same as GO molecular function
- molecular function
- GO:0003674
- Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
- gene product or complex activity
- molecular_function
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- A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
- GOC:pdt
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- true
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- Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
- E2
- E3
- KEGG_REACTION:R03876
- Reactome:R-HSA-1169394
- Reactome:R-HSA-1169395
- Reactome:R-HSA-1169397
- Reactome:R-HSA-1169398
- Reactome:R-HSA-1169402
- Reactome:R-HSA-1169405
- Reactome:R-HSA-1169406
- Reactome:R-HSA-1234163
- Reactome:R-HSA-1234172
- Reactome:R-HSA-1253282
- Reactome:R-HSA-1358789
- Reactome:R-HSA-1358790
- Reactome:R-HSA-1358792
- Reactome:R-HSA-1363331
- Reactome:R-HSA-168915
- Reactome:R-HSA-173542
- Reactome:R-HSA-173545
- Reactome:R-HSA-174057
- Reactome:R-HSA-174104
- Reactome:R-HSA-174144
- Reactome:R-HSA-174159
- Reactome:R-HSA-174195
- Reactome:R-HSA-174227
- Reactome:R-HSA-179417
- Reactome:R-HSA-180540
- Reactome:R-HSA-180597
- Reactome:R-HSA-182986
- Reactome:R-HSA-182993
- Reactome:R-HSA-183051
- Reactome:R-HSA-183084
- Reactome:R-HSA-183089
- Reactome:R-HSA-1852623
- Reactome:R-HSA-187575
- Reactome:R-HSA-1912357
- Reactome:R-HSA-1912386
- Reactome:R-HSA-1918092
- Reactome:R-HSA-1918095
- Reactome:R-HSA-1977296
- Reactome:R-HSA-1980074
- Reactome:R-HSA-1980118
- Reactome:R-HSA-201425
- Reactome:R-HSA-202453
- Reactome:R-HSA-202534
- Reactome:R-HSA-205118
- Reactome:R-HSA-209063
- Reactome:R-HSA-211734
- Reactome:R-HSA-2169050
- Reactome:R-HSA-2172172
- Reactome:R-HSA-2179276
- Reactome:R-HSA-2186747
- Reactome:R-HSA-2186785
- Reactome:R-HSA-2187368
- Reactome:R-HSA-2213017
- Reactome:R-HSA-264444
- Reactome:R-HSA-2682349
- Reactome:R-HSA-2730904
- Reactome:R-HSA-2737728
- Reactome:R-HSA-2769007
- Reactome:R-HSA-2900765
- Reactome:R-HSA-3000335
- Reactome:R-HSA-3134804
- Reactome:R-HSA-3134946
- Reactome:R-HSA-3249386
- Reactome:R-HSA-3780995
- Reactome:R-HSA-3781009
- Reactome:R-HSA-3788724
- Reactome:R-HSA-3797226
- Reactome:R-HSA-4332236
- Reactome:R-HSA-446877
- Reactome:R-HSA-450358
- Reactome:R-HSA-451418
- Reactome:R-HSA-5357757
- Reactome:R-HSA-5362412
- Reactome:R-HSA-5483238
- Reactome:R-HSA-5607725
- Reactome:R-HSA-5607728
- Reactome:R-HSA-5607756
- Reactome:R-HSA-5607757
- Reactome:R-HSA-5610742
- Reactome:R-HSA-5610745
- Reactome:R-HSA-5610746
- Reactome:R-HSA-5652009
- Reactome:R-HSA-5655170
- Reactome:R-HSA-5660753
- Reactome:R-HSA-5667107
- Reactome:R-HSA-5667111
- Reactome:R-HSA-5668454
- Reactome:R-HSA-5668534
- Reactome:R-HSA-5675470
- Reactome:R-HSA-5684250
- Reactome:R-HSA-5691108
- Reactome:R-HSA-5693108
- Reactome:R-HSA-68712
- Reactome:R-HSA-69598
- Reactome:R-HSA-741386
- Reactome:R-HSA-75824
- Reactome:R-HSA-870449
- Reactome:R-HSA-8948709
- Reactome:R-HSA-8956106
- Reactome:R-HSA-9013069
- Reactome:R-HSA-9013974
- Reactome:R-HSA-9014342
- Reactome:R-HSA-918224
- Reactome:R-HSA-936412
- Reactome:R-HSA-936942
- Reactome:R-HSA-936986
- Reactome:R-HSA-9628444
- Reactome:R-HSA-9645394
- Reactome:R-HSA-9645414
- Reactome:R-HSA-9688831
- Reactome:R-HSA-9701000
- Reactome:R-HSA-9750946
- Reactome:R-HSA-975118
- Reactome:R-HSA-975147
- Reactome:R-HSA-9758604
- Reactome:R-HSA-9766227
- Reactome:R-HSA-9793444
- Reactome:R-HSA-9793485
- Reactome:R-HSA-9793679
- Reactome:R-HSA-9796346
- Reactome:R-HSA-9796387
- Reactome:R-HSA-9796626
- Reactome:R-HSA-9815507
- Reactome:R-HSA-9817362
- Reactome:R-HSA-983140
- Reactome:R-HSA-983153
- Reactome:R-HSA-983156
- Reactome:R-HSA-9833155
- Reactome:R-HSA-9833973
- Reactome:R-HSA-9834070
- Reactome:R-HSA-9861563
- Reactome:R-HSA-9861640
- Reactome:R-HSA-9929350
- Reactome:R-HSA-9934753
- Reactome:R-HSA-9948301
- Reactome:R-HSA-9954721
- ubiquitin conjugating enzyme activity
- ubiquitin ligase activity
- ubiquitin protein ligase activity
- ubiquitin protein-ligase activity
- ubiquitin-conjugating enzyme activity
- GO:0004842
- ubiquitin-protein transferase activity
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-
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- Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
- GOC:BioGRID
- GOC:jh2
- PMID:9635407
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- Reactome:R-HSA-1169394
- ISGylation of IRF3
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- Reactome:R-HSA-1169395
- ISGylation of viral protein NS1
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- Reactome:R-HSA-1169397
- Activation of ISG15 by UBA7 E1 ligase
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- Reactome:R-HSA-1169398
- ISGylation of host protein filamin B
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- Reactome:R-HSA-1169402
- ISGylation of E2 conjugating enzymes
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- Reactome:R-HSA-1169405
- ISGylation of protein phosphatase 1 beta (PP2CB)
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- Reactome:R-HSA-1169406
- ISGylation of host proteins
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- Reactome:R-HSA-1234163
- Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha
-
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- Reactome:R-HSA-1234172
- Nuclear VBC complex ubiquitinylates HIF-alpha
-
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- Reactome:R-HSA-1253282
- ERBB4 ubiquitination by WWP1/ITCH
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- Reactome:R-HSA-1358789
- Self-ubiquitination of RNF41
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- Reactome:R-HSA-1358790
- RNF41 ubiquitinates ERBB3
-
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- Reactome:R-HSA-1358792
- RNF41 ubiquitinates activated ERBB3
-
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- Reactome:R-HSA-1363331
- Ubiquitination of p130 (RBL2) by SCF (Skp2)
-
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- Reactome:R-HSA-168915
- K63-linked ubiquitination of RIP1 bound to the activated TLR complex
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- Reactome:R-HSA-173542
- SMURF2 ubiquitinates SMAD2
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- Reactome:R-HSA-173545
- Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling
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- Reactome:R-HSA-174057
- Multiubiquitination of APC/C-associated Cdh1
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- Reactome:R-HSA-174104
- Ubiquitination of Cyclin A by APC/C:Cdc20 complex
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- Reactome:R-HSA-174144
- Ubiquitination of Securin by phospho-APC/C:Cdc20 complex
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- Reactome:R-HSA-174159
- Ubiquitination of Emi1 by SCF-beta-TrCP
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- Reactome:R-HSA-174195
- Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex
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- Reactome:R-HSA-174227
- Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex
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- Reactome:R-HSA-179417
- Multiubiquitination of Nek2A
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- Reactome:R-HSA-180540
- Multi-ubiquitination of APOBEC3G
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- Reactome:R-HSA-180597
- Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex
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- Reactome:R-HSA-182986
- CBL-mediated ubiquitination of CIN85
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- Reactome:R-HSA-182993
- Ubiquitination of stimulated EGFR (CBL)
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- Reactome:R-HSA-183051
- CBL ubiquitinates Sprouty
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- Reactome:R-HSA-183084
- CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix
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- Reactome:R-HSA-183089
- CBL binds and ubiquitinates phosphorylated Sprouty
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- Reactome:R-HSA-1852623
- Ubiquitination of NICD1 by FBWX7
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- Reactome:R-HSA-187575
- Ubiquitination of phospho-p27/p21
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- Reactome:R-HSA-1912357
- ITCH ubiquitinates DTX
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- Reactome:R-HSA-1912386
- Ubiquitination of NOTCH1 by ITCH in the absence of ligand
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- Reactome:R-HSA-1918092
- CHIP (STUB1) mediates ubiquitination of ERBB2
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- Reactome:R-HSA-1918095
- CUL5 mediates ubiquitination of ERBB2
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- Reactome:R-HSA-1977296
- NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer
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- Reactome:R-HSA-1980074
- Ubiquitination of DLL/JAG ligands upon binding to NOTCH1
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- Reactome:R-HSA-1980118
- ARRB mediates NOTCH1 ubiquitination
-
-
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- Reactome:R-HSA-201425
- Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling
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- Reactome:R-HSA-202453
- Auto-ubiquitination of TRAF6
-
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- Reactome:R-HSA-202534
- Ubiquitination of NEMO by TRAF6
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- Reactome:R-HSA-205118
- TRAF6 polyubiquitinates NRIF
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- Reactome:R-HSA-209063
- Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex
-
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- Reactome:R-HSA-211734
- Ubiquitination of PAK-2p34
-
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-
- Reactome:R-HSA-2169050
- SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7
-
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- Reactome:R-HSA-2172172
- Ubiquitination of DLL/JAG ligands upon binding to NOTCH2
-
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- Reactome:R-HSA-2179276
- SMURF2 monoubiquitinates SMAD3
-
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-
- Reactome:R-HSA-2186747
- Ubiquitination of SKI/SKIL by RNF111/SMURF2
-
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- Reactome:R-HSA-2186785
- RNF111 ubiquitinates SMAD7
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- Reactome:R-HSA-2187368
- STUB1 (CHIP) ubiquitinates SMAD3
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-
- Reactome:R-HSA-2213017
- Auto-ubiquitination of TRAF3
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- Reactome:R-HSA-264444
- Autoubiquitination of phospho-COP1(Ser-387 )
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- Reactome:R-HSA-2682349
- RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels
-
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- Reactome:R-HSA-2730904
- Auto-ubiquitination of TRAF6
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- Reactome:R-HSA-2737728
- Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants
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- Reactome:R-HSA-2769007
- Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants
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- Reactome:R-HSA-2900765
- Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants
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- Reactome:R-HSA-3000335
- SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA
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- Reactome:R-HSA-3134804
- STING ubiquitination by TRIM32 or TRIM56
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- Reactome:R-HSA-3134946
- DDX41 ubiquitination by TRIM21
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- Reactome:R-HSA-3249386
- DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1
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- Reactome:R-HSA-3780995
- NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2
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- Reactome:R-HSA-3781009
- NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1
-
-
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- Reactome:R-HSA-3788724
- Cdh1:APC/C ubiquitinates EHMT1 and EHMT2
-
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- Reactome:R-HSA-3797226
- Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease)
-
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- Reactome:R-HSA-4332236
- CBL neddylates TGFBR2
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-
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- Reactome:R-HSA-446877
- TRAF6 is K63 poly-ubiquitinated
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- Reactome:R-HSA-450358
- Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation
-
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- Reactome:R-HSA-451418
- Pellino ubiquitinates IRAK1
-
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-
-
- Reactome:R-HSA-5357757
- BIRC(cIAP1/2) ubiquitinates RIPK1
-
-
-
-
- Reactome:R-HSA-5362412
- SYVN1 ubiquitinates Hh C-terminal fragments
-
-
-
-
- Reactome:R-HSA-5483238
- Hh processing variants are ubiquitinated
-
-
-
-
- Reactome:R-HSA-5607725
- SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP
-
-
-
-
- Reactome:R-HSA-5607728
- beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex
-
-
-
-
- Reactome:R-HSA-5607756
- TRAF6 oligomer autoubiquitinates
-
-
-
-
- Reactome:R-HSA-5607757
- K63polyUb-TRAF6 ubiquitinates TAK1
-
-
-
-
- Reactome:R-HSA-5610742
- SCF(beta-TrCP) ubiquitinates p-GLI1
-
-
-
-
- Reactome:R-HSA-5610745
- SCF(beta-TrCP) ubiquitinates p-GLI2
-
-
-
-
- Reactome:R-HSA-5610746
- SCF(beta-TrCP) ubiquitinates p-GLI3
-
-
-
-
- Reactome:R-HSA-5652009
- RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA
-
-
-
-
- Reactome:R-HSA-5655170
- RCHY1 monoubiquitinates POLH
-
-
-
-
- Reactome:R-HSA-5660753
- SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA
-
-
-
-
- Reactome:R-HSA-5667107
- SIAH1, SIAH2 ubiquitinate SNCAIP
-
-
-
-
- Reactome:R-HSA-5667111
- PARK2 K63-Ubiquitinates SNCAIP
-
-
-
-
- Reactome:R-HSA-5668454
- K63polyUb-cIAP1,2 ubiquitinates TRAF3
-
-
-
-
- Reactome:R-HSA-5668534
- cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK
-
-
-
-
- Reactome:R-HSA-5675470
- BIRC2/3 (cIAP1/2) is autoubiquitinated
-
-
-
-
- Reactome:R-HSA-5684250
- SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2
-
-
-
-
- Reactome:R-HSA-5691108
- SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2
-
-
-
-
- Reactome:R-HSA-5693108
- TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains
-
-
-
-
- Reactome:R-HSA-68712
- The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1
-
-
-
-
- Reactome:R-HSA-69598
- Ubiquitination of phosphorylated CDC25A
-
-
-
-
- Reactome:R-HSA-741386
- RIP2 induces K63-linked ubiquitination of NEMO
-
-
-
-
- Reactome:R-HSA-75824
- Ubiquitination of Cyclin D1
-
-
-
-
- Reactome:R-HSA-870449
- TRIM33 monoubiquitinates SMAD4
-
-
-
-
- Reactome:R-HSA-8948709
- DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3
-
-
-
-
- Reactome:R-HSA-8956106
- VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha
-
-
-
-
- Reactome:R-HSA-9013069
- Ubiquitination of DLL/JAG ligands upon binding to NOTCH3
-
-
-
-
- Reactome:R-HSA-9013974
- Auto-ubiquitination of TRAF3 within activated TLR3 complex
-
-
-
-
- Reactome:R-HSA-9014342
- K63-linked ubiquitination of RIP1 bound to the activated TLR complex
-
-
-
-
- Reactome:R-HSA-918224
- DDX58 is K63 polyubiquitinated
-
-
-
-
- Reactome:R-HSA-936412
- RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS
-
-
-
-
- Reactome:R-HSA-936942
- Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2
-
-
-
-
- Reactome:R-HSA-936986
- Activated TRAF6 synthesizes unanchored polyubiquitin chains
-
-
-
-
- Reactome:R-HSA-9628444
- Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation
-
-
-
-
- Reactome:R-HSA-9645394
- Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation
-
-
-
-
- Reactome:R-HSA-9645414
- Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer
-
-
-
-
- Reactome:R-HSA-9688831
- STUB1 ubiquitinates RIPK3 at K55, K363
-
-
-
-
- Reactome:R-HSA-9701000
- BRCA1:BARD1 heterodimer autoubiquitinates
-
-
-
-
- Reactome:R-HSA-9750946
- TRAF2,6 ubiquitinates NLRC5
-
-
-
-
- Reactome:R-HSA-975118
- TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex
-
-
-
-
- Reactome:R-HSA-975147
- Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane
-
-
-
-
- Reactome:R-HSA-9758604
- Ubiquitination of IKBKG by TRAF6
-
-
-
-
- Reactome:R-HSA-9766227
- MDM2 mediates CDH1 ubiquitination
-
-
-
-
- Reactome:R-HSA-9793444
- ITCH polyubiquitinates MLKL at K50
-
-
-
-
- Reactome:R-HSA-9793485
- PRKN polyubiquitinates RIPK3
-
-
-
-
- Reactome:R-HSA-9793679
- LUBAC ubiquitinates RIPK1 at K627
-
-
-
-
- Reactome:R-HSA-9796346
- MIB2 ubiquitinates RIPK1 at K377, K604, K634
-
-
-
-
- Reactome:R-HSA-9796387
- STUB1 ubiquitinates RIPK1 at K571, K604, K627
-
-
-
-
- Reactome:R-HSA-9796626
- MIB2 ubiquitinates CFLAR
-
-
-
-
- Reactome:R-HSA-9815507
- MIB2 ubiquitinates CYLD at K338, K530
-
-
-
-
- Reactome:R-HSA-9817362
- SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex
-
-
-
-
- Reactome:R-HSA-983140
- Transfer of Ub from E2 to substrate and release of E2
-
-
-
-
- Reactome:R-HSA-983153
- E1 mediated ubiquitin activation
-
-
-
-
- Reactome:R-HSA-983156
- Polyubiquitination of substrate
-
-
-
-
- Reactome:R-HSA-9833155
- Ubiquitination of STAT2
-
-
-
-
- Reactome:R-HSA-9833973
- ISGylation of PKR
-
-
-
-
- Reactome:R-HSA-9834070
- PRKN ubiquitinates MOM substrates
-
-
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-
- Reactome:R-HSA-9861563
- CTLH E3 ligase ubiquitinates LDHA
-
-
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-
- Reactome:R-HSA-9861640
- CTLH E3 ligase ubiquitinates PKM-1
-
-
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-
- Reactome:R-HSA-9929350
- Ubiquitination of CD274 by BTRC-SCF E3-ligase complex
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-
- Reactome:R-HSA-9934753
- CBLL1 ubiquitinates CDH1
-
-
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-
- Reactome:R-HSA-9948301
- ZNF598 K63 polyubiquitinates RPS10 (eS10) and RPS20 (uS10) of the 40S ribosomal subunit
-
-
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-
- Reactome:R-HSA-9954721
- NEDD8-K699-CUL2:ELOB:ELOC:RBX1:KLHDC10 K48 polyubiquitinates alanine-tailed nascent peptide
-
-
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-
- A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
- NIF_Subcellular:sao1702920020
- Wikipedia:Cell_nucleus
- cell nucleus
- horsetail nucleus
- GO:0005634
- nucleus
-
-
-
-
- A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
- GOC:go_curators
-
-
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-
- horsetail nucleus
- GOC:al
- GOC:mah
- GOC:vw
- PMID:15030757
-
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-
- A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
- jl
- 2012-09-19T15:05:24Z
- Wikipedia:Biological_process
- biological process
- physiological process
- single organism process
- single-organism process
- GO:0008150
- Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
- biological process
- biological_process
-
-
-
-
- A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
- GOC:pdt
-
-
-
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-
-
-
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-
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-
- true
-
-
- Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
- Reactome:R-HSA-6788855
- Reactome:R-HSA-6788867
- phosphokinase activity
- GO:0016301
- Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
- kinase activity
-
-
-
-
- Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
- ISBN:0198506732
-
-
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-
- Reactome:R-HSA-6788855
- FN3KRP phosphorylates PsiAm, RibAm
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-
- Reactome:R-HSA-6788867
- FN3K phosphorylates ketosamines
-
-
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-
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-
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-
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- true
-
-
- Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.
- Reactome:R-HSA-141367
- Reactome:R-HSA-162914
- GO:0019107
- myristoyltransferase activity
-
-
-
-
- Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.
- GOC:ai
-
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-
- Reactome:R-HSA-141367
- Myristoylation of tBID by NMT1
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-
- Reactome:R-HSA-162914
- Myristoylation of Nef
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- curation status specification
-
- The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
- Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
- PERSON:Bill Bug
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- OBI_0000266
- curation status specification
-
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- assay
- Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
-
- A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.
- 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
- Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683.
- PlanAndPlannedProcess Branch
- measuring
- scientific observation
- OBI branch derived
- assay
-
-
-
-
-
-
-
- container
-
- A device that can be used to restrict the location of material entities over time
- 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
- PERSON: Bjoern Peters
- container
-
-
-
-
-
-
-
-
- A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
- disease
-
-
-
-
-
-
-
-
- A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
- PATO:0000001
- quality
-
-
-
-
- A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
- PATOC:GVG
-
-
-
-
-
-
-
-
- A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
-
- ramified
- ramiform
- PATO:0000402
- branched
-
-
-
-
- A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
- WordNet:WordNet
-
-
-
-
-
-
-
-
- A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
- PATO:0001199
- linear
-
-
-
-
- A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
- ISBN:0881923214
-
-
-
-
-
-
-
-
- A quality inhering in a bearer by virtue of the bearer's magnitude in proportion to the magnitude of another entity.
- proportion
- proportionality
- proportionality to
- quotient
- rate
- PATO:0001470
- Examples: height to weight; brain size to body size; root to shoot ratio; urinary sodium to potassium ratio. waist-hip ratio.
- ratio
-
-
-
-
- A quality inhering in a bearer by virtue of the bearer's magnitude in proportion to the magnitude of another entity.
- https://orcid.org/0000-0001-8314-2140
-
-
-
-
- Examples: height to weight; brain size to body size; root to shoot ratio; urinary sodium to potassium ratio. waist-hip ratio.
- https://orcid.org/0000-0001-8314-2140
-
-
-
-
-
-
-
-
- A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
-
- 2009-10-06T04:37:14Z
- PATO:0002124
- laminar
-
-
-
-
- A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
- PATOC:GVG
-
-
-
-
-
-
-
- An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human,
- An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes.
- OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.
- This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions.
-
-
- 2017-06-05T17:55:39Z
- obsolete exposure event or process
- https://github.com/oborel/obo-relations/pull/173
- true
-
-
-
-
-
-
-
-
-
-
-
-
-
- Any entity that is ordered in discrete units along a linear axis.
-
- sequentially ordered entity
-
-
-
-
-
-
-
-
- Any individual unit of a collection of like units arranged in a linear order
-
- An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair.
- sequence atomic unit
-
-
-
-
-
-
-
-
- Any entity that can be divided into parts such that each part is an atomical unit of a sequence
-
- Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence.
- sequence bearer
-
-
-
-
-
-
-
-
- A material entity consisting of multiple components that are causally integrated.
- May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
-
- http://www.jbiomedsem.com/content/4/1/43
- system
-
-
-
-
-
-
-
-
- Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
-
-
- AAO:0010825
- AEO:0000003
- BILA:0000003
- CARO:0000003
- EHDAA2:0003003
- EMAPA:0
- FAO:0000001
- FMA:305751
- FMA:67135
- GAID:781
- HAO:0000003
- MA:0003000
- MESH:D000825
- SCTID:362889002
- TAO:0000037
- TGMA:0001823
- VHOG:0001759
- XAO:0003000
- ZFA:0000037
- http://dbpedia.org/ontology/AnatomicalStructure
- biological structure
- connected biological structure
- UBERON:0000061
-
-
-
-
-
- anatomical structure
-
-
-
-
- Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
- CARO:0000003
-
-
-
-
- connected biological structure
- CARO:0000003
-
-
-
-
-
-
-
-
- A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
- CARO:0001001
- NLX:147821
- funiculus
- nerve fiber bundle
- neural fiber bundle
- UBERON:0000122
-
-
- neuron projection bundle
-
-
-
-
- A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
- CARO:0001001
- FBC:DOS
- FBbt:00005099
-
-
-
-
- nerve fiber bundle
- FBbt:00005099
-
-
-
-
-
-
-
-
-
-
- Anatomical entity that has mass.
-
-
- AAO:0010264
- AEO:0000006
- BILA:0000006
- CARO:0000006
- EHDAA2:0003006
- FMA:67165
- HAO:0000006
- TAO:0001836
- TGMA:0001826
- VHOG:0001721
- UBERON:0000465
-
-
-
-
- material anatomical entity
-
-
-
-
- Anatomical entity that has mass.
- http://orcid.org/0000-0001-9114-8737
-
-
-
-
-
-
-
-
-
- Anatomical entity that has no mass.
-
-
- AAO:0010265
- AEO:0000007
- BILA:0000007
- CARO:0000007
- EHDAA2:0003007
- FMA:67112
- HAO:0000007
- TAO:0001835
- TGMA:0001827
- VHOG:0001727
- immaterial physical anatomical entity
- UBERON:0000466
-
-
-
-
- immaterial anatomical entity
-
-
-
-
- Anatomical entity that has no mass.
- http://orcid.org/0000-0001-9114-8737
-
-
-
-
- immaterial physical anatomical entity
- FMA:67112
-
-
-
-
-
-
-
-
-
-
- true
-
-
-
- Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
-
-
- AAO:0010841
- AEO:0000000
- BFO:0000004
- BILA:0000000
- BIRNLEX:6
- CARO:0000000
- EHDAA2:0002229
- FMA:62955
- HAO:0000000
- MA:0000001
- NCIT:C12219
- TAO:0100000
- TGMA:0001822
- UMLS:C1515976
- WBbt:0000100
- XAO:0000000
- ZFA:0100000
- UBERON:0001062
-
-
-
-
- anatomical entity
-
-
-
-
- Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
- FMA:62955
- http://orcid.org/0000-0001-9114-8737
-
-
-
-
- UMLS:C1515976
- ncithesaurus:Anatomic_Structure_System_or_Substance
-
-
-
-
-
-
-
-
- A vessel through which blood circulates in the body.
- consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
- vascular element
- AAO:0011004
- AEO:0000207
- BTO:0001102
- CALOHA:TS-0080
- EFO:0000817
- EHDAA2:0003252
- EHDAA:240
- EMAPA:32743
- EMAPA:35993
- FMA:50722
- FMA:63183
- GAID:169
- MA:0000060
- MAT:0000393
- MESH:D001808
- NCIT:C12679
- NLXANAT:090901
- SCTID:361097006
- TAO:0002137
- UMLS:C0005847
- VHOG:0001250
- Wikipedia:Blood_vessel
- XAO:0001011
- ZFA:0005314
- region of vascular tree organ
- vascular tree organ region
- UBERON:0001981
-
-
-
-
-
-
-
- blood vessel
-
-
-
-
- A vessel through which blood circulates in the body.
- BTO:0001102
- Wikipedia:Blood_vessel
-
-
-
-
- vascular element
- EMAPA:35993
-
-
-
-
- UMLS:C0005847
- ncithesaurus:Blood_Vessel
-
-
-
-
- region of vascular tree organ
- FMA:50722
-
-
-
-
- vascular tree organ region
- FMA:50722
-
-
-
-
-
-
-
-
- Any of the smallest blood vessels connecting arterioles with venules.
- not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
- AAO:0010252
- BTO:0002045
- CALOHA:TS-2006
- EFO:0001906
- EMAPA:35198
- EV:0100035
- FMA:63194
- MA:0000065
- MESH:D002196
- NCIT:C12685
- NLXANAT:090902
- TAO:0005250
- UMLS:C0935624
- VHOG:0001253
- Wikipedia:Capillary
- XAO:0000116
- ZFA:0005250
- blood capillary
- capillary vessel
- UBERON:0001982
-
-
-
-
-
-
-
- capillary
- https://github.com/obophenotype/uberon/issues/2186
-
-
-
-
- Any of the smallest blood vessels connecting arterioles with venules.
- ISBN:0073040584
- Wikipedia:Capillary
- https://github.com/obophenotype/uberon/issues/137
-
-
-
-
- UMLS:C0935624
- ncithesaurus:Capillary
-
-
-
-
-
-
-
-
- An anatomical structure that has more than one cell as a part.
-
-
- CARO:0010000
- multicellular structure
- UBERON:0010000
-
-
-
-
- multicellular anatomical structure
-
-
-
-
- An anatomical structure that has more than one cell as a part.
- CARO:0010000
-
-
-
-
- multicellular structure
- FBbt:00100313
-
-
-
-
-
-
-
-
- phenotype
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 2019-03-05T17:25:21Z
- Western Australia Ecoregion
- WWF:AA1310
- https://www.worldwildlife.org/ecoregions/aa1310
- Western Australian Mulga Shrublands Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-05T17:51:32Z
- https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands
- Australasia Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-05T17:52:41Z
- Southern central Australia Ecoregion
- WWF:AA1309
- https://www.worldwildlife.org/ecoregions/aa1309
- Tirari-Sturt Stony Desert Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-05T17:54:35Z
- Eastern central Australia Ecoregion
- WWF:AA1308
- https://www.worldwildlife.org/ecoregions/aa1308
- Simpson Desert Region
-
-
-
-
-
-
-
-
-
- 2019-03-05T17:56:13Z
- Western Australia Ecoregion
- WWF:AA1307
- https://www.worldwildlife.org/ecoregions/aa1307
- Pilbara Shrublands Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-05T18:10:52Z
- Western coast of Australia Ecoregion
- WWF:AA1301
- https://www.worldwildlife.org/ecoregions/aa1301
- Carnarvon Xeric Shrublands Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-05T18:12:28Z
- Central Australia Ecoregion
- WWF:AA1302
- https://www.worldwildlife.org/ecoregions/aa1302
- Central Ranges Xeric Shrub Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-05T18:15:11Z
- Western central Australia
- WWF:AA1303
- https://www.worldwildlife.org/ecoregions/aa1303
- Gibson Desert Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-05T18:17:15Z
- Northwestern Australia
- WWF:AA1304
- https://www.worldwildlife.org/ecoregions/aa1304
- The Great Sandy-Tanami Desert Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-05T18:24:06Z
- Southern Australia Ecoregion
- WWF:AA1305
- https://www.worldwildlife.org/ecoregions/aa1305
- Great Victoria Desert Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-05T18:26:16Z
- Southern Australia Ecoregion
- WWF:AA1306
- https://www.worldwildlife.org/ecoregions/aa1306
- Nullarbor Plains Xeric Shrubland Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:01:41Z
- https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands
- Afrotropical Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-06T22:02:37Z
- Southern Africa: Southern Namibia into South Africa
- WWF:AT1322
- https://www.worldwildlife.org/ecoregions/at1322
- Succulent Karoo Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-06T22:07:38Z
- WWF:AT1321
- https://www.worldwildlife.org/ecoregions/at1321
- Arabian Peninsula: Yemen and Saudi Arabia
- Yemen and Saudi Arabia Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-06T22:11:38Z
- WWF:AT1320
- https://www.worldwildlife.org/ecoregions/at1320
- Arabian Peninsula: Yemen, Saudi Arabia, and Oman
- Yemen, Saudi Arabia, and Oman Ecoregion
-
-
-
-
-
-
-
-
-
- 2019-03-06T22:13:00Z
- WWF:AT1319
- https://www.worldwildlife.org/ecoregions/at1319
- Somali montane xeric woodlands ecoregion
- Somali Montane Xeric Woodland Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:15:07Z
- Islands east of the Horn of Africa and south of Yemen Ecoregion
- WWF:AT1318
- https://www.worldwildlife.org/ecoregions/at1318
- Socotran Archipelago Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:18:55Z
- WWF:AT1317
- https://www.worldwildlife.org/ecoregions/at1317
- Red Sea Coastal Desert Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:20:56Z
- WWF:AT1316
- https://www.worldwildlife.org/ecoregions/at1316
- Namibian Savanna Woodland Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:24:28Z
- Africa: Namibia Ecoregion
- WWF:AT1315
- https://www.worldwildlife.org/ecoregions/at1315
- Namib Desert Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:26:15Z
- WWF:AT1314
- https://www.worldwildlife.org/ecoregions/at1314
- Nama Karoo Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:28:43Z
- WWF:AT1313
- https://www.worldwildlife.org/ecoregions/at1313
- Masai Xeric Grasslands and Shrublands Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:30:23Z
- WWF:AT1312
- https://www.worldwildlife.org/ecoregions/at1312
- Madagascar Succulent Woodlands Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:31:29Z
- WWF:AT1311
- https://www.worldwildlife.org/ecoregions/at1311
- Madagascar spiny desert ecoregion
- Madagascar Spiny Thickets Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:39:32Z
- WWF:AT1310
- https://www.worldwildlife.org/ecoregions/at1310
- Africa: Coastal Namibia and Angola Ecoregion
- Kaokoveld Desert Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:42:47Z
- WWF:AT1309
- https://www.worldwildlife.org/ecoregions/at1309
- Kalahari Xeric Savanna Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:44:54Z
- WWF:AT1308
- https://www.worldwildlife.org/ecoregions/at1308
- Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion
- Ile Europa and Bassas da India Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:46:58Z
- Eastern Africa: Somalia
- WWF:AT1307
- https://www.worldwildlife.org/ecoregions/at1307
- Hobyo Grassland and Shrubland Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-06T22:54:57Z
- WWF:AT1306
- https://www.worldwildlife.org/ecoregions/at1306
- Arabian Peninsula: Oman and United Arab Emirates Ecoregion
- Oman and United Arab Emirates Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-07T00:08:06Z
- WWF:AT1305
- https://www.worldwildlife.org/ecoregions/at1305
- Ethiopian Xeric Grasslands and Shrublands Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-07T00:11:29Z
- WWF:AT1304
- https://www.worldwildlife.org/ecoregions/at1304
- Eritrean Coastal Desert Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-07T00:13:33Z
- WWF:AT1303
- https://www.worldwildlife.org/ecoregions/at1303
- North central Africa: Eastern Chad and small area of western Sudan
- East Saharan Montane Xeric Woodland Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-07T00:16:12Z
- WWF:AT1302
- https://www.worldwildlife.org/ecoregions/at1302
- Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion
- Oman, Yemen, and Saudi Arabia Ecoregion
-
-
-
-
-
-
-
-
- 2019-03-07T00:18:09Z
- WWF:AT1301
- https://www.worldwildlife.org/ecoregions/at1301
- Aldabra Island Xeric Scrub Ecoregion
-
-
-
-
-
-
-
- 2019-04-26T23:38:50Z
-
- Indo-Malay Ecoregion
-
-
-
-
-
-
-
-
- 2019-04-26T23:40:13Z
-
- WWF:IM1304
- Southern Asia: Western India into Pakistan
- Thar Desert
-
-
-
-
-
-
-
-
- 2019-04-27T00:12:51Z
-
- WWF:IM1303
- Southern Asia: Eastern India and western Pakistan
- Northwestern Thorn Scrub Forests
-
-
-
-
-
-
-
- A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth.
- envoAtmo
- envoPolar
- Arctic front
-
-
-
-
- A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth.
-
-
-
-
-
-
-
-
- A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth.
- envoAtmo
- envoPolar
- Antarctic front
-
-
-
-
- A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth.
-
-
-
-
-
-
-
-
-
- Stellar radiation emitted from Sol.
- Solar radiation
-
-
-
-
-
-
-
- example to be eventually removed
- example to be eventually removed
-
-
-
-
-
-
-
- metadata complete
- Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
- metadata complete
-
-
-
-
-
-
-
- organizational term
- The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release.
- organizational term
-
-
-
-
-
-
-
- ready for release
-
- Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
- ready for release
-
-
-
-
-
-
-
- metadata incomplete
- Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
- metadata incomplete
-
-
-
-
-
-
-
- uncurated
- Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
- uncurated
-
-
-
-
-
-
-
-
- pending final vetting
-
- All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
- pending final vetting
-
-
-
-
-
-
-
- to be replaced with external ontology term
- Terms with this status should eventually replaced with a term from another ontology.
- Alan Ruttenberg
- group:OBI
- to be replaced with external ontology term
-
-
-
-
-
-
-
-
- requires discussion
-
- A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
- Alan Ruttenberg
- group:OBI
- requires discussion
-
-
-
-
-
-
-
- ## Elucidation
-
-This is used when the statement/axiom is assumed to hold true 'eternally'
-
-## How to interpret (informal)
-
-First the "atemporal" FOL is derived from the OWL using the standard
-interpretation. This axiom is temporalized by embedding the axiom
-within a for-all-times quantified sentence. The t argument is added to
-all instantiation predicates and predicates that use this relation.
-
-## Example
-
- Class: nucleus
- SubClassOf: part_of some cell
-
- forall t :
- forall n :
- instance_of(n,Nucleus,t)
- implies
- exists c :
- instance_of(c,Cell,t)
- part_of(n,c,t)
-
-## Notes
-
-This interpretation is *not* the same as an at-all-times relation
- axiom holds for all times
-
-
-
-
-
-
-
- ## Elucidation
-
-This is used when the first-order logic form of the relation is
-binary, and takes no temporal argument.
-
-## Example:
-
- Class: limb
- SubClassOf: develops_from some lateral-plate-mesoderm
-
- forall t, t2:
- forall x :
- instance_of(x,Limb,t)
- implies
- exists y :
- instance_of(y,LPM,t2)
- develops_from(x,y)
- relation has no temporal argument
-
-
-
-
-
-
-
- researcher
- Nicole Vasilevsky
-
-
-
-
- researcher
-
-
-
-
-
- Nicole Vasilevsky
-
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-
-
-
-
-
-
- researcher
- Darren A. Natale
-
-
-
-
- researcher
-
-
-
-
-
- Darren A. Natale
-
-
-
-
-
-
-
-
- researcher ORCID ID = 0000-0001-5948-3092
- Marta Costa
-
-
-
-
- researcher ORCID ID = 0000-0001-5948-3092
-
-
-
-
-
- Marta Costa
-
-
-
-
-
-
-
-
- Researcher ORCID=0000-0001-6677-8489
- Aleix Puig-Barbé
-
-
-
-
- Researcher ORCID=0000-0001-6677-8489
-
-
-
-
-
- Aleix Puig-Barbé
-
-
-
-
-
-
-
-
- Researcher
- Austin Meier
-
-
-
-
- Researcher
-
-
-
-
-
- Austin Meier
-
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-
-
-
-
-
-
- researcher
- Katja S Schulz
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- researcher
-
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-
-
- Katja S Schulz
-
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- researcher
- Shawn Zheng Kai Tan
-
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- researcher
-
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-
-
- Shawn Zheng Kai Tan
-
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- researcher
- David P Hill
-
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- researcher
-
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- David P Hill
-
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- researcher
- Raymund Stefancsik
-
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- researcher
-
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-
-
-
- Raymund Stefancsik
-
-
-
-
-
-
-
-
- researcher, metadata, diseases, University of Maryland
- Lynn Schriml
-
-
-
-
- researcher, metadata, diseases, University of Maryland
-
-
-
-
-
- Lynn Schriml
-
-
-
-
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-
-
-
- American epidemiologist and ontologist
- Melissa Haendel
-
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-
-
- American epidemiologist and ontologist
-
-
-
-
-
- Melissa Haendel
-
-
-
-
-
-
-
-
- researcher
- Jennifer Deegan
-
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-
-
- researcher
-
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-
-
-
- Jennifer Deegan
-
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- researcher
- William D Duncan
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- researcher
-
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-
- William D Duncan
-
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-
- researcher
- Alexander D Diehl
-
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- researcher
-
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-
-
- Alexander D Diehl
-
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-
-
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-
- researcher
- Matthew Brush
-
-
-
-
- researcher
-
-
-
-
-
- Matthew Brush
-
-
-
-
-
-
-
-
- researcher (ORCID 0000-0002-1373-1705)
- Clare Pilgrim
-
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-
-
- researcher (ORCID 0000-0002-1373-1705)
-
-
-
-
-
- Clare Pilgrim
-
-
-
-
-
-
-
-
- data scientist
- Anne Thessen
-
-
-
-
- data scientist
-
-
-
-
-
- Anne Thessen
-
-
-
-
-
-
-
-
- researcher (ORCID 0000-0002-2999-0103)
- Jie Zheng
-
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-
-
- researcher (ORCID 0000-0002-2999-0103)
-
-
-
-
-
- Jie Zheng
-
-
-
-
-
-
-
-
- researcher
- Tanya Z Berardini
-
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-
-
- researcher
-
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-
-
-
- Tanya Z Berardini
-
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-
-
-
-
-
- researcher
- Sabrina Toro
-
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-
-
- researcher
-
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-
-
-
- Sabrina Toro
-
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-
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-
- researcher
- Pier Luigi Buttigieg
-
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-
- researcher
-
-
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-
-
- Pier Luigi Buttigieg
-
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-
-
- Researcher ORCID=0000-0002-5260-9315
- Patrick Ray
-
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-
-
- Researcher ORCID=0000-0002-5260-9315
-
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-
-
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- Patrick Ray
-
-
-
-
-
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-
-
- researcher
- Christian J Stoeckert
-
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-
-
- researcher
-
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-
-
- Christian J Stoeckert
-
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-
-
- bioinformatics researcher
- Christopher J. Mungall
-
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-
- bioinformatics researcher
-
-
-
-
-
- Christopher J. Mungall
-
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-
-
-
-
-
- researcher
- David Osumi-Sutherland
-
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-
- researcher
-
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-
-
- David Osumi-Sutherland
-
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-
-
-
-
-
- researcher
- Lauren E. Chan
-
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-
- researcher
-
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-
-
- Lauren E. Chan
-
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-
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-
-
- researcher
- Marie-Angélique Laporte
-
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-
-
- researcher
-
-
-
-
-
- Marie-Angélique Laporte
-
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-
-
-
-
-
- researcher
- James P. Balhoff
-
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-
- researcher
-
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-
-
- James P. Balhoff
-
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- researcher
- Damion M Dooley
-
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- researcher
-
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- Damion M Dooley
-
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- researcher
- Lindsay G Cowell
-
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- researcher
-
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- Lindsay G Cowell
-
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- Canadian biocurator
- Pascale Gaudet
-
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- Canadian biocurator
-
-
-
-
-
- Pascale Gaudet
-
-
-
-
-
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- researcher
- Mathias Brochhausen
-
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- researcher
-
-
-
-
-
- Mathias Brochhausen
-
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-
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-
-
- Researcher ORCID=0000-0003-1909-9269
- S. Clint Dowland
-
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-
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- Researcher ORCID=0000-0003-1909-9269
-
-
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-
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- S. Clint Dowland
-
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-
-
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-
- researcher
- Anna Maria Masci
-
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-
- researcher
-
-
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-
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- Anna Maria Masci
-
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- researcher
- Terrence F Meehan
-
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- researcher
-
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- Terrence F Meehan
-
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- Researcher ORCID=0000-0003-2620-0345
- Asiyah Yu Lin
-
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- Researcher ORCID=0000-0003-2620-0345
-
-
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-
- Asiyah Yu Lin
-
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- software/data engineer
- Jorrit Poelen
-
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- software/data engineer
-
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- Jorrit Poelen
-
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- American chemist
- Charles Tapley Hoyt
-
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- American chemist
-
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- Charles Tapley Hoyt
-
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- researcher
- Vasundra Touré
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- researcher
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- Vasundra Touré
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- data item
- data item
-
-
- information content entity
- information content entity
-
-
- data about an ontology part
- Data about an ontology part is a data item about a part of an ontology, for example a term
- Person:Alan Ruttenberg
- data about an ontology part
-
-
- failed exploratory term
- The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job.
- Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification.
- Person:Alan Ruttenberg
- failed exploratory term
-
-
- in branch
- An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
- GROUP:OBI
- OBI_0000277
- in branch
-
-
- Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
- PERSON: Alan Ruttenberg
- PERSON: Melanie Courtot
- obsolete_core
-
-
- obsolescence reason specification
-
- The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
- The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
- PERSON: Alan Ruttenberg
- PERSON: Melanie Courtot
- obsolescence reason specification
-
-
- placeholder removed
- The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined.
- This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider.
- placeholder removed
-
-
- terms merged
- The term has been combined with one or more other terms to create a more encompassing (merged) term.
- The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge.
- terms merged
-
-
- term imported
- The term has been replaced by a term imported from another ontology.
- This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001.
- term imported
-
-
- term split
- The term has been split into two or more new terms.
- This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001.
- term split
-
-
- has obsolescence reason
- Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
- PERSON:Alan Ruttenberg
- PERSON:Melanie Courtot
- has obsolescence reason
-
-
- ontology term requester
-
- The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
- Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
- Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
- The 'term requester' can credit the person, organization or project who request the ontology term.
- ontology term requester
-
-
- denotator type
- The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
- A denotator type indicates how a term should be interpreted from an ontological perspective.
- Alan Ruttenberg
- Barry Smith, Werner Ceusters
- denotator type
-
-
- universal
- Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
- Alan Ruttenberg
- A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
- universal
-
-
- is denotator type
- Relates an class defined in an ontology, to the type of it's denotator
- In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
- Alan Ruttenberg
- is denotator type
-
-
- defined class
- A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
- "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
- Alan Ruttenberg
- defined class
-
-
- named class expression
- A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
- named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
- Alan Ruttenberg
- named class expression
-
-
- antisymmetric property
- part_of antisymmetric property xsd:true
- Use boolean value xsd:true to indicate that the property is an antisymmetric property
- Alan Ruttenberg
- antisymmetric property
-
-
- has ID digit count
- Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
- Annotations:
- 'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
- 'has ID digit count' : 7,
- rdfs:label "RO id policy"
- 'has ID policy for': "RO"
- Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
- Person:Alan Ruttenberg
- has ID digit count
-
-
- has ID range allocated
- Datatype: idrange:1
-Annotations: 'has ID range allocated to': "Chris Mungall"
-EquivalentTo: xsd:integer[> 2151 , <= 2300]
-
- Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
- Person:Alan Ruttenberg
- has ID range allocated to
-
-
- has ID policy for
- Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
- Annotations:
- 'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
- 'has ID digit count' : 7,
- rdfs:label "RO id policy"
- 'has ID policy for': "RO"
- Relating an ontology used to record id policy to the ontology namespace whose policy it manages
- Person:Alan Ruttenberg
- has ID policy for
-
-
- has ID prefix
- Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
- Annotations:
- 'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
- 'has ID digit count' : 7,
- rdfs:label "RO id policy"
- 'has ID policy for': "RO"
- Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
- Person:Alan Ruttenberg
- has ID prefix
-
-
- has associated axiom(nl)
- Person:Alan Ruttenberg
- Person:Alan Ruttenberg
- An axiom associated with a term expressed using natural language
- has associated axiom(nl)
-
-
- has associated axiom(fol)
- Person:Alan Ruttenberg
- Person:Alan Ruttenberg
- An axiom expressed in first order logic using CLIF syntax
- has associated axiom(fol)
-
-
- is allocated id range
- Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
- PERSON:Alan Ruttenberg
- Add as annotation triples in the granting ontology
- is allocated id range
-
-
- has ontology root term
- Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
- Nicolas Matentzoglu
- has ontology root term
-
-
- may be identical to
- A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
- David Osumi-Sutherland
- Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
- may be identical to
-
-
- scheduled for obsoletion on or after
- Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
- Chris Mungall, Jie Zheng
- scheduled for obsoletion on or after
-
-
- has axiom id
- Person:Alan Ruttenberg
- Person:Alan Ruttenberg
- A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
- has axiom label
-
-
- ontology module
- I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
- ontology file
- This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
- ontology module
-
-
- base ontology module
- An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
- base ontology module
-
-
-
- editors ontology module
- An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
- source ontology module
- editors ontology module
-
-
- main release ontology module
- An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
- TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
- main release ontology module
-
-
- bridge ontology module
- An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
- bridge ontology module
-
-
-
- import ontology module
- A subset ontology module that is intended to be imported from another ontology.
- TODO: add axioms that indicate this is the output of a module extraction process.
- import file
- import ontology module
-
-
-
- subset ontology module
- An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
- ontology slim
- subset ontology
- subset ontology module
-
-
-
-
- curation subset ontology module
- A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
- curation subset ontology module
-
-
- analysis ontology module
- An ontology module that is intended for usage in analysis or discovery applications.
- analysis subset ontology module
-
-
- single layer ontology module
- A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
- ribbon subset
- single layer subset ontology module
-
-
- exclusion subset ontology module
- A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
- antislim
- exclusion subset ontology module
-
-
- external import ontology module
- An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
- external import
- external import ontology module
-
-
- species subset ontology module
- A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
- taxon subset
- species subset ontology module
-
-
-
- reasoned ontology module
- An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
- reasoned ontology module
-
-
-
- generated ontology module
- An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
- TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
- generated ontology module
-
-
- template generated ontology module
- An ontology module that is automatically generated from a template specification and fillers for slots in that template.
- template generated ontology module
-
-
-
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-
- taxonomic bridge ontology module
- taxonomic bridge ontology module
-
-
- ontology module subsetted by expressivity
- ontology module subsetted by expressivity
-
-
- obo basic subset ontology module
- A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.
-
-Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).
-
-An ontology is OBO Basic if and only if it has the following characteristics:
-DAG
-Unidirectional
-No Dangling Clauses
-Fully Asserted
-Fully Labeled
-No equivalence axioms
-Singly labeled edges
-No qualifier lists
-No disjointness axioms
-No owl-axioms header
-No imports
- obo basic subset ontology module
-
-
-
- ontology module subsetted by OWL profile
- ontology module subsetted by OWL profile
-
-
- EL++ ontology module
- EL++ ontology module
-
-
- The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
- This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype.
-
- out of scope
-
-
- This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
- OBO Operations call
-
- logical characteristic of object property
-
-
- The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality.
- This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore).
-
- domain entity does not exist
-
-
- The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing).
- A provenance property that denotes a synonym to be the preferred one for a specific community.
-
- 2025-06-02
- preferred label for community
-
-
- CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
- A synonym type for describing abbreviations or initalisms
-
- 2023-03-03
- abbreviation
-
-
- A synonym type for describing ambiguous synonyms
-
- 2023-03-03
- ambiguous synonym
-
-
- A synonym type for describing dubious synonyms
-
- 2023-03-03
- dubious synonym
-
-
- EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
- A synonym type for describing layperson or colloquial synonyms
-
- 2023-03-03
- layperson synonym
-
-
- CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
- A synonym type for describing pluralization synonyms
-
- 2023-03-03
- plural form
-
-
- CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
- A synonym type for describing UK spelling variants
-
- 2023-03-03
- UK spelling synonym
-
-
- A synonym type for common misspellings
-
- 2023-03-03
- misspelling
-
-
- A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
-
- 2023-03-03
- misnomer
-
-
- MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
- A synonym type for names that have been used as primary labels in the past.
-
- 2023-07-25
- previous name
-
-
- The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
- A synonym type for the legal entity name
-
- 2023-07-27
- legal name
-
-
- CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label
- The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.
-
- 2023-09-30
- INN
- International Nonproprietary Name
-
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- nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
- A synonym type for describing Latin term synonyms.
-
- 2023-10-12
- latin term
-
-
- NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
- A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
-
- 2023-11-01
- acronym
-
-
- A serial number such as "12324X"; a stop sign; a written proper name such as "OBI
- An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
-
- 2024-03-25
- has symbol
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- if effector directly negatively regulates X, its parent MF directly negatively regulates X
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- 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
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- 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
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- true
- MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
- infer input from direct reg
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- GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
-e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
- enabling an MF enables its parts
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- GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
- involved in BP
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- If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
- inferring direct reg edge from input to regulatory subfunction
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- inferring direct neg reg edge from input to regulatory subfunction
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- inferring direct positive reg edge from input to regulatory subfunction
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- effector input is compound function input
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- Input of effector is input of its parent MF
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- if effector directly regulates X, its parent MF directly regulates X
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- if effector directly positively regulates X, its parent MF directly positively regulates X
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diff --git a/03_TECHNICAL_CORE/ontology/imports/ro_bot.owl b/03_TECHNICAL_CORE/ontology/imports/ro_bot.owl
new file mode 100644
index 0000000..a6f3927
--- /dev/null
+++ b/03_TECHNICAL_CORE/ontology/imports/ro_bot.owl
@@ -0,0 +1,4759 @@
+
+
+
+ The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
+
+ OBO Relations Ontology
+ 2025-12-17
+ https://github.com/oborel/obo-relations/
+
+
+
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+ If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
+
+ is a defining property chain axiom
+
+
+
+
+
+
+
+ If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
+
+ is a defining property chain axiom where second argument is reflexive
+
+
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+
+
+ is part of
+ my brain is part of my body (continuant parthood, two material entities)
+ my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
+ this day is part of this year (occurrent parthood)
+ a core relation that holds between a part and its whole
+ Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
+ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
+ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
+
+A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
+ part_of
+
+
+
+
+
+
+
+
+
+
+
+
+
+ part of
+
+
+ http://www.obofoundry.org/ro/#OBO_REL:part_of
+ https://wiki.geneontology.org/Part_of
+
+
+
+
+
+
+
+
+
+ has part
+ my body has part my brain (continuant parthood, two material entities)
+ my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
+ this year has part this day (occurrent parthood)
+ a core relation that holds between a whole and its part
+ Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
+ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
+ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
+
+A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
+ has_part
+
+
+
+
+
+ has part
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ preceded by
+ x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
+ An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
+ is preceded by
+ preceded_by
+ http://www.obofoundry.org/ro/#OBO_REL:preceded_by
+
+
+ preceded by
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ precedes
+ x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
+
+
+ precedes
+
+
+
+
+
+
+
+
+
+
+ inheres in
+ this fragility is a characteristic of this vase
+ this red color is a characteristic of this apple
+ a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
+ inheres_in
+
+ Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
+
+ characteristic of
+
+
+
+
+
+
+
+
+
+ bearer of
+ this apple is bearer of this red color
+ this vase is bearer of this fragility
+ Inverse of characteristic_of
+ A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
+ bearer_of
+ is bearer of
+
+
+ has characteristic
+
+
+
+
+
+
+
+
+
+
+ participates in
+ this blood clot participates in this blood coagulation
+ this input material (or this output material) participates in this process
+ this investigator participates in this investigation
+ a relation between a continuant and a process, in which the continuant is somehow involved in the process
+ participates_in
+
+ participates in
+
+
+
+
+
+
+
+
+
+
+
+
+
+ has participant
+ this blood coagulation has participant this blood clot
+ this investigation has participant this investigator
+ this process has participant this input material (or this output material)
+ a relation between a process and a continuant, in which the continuant is somehow involved in the process
+ Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
+ has_participant
+ http://www.obofoundry.org/ro/#OBO_REL:has_participant
+
+ has participant
+
+
+
+
+
+
+
+
+
+
+ this catalysis function is a function of this enzyme
+ a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
+ A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
+ function_of
+ is function of
+ This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
+
+ function of
+
+
+
+
+
+
+
+
+
+ this red color is a quality of this apple
+ a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
+ A quality inheres in its bearer at all times for which the quality exists.
+ is quality of
+ quality_of
+ This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
+
+ quality of
+
+
+
+
+
+
+
+
+
+ this investigator role is a role of this person
+ a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
+ A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
+ is role of
+ role_of
+ This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
+
+ role of
+
+
+
+
+
+
+
+
+
+
+ this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
+ a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
+ A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
+ has_function
+
+ has function
+
+
+
+
+
+
+
+
+
+ this apple has quality this red color
+ a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
+ A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
+ has_quality
+
+ has quality
+
+
+
+
+
+
+
+
+
+
+ this person has role this investigator role (more colloquially: this person has this role of investigator)
+ a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
+ A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
+ has_role
+
+ has role
+
+
+
+
+
+
+
+
+
+
+
+ a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
+
+ has disposition
+
+
+
+
+
+
+
+
+ inverse of has disposition
+
+ This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
+
+ disposition of
+
+
+
+
+
+
+
+
+
+ A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
+
+ 2017-05-24T09:30:46Z
+
+ has regulatory component activity
+
+
+
+
+
+
+
+
+
+ A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
+
+ 2017-05-24T09:31:01Z
+ By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
+
+ has negative regulatory component activity
+
+
+
+
+
+
+
+
+
+ A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
+
+ 2017-05-24T09:31:17Z
+ By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
+
+ has positive regulatory component activity
+
+
+
+
+
+
+
+
+
+ 2017-05-24T09:44:33Z
+ A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
+
+ has component activity
+
+
+
+
+
+
+
+
+
+
+ w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
+
+ 2017-05-24T09:49:21Z
+
+ has component process
+
+
+
+
+
+
+
+
+
+
+ 2017-09-17T13:52:24Z
+ Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
+
+ directly regulated by
+
+
+
+
+ Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
+
+
+
+
+
+
+
+
+
+
+ Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
+
+ 2017-09-17T13:52:38Z
+
+ directly negatively regulated by
+
+
+
+
+ Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
+
+
+
+
+
+
+
+
+
+
+ Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
+
+ 2017-09-17T13:52:47Z
+
+ directly positively regulated by
+
+
+
+
+ Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
+
+
+
+
+
+
+
+
+
+
+ A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
+
+ 2017-09-22T14:14:36Z
+ This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
+
+ has effector activity
+
+
+
+
+ A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
+
+
+
+
+
+
+
+
+
+
+
+
+ X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
+
+ ends after
+
+
+
+
+
+
+
+
+
+
+ starts_at_end_of
+ X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
+
+ immediately preceded by
+
+
+
+
+
+
+
+
+
+ ends_at_start_of
+ meets
+
+
+ X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
+
+ immediately precedes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ x overlaps y if and only if there exists some z such that x has part z and z part of y
+ http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
+
+
+
+
+
+ overlaps
+
+
+
+
+
+
+
+
+ true
+
+
+
+
+
+
+
+
+
+ w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
+ The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
+ For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
+
+
+
+ has component
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
+
+
+
+
+ GO
+ Regulation precludes parthood; the regulatory process may not be within the regulated process.
+ regulates (processual)
+ false
+
+
+
+
+ regulates
+
+
+
+
+
+
+
+
+
+
+ p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
+
+
+ negatively regulates (process to process)
+
+
+
+
+
+ negatively regulates
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
+
+
+ positively regulates (process to process)
+
+
+
+
+
+ positively regulates
+
+
+
+
+
+
+
+
+
+
+ mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
+ osteoclast SubClassOf 'capable of' some 'bone resorption'
+ A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
+
+ has function realized in
+
+
+ For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
+
+
+ capable of
+
+
+
+
+
+
+
+
+
+
+
+
+
+ c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
+
+ has function in
+
+ capable of part of
+
+
+
+
+
+
+
+
+
+ true
+
+
+
+
+
+
+
+
+
+
+
+
+ Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
+ https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
+
+ A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
+
+ temporally related to
+
+
+
+
+
+
+
+
+
+
+
+ p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
+
+ consumes
+
+
+
+
+
+ has input
+ https://wiki.geneontology.org/Has_input
+
+
+
+
+
+
+
+
+
+
+
+
+ A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
+ c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
+
+
+ acts upstream of
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
+ c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
+ affects
+
+
+ acts upstream of or within
+ https://wiki.geneontology.org/Acts_upstream_of_or_within
+
+
+
+
+
+
+
+
+
+ p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
+
+
+
+
+ holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
+
+ causally upstream of, positive effect
+
+
+
+
+
+
+
+
+
+
+ p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
+
+
+
+
+
+ causally upstream of, negative effect
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
+ Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
+
+ inheres in part of
+
+
+
+ characteristic of part of
+
+
+
+
+
+
+
+
+
+ true
+
+
+
+
+
+
+
+ A mereological relationship or a topological relationship
+
+ Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
+
+
+ mereotopologically related to
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ a particular instances of akt-2 enables some instance of protein kinase activity
+ c enables p iff c is capable of p and c acts to execute p.
+
+ catalyzes
+ executes
+ has
+ is catalyzing
+ is executing
+ This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
+
+
+ enables
+ https://wiki.geneontology.org/Enables
+
+
+
+
+
+
+
+ A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
+
+ This is a grouping relation that collects relations used for the purpose of connecting structure and function
+
+ functionally related to
+
+
+
+
+
+
+
+
+
+
+
+
+ this relation holds between c and p when c is part of some c', and c' is capable of p.
+
+ false
+
+ part of structure that is capable of
+
+
+
+
+
+
+
+
+ true
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ c involved_in p if and only if c enables some process p', and p' is part of p
+
+ actively involved in
+ enables part of
+
+ involved in
+ https://wiki.geneontology.org/Involved_in
+
+
+
+
+
+
+
+
+
+ inverse of enables
+
+
+
+ enabled by
+ https://wiki.geneontology.org/Enabled_by
+
+
+
+
+
+
+
+
+
+
+
+ inverse of regulates
+
+ regulated by (processual)
+
+
+ regulated by
+
+
+
+
+
+
+
+
+ inverse of negatively regulates
+
+
+
+ negatively regulated by
+
+
+
+
+
+
+
+
+ inverse of positively regulates
+
+
+
+ positively regulated by
+
+
+
+
+
+
+
+
+
+ inverse of has input
+
+
+
+
+ input of
+
+
+
+
+
+
+
+
+
+
+
+ inverse of upstream of
+
+
+ causally downstream of
+
+
+
+
+
+
+
+
+
+
+
+
+
+ immediately causally downstream of
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
+
+ indirectly activates
+
+
+ indirectly positively regulates
+ https://wiki.geneontology.org/Indirectly_positively_regulates
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
+
+ indirectly inhibits
+
+
+ indirectly negatively regulates
+ https://wiki.geneontology.org/Indirectly_negatively_regulates
+
+
+
+
+
+
+
+ relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
+ This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
+
+To define causal relations in an activity-flow type network, we make use of 3 primitives:
+
+ * Temporal: how do the intervals of the two occurrents relate?
+ * Is the causal relation regulatory?
+ * Is the influence positive or negative?
+
+The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
+
+For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
+
+For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
+
+Each of these 3 primitives can be composed to yield a cross-product of different relation types.
+
+ Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
+
+ causally related to
+
+
+
+
+ relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
+ https://en.wikipedia.org/wiki/Causality
+
+
+
+
+
+
+
+
+
+
+ p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
+
+
+
+
+ causally upstream of
+
+
+
+
+
+
+
+
+
+ p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
+
+
+
+ immediately causally upstream of
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
+ We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
+
+ influences (processual)
+ affects
+
+ causally upstream of or within
+
+
+
+
+
+
+
+
+
+ inverse of causally upstream of or within
+
+
+
+
+ causally downstream of or within
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ c involved in regulation of p if c is involved in some p' and p' regulates some p
+
+
+ involved in regulation of
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ c involved in regulation of p if c is involved in some p' and p' positively regulates some p
+
+
+
+ involved in positive regulation of
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
+
+
+
+ involved in negative regulation of
+
+
+
+
+
+
+
+
+
+
+ c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
+ OWL does not allow defining object properties via a Union
+
+ involved in or reguates
+
+ involved in or involved in regulation of
+
+
+
+
+
+
+
+
+
+
+ A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
+ This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
+ Considering relabeling as 'pairwise interacts with'
+
+ Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
+ in pairwise interaction with
+
+
+ interacts with
+ http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
+ http://purl.obolibrary.org/obo/MI_0914
+
+
+
+
+
+
+
+
+
+ An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
+
+ binds
+ molecularly binds with
+
+ molecularly interacts with
+
+ http://purl.obolibrary.org/obo/MI_0915
+
+
+
+
+
+
+
+
+ Axiomatization to GO to be added later
+
+ An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
+
+ phosphorylates
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
+
+A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
+
+
+ molecularly controls
+
+ directly regulates activity of
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
+For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
+
+
+ directly inhibits
+ molecularly decreases activity of
+
+ directly negatively regulates activity of
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
+For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
+
+
+ directly activates
+ molecularly increases activity of
+
+ directly positively regulates activity of
+
+
+
+
+
+
+
+
+ This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
+
+ helper property (not for use in curation)
+
+
+
+
+
+
+
+
+
+
+ is kinase activity
+
+
+
+
+
+
+
+
+
+ A relationship between a material entity and a process where the material entity has some causal role that influences the process
+
+
+ causal agent in process
+
+
+
+
+
+
+
+
+
+
+ p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
+
+
+ Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
+
+ causal relation between processes
+
+
+
+
+
+
+
+
+
+ depends on
+
+
+
+
+
+
+
+
+
+
+
+ The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
+
+
+ Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
+
+ causal relation between entities
+
+
+
+
+
+
+
+
+
+
+
+ causally influenced by (entity-centric)
+
+ causally influenced by
+
+
+
+
+
+
+
+
+
+
+ interaction relation helper property
+
+ http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
+
+
+
+
+
+
+
+
+
+
+ molecular interaction relation helper property
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
+
+
+
+ causally influences (entity-centric)
+
+ causally influences
+
+
+
+
+
+
+
+
+
+ p directly regulates q iff p is immediately causally upstream of q and p regulates q.
+
+
+ directly regulates (processual)
+
+
+
+
+
+ directly regulates
+
+
+
+
+
+
+
+
+
+
+
+
+
+ gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
+ s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
+
+
+ has part structure that is capable of
+
+
+
+
+
+
+
+
+
+
+ A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
+ Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
+
+
+
+ causal relation between material entity and a process
+
+
+
+
+
+
+
+
+
+
+
+
+ pyrethroid -> growth
+ Holds between c and p if and only if c is capable of some activity a, and a regulates p.
+
+
+ capable of regulating
+
+
+
+
+
+
+
+
+
+
+
+
+ Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
+
+
+ capable of negatively regulating
+
+
+
+
+
+
+
+
+
+
+
+
+ renin -> arteriolar smooth muscle contraction
+ Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
+
+
+ capable of positively regulating
+
+
+
+
+
+
+
+
+ Inverse of 'causal agent in process'
+
+
+ process has causal agent
+
+
+
+
+
+
+
+
+
+ p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
+
+ directly positively regulates (process to process)
+
+
+
+
+
+ directly positively regulates
+ https://wiki.geneontology.org/Directly_positively_regulates
+
+
+
+
+
+
+
+
+
+ p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
+
+ directly negatively regulates (process to process)
+
+
+
+
+
+ directly negatively regulates
+ https://wiki.geneontology.org/Directly_negatively_regulates
+
+
+
+
+
+
+
+
+
+
+
+
+ Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
+
+ 2018-01-25T23:20:13Z
+
+ enables subfunction
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 2018-01-26T23:49:30Z
+
+
+ acts upstream of or within, positive effect
+ https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 2018-01-26T23:49:51Z
+
+
+ acts upstream of or within, negative effect
+ https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect
+
+
+
+
+
+
+
+
+
+
+
+
+
+ c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
+
+
+ 2018-01-26T23:53:14Z
+
+
+ acts upstream of, positive effect
+ https://wiki.geneontology.org/Acts_upstream_of,_positive_effect
+
+
+
+
+
+
+
+
+
+
+
+
+
+ c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
+
+
+ 2018-01-26T23:53:22Z
+
+
+ acts upstream of, negative effect
+ https://wiki.geneontology.org/Acts_upstream_of,_negative_effect
+
+
+
+
+
+
+
+
+
+
+ 2018-03-13T23:55:05Z
+
+ causally upstream of or within, negative effect
+ https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect
+
+
+
+
+
+
+
+
+
+
+ 2018-03-13T23:55:19Z
+
+ causally upstream of or within, positive effect
+
+
+
+
+
+
+
+
+
+
+
+ The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
+
+
+ regulates activity of
+
+
+
+
+
+
+
+
+ p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
+
+ 2022-09-26T06:07:17Z
+
+ indirectly causally upstream of
+
+
+
+
+
+
+
+
+
+ p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
+
+ 2022-09-26T06:08:01Z
+
+ indirectly regulates
+
+
+
+
+
+
+
+
+
+
+
+ A diagnostic testing device utilizes a specimen.
+ X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
+ A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
+ See github ticket https://github.com/oborel/obo-relations/issues/497
+
+
+ 2021-11-08T12:00:00Z
+ utilizes
+
+ device utilizes material
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
+
+
+ regulates characteristic
+
+
+
+
+
+
+
+
+
+
+
+
+ A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
+
+
+ positively regulates characteristic
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
+
+
+ negatively regulates characteristic
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
+
+ continuant
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ An entity that has temporal parts and that happens, unfolds or develops through time.
+
+ occurrent
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
+ A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
+
+ independent continuant
+
+
+
+
+
+
+
+
+ p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
+ An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
+
+ process
+
+
+
+
+
+
+
+
+
+
+ disposition
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
+
+ realizable entity
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ quality
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
+ A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
+
+ specifically dependent continuant
+
+
+
+
+
+
+
+
+ A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
+
+ role
+
+
+
+
+
+
+
+
+
+ function
+
+
+
+
+
+
+
+
+ An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
+ Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
+
+ material entity
+
+
+
+
+
+
+
+
+ A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
+ This is the same as GO molecular function
+ molecular function
+ GO:0003674
+ Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
+
+ gene product or complex activity
+ molecular_function
+
+
+
+
+ A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
+ GOC:pdt
+
+
+
+
+
+
+
+
+ A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
+ jl
+ 2012-09-19T15:05:24Z
+ Wikipedia:Biological_process
+ biological process
+ physiological process
+ single organism process
+ single-organism process
+ GO:0008150
+ Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
+
+ biological process
+ biological_process
+
+
+
+
+ A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
+ GOC:pdt
+
+
+
+
+
+
+
+
+
+
+
+ true
+
+
+ Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
+ Reactome:R-HSA-6788855
+ Reactome:R-HSA-6788867
+ phosphokinase activity
+ GO:0016301
+ Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
+
+ kinase activity
+
+
+
+
+ Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
+ ISBN:0198506732
+
+
+
+
+ Reactome:R-HSA-6788855
+ FN3KRP phosphorylates PsiAm, RibAm
+
+
+
+
+ Reactome:R-HSA-6788867
+ FN3K phosphorylates ketosamines
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ curation status specification
+
+ The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
+ Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
+ PERSON:Bill Bug
+ GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
+ OBI_0000266
+
+ curation status specification
+
+
+
+
+
+
+
+
+ A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
+ PATO:0000001
+
+ quality
+
+
+
+
+ A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
+ PATOC:GVG
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 2019-03-05T17:25:21Z
+ Western Australia Ecoregion
+ WWF:AA1310
+ https://www.worldwildlife.org/ecoregions/aa1310
+
+ Western Australian Mulga Shrublands Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-05T17:51:32Z
+ https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands
+
+ Australasia Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-05T17:52:41Z
+ Southern central Australia Ecoregion
+ WWF:AA1309
+ https://www.worldwildlife.org/ecoregions/aa1309
+
+ Tirari-Sturt Stony Desert Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-05T17:54:35Z
+ Eastern central Australia Ecoregion
+ WWF:AA1308
+ https://www.worldwildlife.org/ecoregions/aa1308
+
+ Simpson Desert Region
+
+
+
+
+
+
+
+
+
+ 2019-03-05T17:56:13Z
+ Western Australia Ecoregion
+ WWF:AA1307
+ https://www.worldwildlife.org/ecoregions/aa1307
+
+ Pilbara Shrublands Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-05T18:10:52Z
+ Western coast of Australia Ecoregion
+ WWF:AA1301
+ https://www.worldwildlife.org/ecoregions/aa1301
+
+ Carnarvon Xeric Shrublands Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-05T18:12:28Z
+ Central Australia Ecoregion
+ WWF:AA1302
+ https://www.worldwildlife.org/ecoregions/aa1302
+
+ Central Ranges Xeric Shrub Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-05T18:15:11Z
+ Western central Australia
+ WWF:AA1303
+ https://www.worldwildlife.org/ecoregions/aa1303
+
+ Gibson Desert Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-05T18:17:15Z
+ Northwestern Australia
+ WWF:AA1304
+ https://www.worldwildlife.org/ecoregions/aa1304
+
+ The Great Sandy-Tanami Desert Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-05T18:24:06Z
+ Southern Australia Ecoregion
+ WWF:AA1305
+ https://www.worldwildlife.org/ecoregions/aa1305
+
+ Great Victoria Desert Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-05T18:26:16Z
+ Southern Australia Ecoregion
+ WWF:AA1306
+ https://www.worldwildlife.org/ecoregions/aa1306
+
+ Nullarbor Plains Xeric Shrubland Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:01:41Z
+ https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands
+
+ Afrotropical Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-06T22:02:37Z
+ Southern Africa: Southern Namibia into South Africa
+ WWF:AT1322
+ https://www.worldwildlife.org/ecoregions/at1322
+
+ Succulent Karoo Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-06T22:07:38Z
+ WWF:AT1321
+ https://www.worldwildlife.org/ecoregions/at1321
+ Arabian Peninsula: Yemen and Saudi Arabia
+
+ Yemen and Saudi Arabia Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-06T22:11:38Z
+ WWF:AT1320
+ https://www.worldwildlife.org/ecoregions/at1320
+ Arabian Peninsula: Yemen, Saudi Arabia, and Oman
+
+ Yemen, Saudi Arabia, and Oman Ecoregion
+
+
+
+
+
+
+
+
+
+ 2019-03-06T22:13:00Z
+ WWF:AT1319
+ https://www.worldwildlife.org/ecoregions/at1319
+ Somali montane xeric woodlands ecoregion
+
+ Somali Montane Xeric Woodland Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:15:07Z
+ Islands east of the Horn of Africa and south of Yemen Ecoregion
+ WWF:AT1318
+ https://www.worldwildlife.org/ecoregions/at1318
+
+ Socotran Archipelago Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:18:55Z
+ WWF:AT1317
+ https://www.worldwildlife.org/ecoregions/at1317
+
+ Red Sea Coastal Desert Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:20:56Z
+ WWF:AT1316
+ https://www.worldwildlife.org/ecoregions/at1316
+
+ Namibian Savanna Woodland Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:24:28Z
+ Africa: Namibia Ecoregion
+ WWF:AT1315
+ https://www.worldwildlife.org/ecoregions/at1315
+
+ Namib Desert Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:26:15Z
+ WWF:AT1314
+ https://www.worldwildlife.org/ecoregions/at1314
+
+ Nama Karoo Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:28:43Z
+ WWF:AT1313
+ https://www.worldwildlife.org/ecoregions/at1313
+
+ Masai Xeric Grasslands and Shrublands Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:30:23Z
+ WWF:AT1312
+ https://www.worldwildlife.org/ecoregions/at1312
+
+ Madagascar Succulent Woodlands Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:31:29Z
+ WWF:AT1311
+ https://www.worldwildlife.org/ecoregions/at1311
+ Madagascar spiny desert ecoregion
+
+ Madagascar Spiny Thickets Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:39:32Z
+ WWF:AT1310
+ https://www.worldwildlife.org/ecoregions/at1310
+ Africa: Coastal Namibia and Angola Ecoregion
+
+ Kaokoveld Desert Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:42:47Z
+ WWF:AT1309
+ https://www.worldwildlife.org/ecoregions/at1309
+
+ Kalahari Xeric Savanna Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:44:54Z
+ WWF:AT1308
+ https://www.worldwildlife.org/ecoregions/at1308
+ Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion
+
+ Ile Europa and Bassas da India Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:46:58Z
+ Eastern Africa: Somalia
+ WWF:AT1307
+ https://www.worldwildlife.org/ecoregions/at1307
+
+ Hobyo Grassland and Shrubland Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-06T22:54:57Z
+ WWF:AT1306
+ https://www.worldwildlife.org/ecoregions/at1306
+ Arabian Peninsula: Oman and United Arab Emirates Ecoregion
+
+ Oman and United Arab Emirates Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-07T00:08:06Z
+ WWF:AT1305
+ https://www.worldwildlife.org/ecoregions/at1305
+
+ Ethiopian Xeric Grasslands and Shrublands Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-07T00:11:29Z
+ WWF:AT1304
+ https://www.worldwildlife.org/ecoregions/at1304
+
+ Eritrean Coastal Desert Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-07T00:13:33Z
+ WWF:AT1303
+ https://www.worldwildlife.org/ecoregions/at1303
+ North central Africa: Eastern Chad and small area of western Sudan
+
+ East Saharan Montane Xeric Woodland Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-07T00:16:12Z
+ WWF:AT1302
+ https://www.worldwildlife.org/ecoregions/at1302
+ Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion
+
+ Oman, Yemen, and Saudi Arabia Ecoregion
+
+
+
+
+
+
+
+
+ 2019-03-07T00:18:09Z
+ WWF:AT1301
+ https://www.worldwildlife.org/ecoregions/at1301
+
+ Aldabra Island Xeric Scrub Ecoregion
+
+
+
+
+
+
+
+ 2019-04-26T23:38:50Z
+
+
+ Indo-Malay Ecoregion
+
+
+
+
+
+
+
+
+ 2019-04-26T23:40:13Z
+
+ WWF:IM1304
+ Southern Asia: Western India into Pakistan
+
+ Thar Desert
+
+
+
+
+
+
+
+
+ 2019-04-27T00:12:51Z
+
+ WWF:IM1303
+ Southern Asia: Eastern India and western Pakistan
+
+ Northwestern Thorn Scrub Forests
+
+
+
+
+
+
+
+
+ Stellar radiation emitted from Sol.
+
+ Solar radiation
+
+
+
+
+
+
+
+ example to be eventually removed
+
+ example to be eventually removed
+
+
+
+
+
+
+
+ metadata complete
+ Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
+
+ metadata complete
+
+
+
+
+
+
+
+ organizational term
+ The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release.
+
+ organizational term
+
+
+
+
+
+
+
+ ready for release
+
+ Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
+
+ ready for release
+
+
+
+
+
+
+
+ metadata incomplete
+ Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
+
+ metadata incomplete
+
+
+
+
+
+
+
+ uncurated
+ Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
+
+ uncurated
+
+
+
+
+
+
+
+
+ pending final vetting
+
+ All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
+
+ pending final vetting
+
+
+
+
+
+
+
+ to be replaced with external ontology term
+ Terms with this status should eventually replaced with a term from another ontology.
+ Alan Ruttenberg
+ group:OBI
+
+ to be replaced with external ontology term
+
+
+
+
+
+
+
+
+ requires discussion
+
+ A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
+ Alan Ruttenberg
+ group:OBI
+
+ requires discussion
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+ true
+ MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
+ infer input from direct reg
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+ GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
+e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
+ enabling an MF enables its parts
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+ true
+ GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
+ involved in BP
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+ If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
+ inferring direct reg edge from input to regulatory subfunction
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+ inferring direct neg reg edge from input to regulatory subfunction
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+ inferring direct positive reg edge from input to regulatory subfunction
+
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+ effector input is compound function input
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+ Input of effector is input of its parent MF
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+ if effector directly regulates X, its parent MF directly regulates X
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+ if effector directly positively regulates X, its parent MF directly positively regulates X
+
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+ if effector directly negatively regulates X, its parent MF directly negatively regulates X
+
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+ 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
+
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+ 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
+
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diff --git a/03_TECHNICAL_CORE/ontology/imports/seeds/cco_seed.txt b/03_TECHNICAL_CORE/ontology/imports/seeds/cco_seed.txt
new file mode 100644
index 0000000..772bef9
--- /dev/null
+++ b/03_TECHNICAL_CORE/ontology/imports/seeds/cco_seed.txt
@@ -0,0 +1,6 @@
+http://www.ontologyrepository.com/CommonCoreOntologies/Organization
+http://www.ontologyrepository.com/CommonCoreOntologies/DirectiveInformationContentEntity
+http://www.ontologyrepository.com/CommonCoreOntologies/DescriptiveInformationContentEntity
+http://www.ontologyrepository.com/CommonCoreOntologies/prescribes
+http://www.ontologyrepository.com/CommonCoreOntologies/has_output
+http://www.ontologyrepository.com/CommonCoreOntologies/Person
diff --git a/03_TECHNICAL_CORE/ontology/imports/seeds/iao_seed.txt b/03_TECHNICAL_CORE/ontology/imports/seeds/iao_seed.txt
new file mode 100644
index 0000000..d6482b7
--- /dev/null
+++ b/03_TECHNICAL_CORE/ontology/imports/seeds/iao_seed.txt
@@ -0,0 +1,2 @@
+http://purl.obolibrary.org/obo/IAO_0000030
+http://purl.obolibrary.org/obo/IAO_0000136
diff --git a/03_TECHNICAL_CORE/ontology/imports/seeds/ro_seed.txt b/03_TECHNICAL_CORE/ontology/imports/seeds/ro_seed.txt
new file mode 100644
index 0000000..988fb42
--- /dev/null
+++ b/03_TECHNICAL_CORE/ontology/imports/seeds/ro_seed.txt
@@ -0,0 +1,7 @@
+http://purl.obolibrary.org/obo/RO_0000052
+http://purl.obolibrary.org/obo/RO_0000053
+http://purl.obolibrary.org/obo/RO_0000057
+http://purl.obolibrary.org/obo/RO_0000087
+http://purl.obolibrary.org/obo/RO_0000091
+http://purl.obolibrary.org/obo/RO_0000092
+http://purl.obolibrary.org/obo/RO_0000056
diff --git a/03_TECHNICAL_CORE/scripts/run_pipeline.py b/03_TECHNICAL_CORE/scripts/run_pipeline.py
index f5a3603..1185692 100644
--- a/03_TECHNICAL_CORE/scripts/run_pipeline.py
+++ b/03_TECHNICAL_CORE/scripts/run_pipeline.py
@@ -38,8 +38,9 @@
GOV = ONTOLOGY_DIR / "ARCO_governance_extension.ttl"
INSTANCES = ONTOLOGY_DIR / "ARCO_instances_sentinel.ttl"
BFO_2020 = ONTOLOGY_DIR / "imports" / "bfo-2020.owl"
-IAO_2026 = ONTOLOGY_DIR / "imports" / "iao.owl"
-RO_2025 = ONTOLOGY_DIR / "imports" / "ro.owl"
+IAO_BOT = ONTOLOGY_DIR / "imports" / "iao_bot.owl"
+RO_BOT = ONTOLOGY_DIR / "imports" / "ro_bot.owl"
+CCO_BOT = ONTOLOGY_DIR / "imports" / "cco_bot.owl"
SHAPES = VALIDATION_DIR / "assessment_documentation_shape.ttl"
@@ -1427,7 +1428,7 @@ def main() -> None:
sub("LOAD")
print("Loading: core ontology + governance extension + instance data")
- g_source = load_union_graph(BFO_2020, IAO_2026, RO_2025, CORE, GOV, INSTANCES)
+ g_source = load_union_graph(BFO_2020, IAO_BOT, RO_BOT, CCO_BOT, CORE, GOV, INSTANCES)
print(f"Triples loaded (asserted): {len(g_source)}")
# ── invalid --system fail-fast (before reasoning) ──────────────
diff --git a/03_TECHNICAL_CORE/scripts/test_scenarios.py b/03_TECHNICAL_CORE/scripts/test_scenarios.py
index 476baee..b7158de 100644
--- a/03_TECHNICAL_CORE/scripts/test_scenarios.py
+++ b/03_TECHNICAL_CORE/scripts/test_scenarios.py
@@ -44,8 +44,9 @@
ONTOLOGY_DIR = REPO_ROOT / "03_TECHNICAL_CORE" / "ontology"
BFO_2020 = ONTOLOGY_DIR / "imports" / "bfo-2020.owl"
-IAO_2026 = ONTOLOGY_DIR / "imports" / "iao.owl"
-RO_2025 = ONTOLOGY_DIR / "imports" / "ro.owl"
+IAO_BOT = ONTOLOGY_DIR / "imports" / "iao_bot.owl"
+RO_BOT = ONTOLOGY_DIR / "imports" / "ro_bot.owl"
+CCO_BOT = ONTOLOGY_DIR / "imports" / "cco_bot.owl"
CORE = ONTOLOGY_DIR / "ARCO_core.ttl"
GOV = ONTOLOGY_DIR / "ARCO_governance_extension.ttl"
@@ -116,7 +117,7 @@
def load_and_reason(instance_file: Path) -> Graph:
g = Graph()
- for p in (BFO_2020, IAO_2026, RO_2025, CORE, GOV, instance_file):
+ for p in (BFO_2020, IAO_BOT, RO_BOT, CCO_BOT, CORE, GOV, instance_file):
if not p.exists():
raise FileNotFoundError(f"Missing: {p}")
fmt = "xml" if p.suffix == ".owl" else "turtle"
diff --git a/README.md b/README.md
index 7165ca4..95efde0 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@ ARCO moves that risk decision upstream. It is a pre-deployment classification en
The output is not a score, a confidence level, or an advisory opinion. It is a deterministic, audit-traceable assessment grounded in formal logic and BFO/RO/IAO-aligned, CCO-informed structure: same structured inputs, same classification, every time.
**TL;DR**
-- ARCO is a deterministic regulatory classification framework grounded in BFO 2020, with full upstream RO and IAO imports and local CCO stubs. The current implementation demonstrates it against the EU AI Act: formal OWL-RL reasoning tells you, before you build, whether your system triggers high-risk conditions per ARCO's encoding of Article 6 and Annex III, and exactly why. The architecture generalizes to any regulatory domain where obligations attach to capability, structure, and role.
+- ARCO is a deterministic regulatory classification framework grounded in BFO 2020, with ROBOT-BOT-extracted slim modules of OBO Relations Ontology, Information Artifact Ontology, and Common Core Ontologies — the OBO Foundry / ODK standard pattern, version-pinned and reproducible from seed files in the repo. The current implementation demonstrates it against the EU AI Act: formal OWL-RL reasoning tells you, before you build, whether your system triggers high-risk conditions per ARCO's encoding of Article 6 and Annex III, and exactly why. The architecture generalizes to any regulatory domain where obligations attach to capability, structure, and role.
- Classifications are deterministic and audit-traceable: formal OWL-RL reasoning + SHACL validation + SPARQL queries over a BFO-aligned ontology, with no probabilistic scoring and no LLMs in the decision loop.
- From a fresh clone, install the Python dependencies and run `python 03_TECHNICAL_CORE/scripts/run_pipeline.py` from the repository root to produce a formal condition assessment certificate with a full evidence path from system components through capabilities to Annex III criteria.
@@ -63,7 +63,7 @@ ARCO CONDITION ASSESSMENT CERTIFICATE
OBLIGATION: PASS
REG. ALIGNED: PASS
- ENTAILED TRIPLES ADDED: +47888
+ ENTAILED TRIPLES ADDED: +19710
Classification layer: PASS
Audit layer: PASS
@@ -107,29 +107,27 @@ This makes ARCO fundamentally different from post-hoc tools that observe behavio
| Ontology | Version / release | IRI namespace used | How it's loaded |
|----------|------------------|--------------------|------------------|
| **BFO** | BFO 2020 (ISO/IEC 21838-2:2021) | `http://purl.obolibrary.org/obo/BFO_` | Full ontology loaded from `03_TECHNICAL_CORE/ontology/imports/bfo-2020.owl` |
-| **RO** | OBO Relations Ontology release `2025-12-17` | `http://purl.obolibrary.org/obo/RO_` | Full ontology loaded from `03_TECHNICAL_CORE/ontology/imports/ro.owl` |
-| **IAO** | Information Artifact Ontology release `2026-03-30` | `http://purl.obolibrary.org/obo/IAO_` | Full ontology loaded from `03_TECHNICAL_CORE/ontology/imports/iao.owl` |
-| **CCO** | CCO pre-integrated release (exact version unverified; local stubs) | `http://www.ontologyrepository.com/CommonCoreOntologies/` | Local stubs only — specific terms declared in `ARCO_governance_extension.ttl` |
+| **RO** | OBO Relations Ontology release `2025-12-17` | `http://purl.obolibrary.org/obo/RO_` | ROBOT BOT-extracted slim module loaded from `03_TECHNICAL_CORE/ontology/imports/ro_bot.owl` |
+| **IAO** | Information Artifact Ontology release `2026-03-30` | `http://purl.obolibrary.org/obo/IAO_` | ROBOT BOT-extracted slim module loaded from `03_TECHNICAL_CORE/ontology/imports/iao_bot.owl` |
+| **CCO** | Common Core Ontologies release `v1.7-2024-11-03` (last release before the v2.0 IRI-namespace migration) | `http://www.ontologyrepository.com/CommonCoreOntologies/` | ROBOT BOT-extracted slim module loaded from `03_TECHNICAL_CORE/ontology/imports/cco_bot.owl`, plus a small set of local bridging assertions in `ARCO_governance_extension.ttl` |
-**BFO 2020** is the second edition of Basic Formal Ontology, standardized as ISO/IEC 21838-2:2021. ARCO uses the OBO Foundry numeric-ID namespace (`BFO_0000015`, `BFO_0000016`, etc.) that is definitive of this release. The earlier BFO 1.1 used a different IRI scheme (`http://www.ifomis.org/bfo/1.1/snap#`, `span#`) and is not used here.
+**BFO 2020** is the second edition of Basic Formal Ontology, standardized as ISO/IEC 21838-2:2021. ARCO uses the OBO Foundry numeric-ID namespace (`BFO_0000015`, `BFO_0000016`, etc.) that is definitive of this release. BFO is loaded as a full local file because it is small (~100 KB), ISO-standardized, and the authoritative grounding for everything else; this matches IAO's own pattern of full-importing BFO while extracting slim modules of any other dependency.
-**RO** and **IAO** are loaded as full upstream releases. The pipeline pulls the entire `ro.owl` and `iao.owl` files into the reasoning graph alongside BFO. This was not always the case: earlier ARCO revisions referenced RO and IAO terms by IRI with only minimal local label declarations and no full `owl:imports`. The promotion from stub-style references to full-file imports was performed under independent verification (alignment audit, OWL 2 DL profile validation under ROBOT, and HermiT consistency check) and confirmed not to change any classification outputs. See `docs/agent/alignment_audit_RO_2026-04-29.md` and `docs/agent/alignment_audit_IAO_2026-04-29.md`.
+**RO**, **IAO**, and **CCO** are loaded as ROBOT-extracted slim modules using `--method BOT`, a syntactic locality variant. The seed term lists ARCO depends on are version-controlled in `03_TECHNICAL_CORE/ontology/imports/seeds/{ro,iao,cco}_seed.txt`, and the slim modules can be regenerated reproducibly from the pinned upstream releases. This is the OBO Foundry / Ontology Development Kit (ODK) standard pattern, used by Gene Ontology, the OBO Relations Ontology itself, and the hundreds of ODK-managed projects.
-**CCO** terms remain declared as local stubs rather than via a full `owl:imports` of the CCO modules. Only the specific CCO classes and properties ARCO requires are declared in-file (`cco:Organization`, `cco:DirectiveInformationContentEntity`, `cco:prescribes`, `cco:has_output`, etc.), using the pre-integrated-release IRI namespace. The pipeline does not depend on fetching external CCO files at runtime.
+**Local CCO bridging assertions.** Upstream CCO has its own `cco:InformationContentEntity` class that is not formally linked to IAO's `iao:0000030`. ARCO's `ARCO_governance_extension.ttl` contains two small bridging assertions (`cco:DirectiveICE rdfs:subClassOf iao:0000030`, `cco:DescriptiveICE rdfs:subClassOf iao:0000030`) that connect the CCO and IAO information-content-entity hierarchies. These are the only stubs that do non-trivial work; the remaining CCO declarations in that file are now redundant with the BOT module and are kept for in-file readability rather than logical effect.
-### Why full upstream imports rather than slim MIREOT modules
+### Why ROBOT BOT slim modules
-The conventional OBO Foundry pattern for depending on an external ontology is to extract a slim "import module" using a tool such as ROBOT's `extract` command (e.g. MIREOT, BOT, or STAR), pulling in only the specific terms a project references plus their ancestors. ARCO instead loads the complete upstream releases. This is a deliberate choice grounded in ARCO's role as a regulatory classification framework rather than a biological ontology fragment.
+Using `robot extract --method BOT` to pull slim, version-pinned modules is the OBO Foundry's standard pattern for depending on external ontologies. The choice rests on five practical points:
-Five reasons full imports are the right default for ARCO:
+1. **Formal entailment-preservation guarantee.** BOT is a syntactic locality module variant (Cuenca Grau, Horrocks, Kazakov, Sattler 2007/2008): for any axiom α whose signature is contained in the seed signature Σ, the extracted module entails α iff the full upstream ontology does. This includes property characteristics (`FunctionalProperty`, `Transitive`, `Symmetric`), property chain axioms, inverse-of axioms, and `rdfs:domain` / `rdfs:range`. ARCO's gate axioms depend on these — particularly anonymous inverse property expressions on `iao:0000136` — so this is the strict property the project needs.
+2. **OBO Foundry / ODK convention.** The Ontology Development Kit, which scaffolds ~hundreds of OBO Foundry projects, hardcodes `module_type_slme: "BOT"` as default. Gene Ontology, OBI, ChEBI, and the OBO Relations Ontology itself all ship BOT-extracted slim modules for their dependencies. ARCO matching this convention shortens the trust chain for any reviewer fluent in OBO practice.
+3. **MIREOT is legacy and unsafe for reasoning-critical projects.** ROBOT's own documentation states MIREOT "preserves the hierarchy of the input ontology (subclass and subproperty relationships), but does not try to preserve the full set of logical entailments." The documented MIREOT failure mode is silently dropping property typing and characteristic axioms. For a project whose headline product is OWL-DL reasoning correctness over inverse-property gate axioms, MIREOT is the wrong choice on principle and BOT is the right one.
+4. **Reproducibility.** Each slim module is regenerable from a pinned upstream release using a single ROBOT command with a version-controlled seed file. The seed lists are in `03_TECHNICAL_CORE/ontology/imports/seeds/`. A reviewer auditing ARCO can re-run the extraction and verify byte-equivalent output.
+5. **Operational scaling.** A pipeline run on Sentinel-ID with the BOT modules loads roughly 7744 asserted triples and produces 27454 post-reasoning (about 19710 derived). The HermiT reasoning step in the ROBOT validation workflow runs in approximately seven minutes on the merged ontology. An earlier intermediate state of ARCO loaded the full upstream releases of RO and IAO, which took the HermiT step to thirty to forty minutes and was projected to grow to one to three hours when CCO was added; this is operationally noisy without adding any reasoning-correctness signal that BOT does not already provide. The full-import experiments are preserved in git history at PRs #24 and #25 and confirmed that the slim modules produce byte-identical classification outputs.
-1. **Audit traceability.** A reviewer, auditor, or regulator can verify with a single hash that ARCO uses BFO 2020, OBO Relations Ontology release `2025-12-17`, and Information Artifact Ontology release `2026-03-30` exactly as published — with no curation step in between. A MIREOT module would itself be an audit surface ("which axioms made the cut, why, and is the slice still consistent with the full upstream?"). Removing that step shortens the chain of trust.
-2. **No silent upstream drift.** When an upstream ontology adds a new property-chain axiom, strengthens a domain or range, or refines a class definition, the full import picks it up automatically on the next release pin. A slim module would freeze the previous slice and quietly miss the change. For a tool whose entire purpose is tracking formal definitions of regulated concepts, this matters.
-3. **Extensibility to new Annex III categories and to peer regulations.** Adding Annex III 1(b), 5(a), or 6 — or modeling GDPR Article 22, FDA pre-cert, NIS2, or sectoral safety regimes — will reach for additional BFO, RO, and IAO terms ARCO does not currently reference. With full imports those terms are already in scope; the only ontology engineering work is the new gate axioms. With slim modules every new category or domain triggers a module-rebuild step.
-4. **Cross-domain generalization is part of the architectural pitch.** The README and the underlying design claim that ARCO generalizes to any regulatory domain where obligations attach to capability, structure, and role. Full imports are consistent with that claim; per-domain slim modules quietly contradict it.
-5. **Stronger independent-reasoner verification.** The HermiT cross-check in CI exists to confirm that the production OWL-RL reasoner agrees with a full DL reasoner over the actual upstream axiomatization. Running HermiT against a slim module would only verify agreement over the axioms ARCO chose to import; running HermiT against the full ontologies verifies agreement over what the upstream specifications actually say.
-
-The cost is operational, not logical. A pipeline run on Sentinel-ID currently loads roughly 17266 asserted triples and produces roughly 65154 post-reasoning triples (about 47888 derived). The overwhelming majority of those derived triples come from OWL-RL closure over upstream axioms ARCO does not directly invoke: BFO upper-level subclass propagation, RO's property-chain and inverse-property axioms firing across every relation in the merged graph, and IAO's information-content-entity hierarchy. Only a small fraction is ARCO-specific (the gate-axiom entailments classifying a system as `HighRiskSystem` or `AnnexIII1aApplicableSystem`, plus supporting traceability triples). With slim MIREOT modules the same classification would emerge, but the post-reasoning graph would be perhaps an order of magnitude smaller because the bulk of upstream axiomatization would not be loaded. ARCO carries the larger graph deliberately: the inflation is observability cost, not reasoning complexity the gate axioms had to traverse. The HermiT step in CI takes roughly thirty to forty minutes on the merged ontology — slow, but informational and non-gating, and confirmed correct under both reasoners. The conventional MIREOT counter-argument (sibling biological ontologies needing slim modules to avoid cyclic imports) does not apply because ARCO has no such cycles.
+The conventional argument for full imports — single-hash audit traceability against published upstream releases — is recovered here by the seed-file plus version-pin pattern: the seed lists are version-controlled, the upstream releases are pinned, and the extraction tool (ROBOT v1.9.10) is pinned in CI. The audit story becomes "ARCO uses BOT-extracted modules of these specific upstream releases, regenerable from these seed files using this specific ROBOT command," which is a tighter and more reproducible claim than "ARCO uses these full upstream releases" because every step is mechanically verifiable.
---
@@ -197,7 +195,7 @@ python 03_TECHNICAL_CORE/scripts/run_pipeline.py
The pipeline will:
1. Load ontology (core + governance extension) and instance data
-2. Run OWL-RL reasoning to materialize entailments (17266 asserted -> 65154 post-reasoning, on the full BFO + RO + IAO + ARCO union)
+2. Run OWL-RL reasoning to materialize entailments (7744 asserted -> 27454 post-reasoning, on the BFO + BOT-extracted RO/IAO/CCO + ARCO union)
3. Validate documentary completeness with SHACL
4. Run two layers of checks:
- **Classification layer (OWL-RL):** SHACL conformance, `HighRiskSystem` latent-risk entailment, Annex III 1(a) three-gate entailment (the formal classification outputs)