diff --git a/data/ontology/provisional_props.ttl b/data/ontology/provisional_props.ttl index ae12b876..c3bf95b5 100644 --- a/data/ontology/provisional_props.ttl +++ b/data/ontology/provisional_props.ttl @@ -492,3 +492,33 @@ bao:BAX_0000082 rdfs:label "has molecular entity potentiator" ; obo:IAO_0000115 "" . + +bao:BAX_0000083 + rdf:type owl:DatatypeProperty ; + rdfs:label "has publication source" ; + obo:IAO_0000115 "" + . + +bao:BAX_0000084 + rdf:type owl:DatatypeProperty ; + rdfs:label "has library source" ; + obo:IAO_0000115 "" + . + +bao:BAX_0000085 + rdf:type owl:DatatypeProperty ; + rdfs:label "has reagent source" ; + obo:IAO_0000115 "" + . + +bao:BAX_0000086 + rdf:type owl:DatatypeProperty ; + rdfs:label "has target HELM" ; + obo:IAO_0000115 "" + . + +bao:BAX_0000087 + rdf:type owl:DatatypeProperty ; + rdfs:label "is activity inverted" ; + obo:IAO_0000115 "" + . diff --git a/data/ontology/provisional_values.ttl b/data/ontology/provisional_values.ttl index 2b710cab..6afb4ea1 100644 --- a/data/ontology/provisional_values.ttl +++ b/data/ontology/provisional_values.ttl @@ -338,4 +338,19 @@ bae:BAE_0000063 obo:IAO_0000115 "" ; . +bae:BAE_0000064 + rdfs:label "boolean" ; + obo:IAO_0000115 "" ; + . +bae:BAE_0000065 + rdfs:label "true" ; + rdfs:subClassOf bao:BAE_0000064 ; + obo:IAO_0000115 "" ; + . + +bae:BAE_0000066 + rdfs:label "false" ; + rdfs:subClassOf bao:BAE_0000064 ; + obo:IAO_0000115 "" ; + . diff --git a/data/template/schema.json b/data/template/schema.json index 79eef20b..0aba4ae6 100644 --- a/data/template/schema.json +++ b/data/template/schema.json @@ -394,7 +394,7 @@ "uri": "http://www.bioassayontology.org/bao#BAO_0003114", "name": "assay biology component", "descr": "", - "spec": "exclude" + "spec": "container" }, { "uri": "http://www.bioassayontology.org/bat#Absence", diff --git a/data/template/schema_hack.json b/data/template/schema_hack.json new file mode 100644 index 00000000..056f6212 --- /dev/null +++ b/data/template/schema_hack.json @@ -0,0 +1,964 @@ +{ + "schemaPrefix": "http://www.bioassayontology.org/basp#", + "root": + { + "name": "common assay template +", + "descr": "The Common Assay Template is designed to capture most of the high value data from in vitro assays, particularly those used for high throughput screening. Modified during the BioITWorld hackathon.", + "groupURI": "", + "assignments": + [ + { + "name": "assay title", + "descr": "A short summary description of the assay.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0002853", + "suggestions": "string", + "values": [] + }, + { + "name": "bioassay type", + "descr": "Categorization of bioassays based on the property or process that the assay is interrogating, e.g. ADMET, functional, etc.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0002854", + "suggestions": "full", + "values": + [ + { + "uri": "http://www.bioassayontology.org/bao#BAO_0000008", + "name": "bioassay type", + "descr": "Categorization of bioassays based on the property or process that the assay is interrogating, e.g. ADMET, functional, etc.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + } + ] + }, + { + "name": "bioassay", + "descr": "Categorization of the general class of bioassay (enyzme activity, gene expression...)", + "propURI": "http://www.bioassayontology.org/bao#BAO_0002855", + "suggestions": "full", + "values": + [ + { + "uri": "http://www.bioassayontology.org/bao#BAO_0000015", + "name": "bioassay", + "descr": "A set of instructions, methodology, operations, required reagents, instruments to carrie out experiments for the purpose of testing the effect of a perturbing agent in a biological model system, measuring one or multiple effect(s) of the agent facilitated by an assay design method translate the perturbation into a detectable signal to arrive at one or multiple endpoint(s) that quantify or qualify the extent of the perturbation. Bioassay is described by multiple bioassay components: assay format, biology (biological participants in various role and processes), design method, physical detection method / technology, screened entity, and endpoint. Bioassay includes one or multiple measure groups to describe panel, profiling, multiparametric (or multiplexed) assays (assays that measure more than one effect of the perturbagen on the system that is screened).", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0000248", + "name": "assay kit", + "descr": "The title of the kit/biologicals used in the assay.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0002933", + "name": "experimental specification", + "descr": "", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0000026", + "name": "bioassay specification", + "descr": "Description of an experiment carried out for the purpose of screening a perturbing agent in a biological system, measuring the effect of the agents using specified technology, and arriving at endpoints that satisfy particular criteria.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0000040", + "name": "measure group", + "descr": "Measure group is used to group and link multiple (different) sets of experimental results to one bioassay. Measure groups thus facilitate the description of multiparametric (or multiplexed) assays, that measure more than one effect of the perturbagen on the system that is screened. It also facilitate the definition of panel and profiling assays, e.g. assays that test compounds against multiple (protein) targets.\nCompare definition of bioassay.\nMeasure group links to those classes that can vary among different measurements of a panel assay, profiling assay, multiparametric assay, e.g. target, assay design method, physical detection method, endpoint. Measure group is also used to define derived endpoints, for example concentration-response endpoints obtained by curve fitting a set of results from the same compound tested in the same assay at different concentrations.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0002185", + "name": "measure group specification", + "descr": "An abstract concept to group one or more assay readout and allow description of an assay that measures one or more effect of a perturbagen on the biological entity. This does not define the physical readout method itself, which is captured in assay design, but rather classifies the data being generated by those readouts.", + "spec": "exclude" + } + ] + }, + { + "name": "assay format", + "descr": "Assay format is a conceptualization of assays based on the biological and / or chemical features of the experimental system. For example assay formats include biochemical assays - referring to assays with purified protein, cell-based - referring to assays in whole cells, or organism-based - referring to assays performed in an organism.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0000205", + "suggestions": "full", + "values": + [ + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0000019", + "name": "assay format", + "descr": "Assay format is a conceptualization of assays based on the biological and / or chemical features of the experimental system. For example assay formats include biochemical assays - referring to assays with purified protein, cell-based - referring to assays in whole cells, or organism-based - referring to assays performed in an organism.", + "spec": "container" + } + ] + }, + { + "name": "assay design method", + "descr": "The assay design method describes how a biological or physical process screened / investigated in the model system is translated into a detectable signal. This relates to the technology / technologies used to make the assay system work, i.e. enable that the screened process can be detected. It typically involves some manipulation of the (biological) model system to detect the process of interest.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0095009", + "suggestions": "full", + "values": + [ + { + "uri": "http://www.bioassayontology.org/bao#BAO_0002202", + "name": "assay design method", + "descr": "The assay design method describes how a biological or physical process screened / investigated in the model system is translated into a detectable signal. This relates to the technology / technologies used to make the assay system work, i.e. enable that the screened process can be detected. It typically involves some manipulation of the (biological) model system to detect the process of interest.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0002429", + "name": "assay supporting method", + "descr": "Assay supporting methods describe the methods to prepare, generate or post-process the assay system or assay screening process. Such methods include the sample preparation, labeling, data processing, etc., which are required to performing the assay, but do not constitute the actual assay (design method).", + "spec": "exclude" + } + ] + }, + { + "name": "assay supporting method", + "descr": "Assay supporting methods describe the methods to prepare, generate or post-process the assay system or assay screening process. Such methods include the sample preparation, labeling, data processing, etc., which are required to performing the assay, but do not constitute the actual assay (design method).", + "propURI": "http://www.bioassayontology.org/bao#BAO_0095010", + "suggestions": "full", + "values": + [ + { + "uri": "http://www.bioassayontology.org/bao#BAO_0002429", + "name": "assay supporting method", + "descr": "Assay supporting methods describe the methods to prepare, generate or post-process the assay system or assay screening process. Such methods include the sample preparation, labeling, data processing, etc., which are required to performing the assay, but do not constitute the actual assay (design method).", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0002202", + "name": "assay design method", + "descr": "The assay design method describes how a biological or physical process screened / investigated in the model system is translated into a detectable signal. This relates to the technology / technologies used to make the assay system work, i.e. enable that the screened process can be detected. It typically involves some manipulation of the (biological) model system to detect the process of interest.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + } + ] + }, + { + "name": "assay cell line", + "descr": "An assay cell line refers to the source of the cells or cell line used in the assay. This may be from primary cells (as annotated) or, more frequently, from an immortal cell line. Due to the continued passaging of immortal cell lines, users must be aware that spontaneous mutations can, and often do, arise in sub-populations, such that the actual cells used in the individual assay may differ from the original source.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0002800", + "suggestions": "full", + "values": + [ + { + "uri": "http://dto.org/DTO/DTO_000", + "name": "BRENDA tissues and cell lines", + "descr": "", + "spec": "container" + }, + { + "uri": "http://purl.obolibrary.org/obo/CLO_0000001", + "name": "cell line cell", + "descr": "", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + } + ] + }, + { + "name": "organism", + "descr": "The organism related to the target / meta-target of the bioassay. It includes both bacterium and eukaryote.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0002921", + "suggestions": "full", + "values": + [ + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0000551", + "name": "organism", + "descr": "The organism related to the target / meta-target of the bioassay. It includes both bacterium and eukaryote.", + "spec": "container" + } + ] + }, + { + "name": "biological process", + "descr": "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end (from GO). For annotated BioAssays, Biological Process is the process that is being (or is presumed to be) affected by an entity with a perturbagen role in the assay.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0002009", + "suggestions": "full", + "values": + [ + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://purl.obolibrary.org/obo/GO_0008150", + "name": "biological process", + "descr": "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end (from GO).", + "spec": "container" + }, + { + "uri": "http://purl.obolibrary.org/obo/GO_0003674", + "name": "molecular function", + "descr": "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0003117", + "name": "function", + "descr": "", + "spec": "container" + } + ] + }, + { + "name": "target", + "descr": "The molecular entity (e.g., protein, carbohydrate, nucleic acid, or other) that is the presumed subject of the assay and whose activity is being effected by an entity with a perturbagen role in the assay. Can encompass the TYPE of biological macromolecule (e.g., enzyme, chaperone, GPCR, etc.) as well as the specific molecular target (e.g., gene name or geneid). An assay can have zero (e.g., if unknown as in assays for cytotoxic compounds) or multiple targets.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0000211", + "suggestions": "full", + "values": + [ + { + "uri": "http://www.bioassayontology.org/bao#BAO_0003111", + "name": "biological macromolecule", + "descr": "", + "spec": "container" + }, + { + "uri": "http://www.drugtargetontology.org/dto/DTO_00200000", + "name": "Gene", + "descr": "", + "spec": "container" + }, + { + "uri": "http://www.drugtargetontology.org/dto/DTO_00100000", + "name": "Protein", + "descr": "", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + } + ] + }, + { + "name": "applies to disease", + "descr": "Disease targets that the assay is designed to affect. This is a more general term than the specific biological target.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0002848", + "suggestions": "full", + "values": + [ + { + "uri": "http://purl.obolibrary.org/obo/DOID_4", + "name": "Disease", + "descr": "A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.\n", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0003114", + "name": "assay biology component", + "descr": "", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + } + ] + }, + { + "name": "assay mode of action", + "descr": "Assay mode of action refers both to the mechanism (binding vs. functional) and the effect of the perturbagen on the target - whether it brings about inhibition, activation, cytotoxicity, etc.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0000196", + "suggestions": "full", + "values": + [ + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0000074", + "name": "mode of action", + "descr": "This refers to the effect of the perturbagen on the target of an assay, whether it brings about inhibition, activation, cytotoxicity, etc. ", + "spec": "container" + } + ] + }, + { + "name": "result", + "descr": "The endpoint is a quantitive or qualitative interpretable standardized representation of a perturbation (a change from a defined reference state of a \"closed\" model system) that is measured by the bioassay. An endpoint consists of a series of data points, one for each perturbing agent (screened entity) tested the assay.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0000208", + "suggestions": "full", + "values": + [ + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0000179", + "name": "endpoint", + "descr": "The endpoint is a quantitive or qualitative interpretable standardized representation of a perturbation (a change from a defined reference state of a \"closed\" model system) that is measured by the bioassay. An endpoint consists of a series of data points, one for each perturbing agent (screened entity) tested the assay.", + "spec": "container" + } + ] + }, + { + "name": "screening campaign stage", + "descr": "The assay stage describes the purpose of the assay in an assay campaign. Assay stage also relates to the order of assays in a screening campaign. For example the primary assay, which is performed first, identifies hits. The primary hits are then confirmed in a confirmatory assay. Subsequent secondary assays are run to eliminate compounds that are not of interest or to confirm hits using an alternate design / technology, or to further characterize compounds.\nWhether an assay is run in single concentration or concentration response is defined in the class 'assay measurement throughput quality'. For example primary assays are typically run in single concentration with single measurements. However, the NCGC runs qHTS primary assays as concentration-response assays.", + "propURI": "http://www.bioassayontology.org/bao#BAO_0000210", + "suggestions": "full", + "values": + [ + { + "uri": "http://www.bioassayontology.org/bat#Absence", + "name": "absence", + "descr": "A group of annotations that explain why an annotation is missing, when it should not be.", + "spec": "container" + }, + { + "uri": "http://www.bioassayontology.org/bat#NotDetermined", + "name": "not determined", + "descr": "The measurement was not made.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bat#SeeGeneID", + "name": "see Gene ID", + "descr": "The target is present in the Gene ID section, but needs to be mapped to a formal ontology.", + "spec": "exclude" + }, + { + "uri": "http://www.bioassayontology.org/bao#BAO_0000029", + "name": "assay screening campaign stage", + "descr": "The assay stage describes the purpose of the assay in an assay campaign. Assay stage also relates to the order of assays in a screening campaign. For example the primary assay, which is performed first, identifies hits. The primary hits are then confirmed in a confirmatory assay. Subsequent secondary assays are run to eliminate compounds that are not of interest or to confirm hits using an alternate design / technology, or to further characterize compounds.\nWhether an assay is run in single concentration or concentration response is defined in the class 'assay measurement throughput quality'. For example primary assays are typically run in single concentration with single measurements. 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