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Add “cryo-EM” and “cryo-ET”. #32

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Merged
gouttegd merged 5 commits into from
Feb 16, 2026
Merged

Add “cryo-EM” and “cryo-ET”. #32

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e7744be
Import the OBO Metadata Ontology (OMO).
gouttegd Feb 16, 2026
d9b0418
Commit re-generated files.
gouttegd Feb 16, 2026
46ae94b
Add "cryo-EM" and "cryo-TEM".
gouttegd Feb 16, 2026
dbc5b92
Split the label of 'transmission electron microscopy (TEM)'.
gouttegd Feb 16, 2026
303b4b3
Typo fix ("nature" -> "native").
gouttegd Feb 16, 2026
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12 changes: 10 additions & 2 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
# More information: https://github.com/INCATools/ontology-development-kit/

# Fingerprint of the configuration file when this Makefile was last generated
CONFIG_HASH= d25d320524c42b89f4a1468da94a2b22a9c25036ffce1890cbe3bf145290e57e
CONFIG_HASH= 098026db9e0812afa65ba3dd4cc8678b97eb80ec518df34154f83ee105d84fa8


# ----------------------------------------
Expand Down Expand Up @@ -193,7 +193,7 @@ all_main: $(MAIN_FILES)
# ----------------------------------------


IMPORTS = ro
IMPORTS = ro omo

IMPORT_ROOTS = $(IMPORTDIR)/merged_import
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
Expand Down Expand Up @@ -457,6 +457,14 @@ mirror-ro: | $(TMPDIR)
curl -L $(OBOBASE)/ro.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 200 && \
$(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl


## ONTOLOGY: omo
.PHONY: mirror-omo
.PRECIOUS: $(MIRRORDIR)/omo.owl
mirror-omo: | $(TMPDIR)
curl -L $(OBOBASE)/omo.owl --create-dirs -o $(TMPDIR)/omo-download.owl --retry 4 --max-time 200 && \
$(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl

ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
MERGE_MIRRORS = true

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40 changes: 38 additions & 2 deletions src/ontology/fbbi-edit.owl
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Expand Up @@ -666,6 +666,8 @@ Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_00100010>))
Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_00100011>))
Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_00100012>))
Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_00100013>))
Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_00100014>))
Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_00100015>))
Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_root_00000000>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/FBbi_00000346>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
Expand All @@ -680,11 +682,13 @@ Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#Sub
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#created_by>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#creation_date>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#default-namespace>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#inSubset>))
Declaration(AnnotationProperty(rdfs:comment))
Expand Down Expand Up @@ -2725,11 +2729,12 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00000257> "s
EquivalentClasses(<http://purl.obolibrary.org/obo/FBbi_00000257> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbi_00000256> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000278>)))
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000257> <http://purl.obolibrary.org/obo/FBbi_00000256>)

# Class: <http://purl.obolibrary.org/obo/FBbi_00000258> (transmission electron microscopy (TEM))
# Class: <http://purl.obolibrary.org/obo/FBbi_00000258> (transmission electron microscopy)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/FBbi_00000258> "image")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/OMO_0003000>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/FBbi_00000258> "TEM")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/FBbi_00000258> "FBbi:00000258")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00000258> "transmission electron microscopy (TEM)")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00000258> "transmission electron microscopy")
EquivalentClasses(<http://purl.obolibrary.org/obo/FBbi_00000258> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbi_00000256> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000277>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000306>)))
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000258> <http://purl.obolibrary.org/obo/FBbi_00000256>)

Expand Down Expand Up @@ -6557,6 +6562,37 @@ AnnotationAssertion(<http://purl.org/dc/terms/date> <http://purl.obolibrary.org/
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00100013> "wide-field fluorescence microscopy")
EquivalentClasses(<http://purl.obolibrary.org/obo/FBbi_00100013> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbi_00000246> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000277>)))

# Class: <http://purl.obolibrary.org/obo/FBbi_00100014> (cryogenic transmission electron microscopy)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:3043536") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbi_00100014> "A form of transmission electron microscopy in which the specimen is maintained in a vitrified state at cryogenic temperature throughout imaging. The specimen is rapidly frozen to preserve its native structure in amorphous ice, avoiding the artefacts associated with chemical fixation, dehydration, and staining. Imaging is performed with the specimen held at cryogenic temperature in a transmission electron microscope.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_00100014> <https://orcid.org/0000-0001-6178-2884>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_00100014> <https://orcid.org/0000-0002-6095-8718>)
AnnotationAssertion(<http://purl.org/dc/terms/date> <http://purl.obolibrary.org/obo/FBbi_00100014> "2026-02-16T12:43:02Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/FBbi_00100014> "cryo-electron microscopy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/FBbi_00100014> "cryogenic electron microscopy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/FBbi_00100014> "cryogenic-sample electron microscopy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FBbi_00100014> "cryo-transmission electron microscopy")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/OMO_0003000>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/FBbi_00100014> "cryo-EM")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/OMO_0003000>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/FBbi_00100014> "cryo-TEM")
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@lubianat lubianat Feb 16, 2026

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is "cryo-TEM" a related or an exact synonym?

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@lubianat lubianat Feb 16, 2026

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maybe the standard is RelatedSynonym for all abbreviations?

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@gouttegd gouttegd Feb 16, 2026

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Yes, exactly. Abbreviations are represented as “related synonyms” with an additional “synonym type“ set to “abbreviation“ (OMO:0003000).

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/OMO_0003000>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/FBbi_00100014> "cryoEM")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00100014> "cryogenic transmission electron microscopy")
EquivalentClasses(<http://purl.obolibrary.org/obo/FBbi_00100014> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbi_00000258> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000013>)))

# Class: <http://purl.obolibrary.org/obo/FBbi_00100015> (cryogenic electron tomography)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:23918936") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbi_00100015> "A form of electron tomography in which a cryo-preserved specimen is tilted incrementally in a cryogenic transmission electron microscope to acquire a series of two-dimensional projection images (tilt series), which are then computationally aligned and reconstructed into a three-dimensional volume (tomogram).")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_00100015> <https://orcid.org/0000-0001-6178-2884 >)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_00100015> <https://orcid.org/0000-0002-6095-8718>)
AnnotationAssertion(<http://purl.org/dc/terms/date> <http://purl.obolibrary.org/obo/FBbi_00100015> "2026-02-16T12:57:59Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FBbi_00100015> "cryo-electron tomography")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FBbi_00100015> "cryogenic-sample electron tomography")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FBbi_00100015> "electron cryotomography")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/OMO_0003000>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/FBbi_00100015> "cryo-ET")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/OMO_0003000>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/FBbi_00100015> "cryoET")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00100015> "cryogenic electron tomography")
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00100015> <http://purl.obolibrary.org/obo/FBbi_00001005>)
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00100015> <http://purl.obolibrary.org/obo/FBbi_00100014>)

# Class: <http://purl.obolibrary.org/obo/FBbi_root_00000000> (method involved in biological imaging)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/FBbi_root_00000000> "image")
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1 change: 1 addition & 0 deletions src/ontology/fbbi-odk.yaml
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Expand Up @@ -7,6 +7,7 @@ import_group:
use_base_merging: true
products:
- id: ro
- id: omo
robot:
reasoner: ELK
repo: fbbi
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