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We will soon start to record abbreviations as "related synonyms of type 'abbreviation'" (formally: a oboInOwl:hasRelaatedSynonym annotation assertion axiom that is itself annotated with a oboInOwl:hasSynonymType annotation with the value OMO:0003000), so we need to import the OBO Metadata Ontology, which defines the OMO:0003000 "abbreviation" synonym type.
We add two terms representing specialised forms of transmission electron microscopy: * `cryogenic transmission electron microscopy` (a form of TEM using a cryofixed sample); * `cryogenic electron tomography` (a form of both TEM and tomography using a cryofixed sample). closes #29
The current label of FBbi:00000258 ("transmission electron microscopy
(TEM)") includes both an actual label and a synonym. These two should
not be conflated in a single annotation.
Make the label simply "transmission electron microscopy", and move "TEM"
to a related synonym with type "abbreviation".
lubianat
reviewed
Feb 16, 2026
lubianat
reviewed
Feb 16, 2026
| 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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is "cryo-TEM" a related or an exact synonym?
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maybe the standard is RelatedSynonym for all abbreviations?
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Yes, exactly. Abbreviations are represented as “related synonyms” with an additional “synonym type“ set to “abbreviation“ (OMO:0003000).
lubianat
reviewed
Feb 16, 2026
| Ontology(<http://purl.obolibrary.org/obo/fbbi/imports/merged_import.owl> | ||
| <http://purl.obolibrary.org/obo/fbbi/releases/2026-01-23/imports/merged_import.owl> | ||
| Annotation(owl:versionInfo "2026-01-23") | ||
| <http://purl.obolibrary.org/obo/fbbi/releases/2026-02-16/imports/merged_import.owl> |
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I went through this file quickly and I see no issues, but I am not sure on what to look for too.
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This file was automatically refreshed because I had to import OMO:0003000 (the “abbreviation” synonym type). :)
lubianat
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just a minor typo-ish, otherwise looks good
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This PR adds the two new terms requested in #29: