Removed TODO definition annotations, added synonyms to 'treatment' an…#200
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dillerm wants to merge 1 commit into
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Removed TODO definition annotations, added synonyms to 'treatment' an…#200dillerm wants to merge 1 commit into
dillerm wants to merge 1 commit into
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…d 'prophylactic treatment', and added COB import.
zhengj2007
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May 23, 2026
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zhengj2007
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No errors were identified directly within the OGMS terms; however, several issues exist regarding imported terms.
- Import term files: Currently, the XXX_terms.txt files (corresponding to XXX_import.owl under src/ontology/imports/) are empty. These must be populated with the relevant terms for each ontology prefix (e.g., bfo, cob, iao). For instance, cob_terms.txt should contain entries such as COB:0000035, COB:0000082 etc.
- Deprecated OBI terms: There are two "planned process" terms in OGMS. The OBI one is deprecated and replaced with COB:0000035. All subclasses should be migrated under COB:0000035 (completely executed planned process) and removed imported OBI "planned process". OBI ‘organism’ should be replaced with the corresponding COB term as well.
- APOLLO_SV terms: OGMS imports APOLLO_SV terms via IAO. We should create a dedicated apollo_sv.owl and apollo_sv_terms.txt to import these terms directly.
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IAO has taken over ownership of those APOLLO-SV classes, they are no longer
imports.
…On Sat, May 23, 2026 at 2:37 PM jie zheng ***@***.***> wrote:
***@***.**** requested changes on this pull request.
No errors were identified directly within the OGMS terms; however, several
issues exist regarding imported terms.
- Import term files: Currently, the XXX_terms.txt files (corresponding
to XXX_import.owl under src/ontology/imports/) are empty. These must be
populated with the relevant terms for each ontology prefix (e.g., bfo, cob,
iao). For instance, cob_terms.txt should contain entries such as
COB:0000035, COB:0000082 etc.
- Deprecated OBI terms: There are two "planned process" terms in OGMS.
The OBI one is deprecated and replaced with COB:0000035. All subclasses
should be migrated under COB:0000035 (completely executed planned process)
and removed imported OBI "planned process". OBI ‘organism’ should be
replaced with the corresponding COB term as well.
- APOLLO_SV terms: OGMS imports APOLLO_SV terms via IAO. We should
create a dedicated apollo_sv.owl and apollo_sv_terms.txt to import these
terms directly.
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…d 'prophylactic treatment', and added COB import.