Removed TODO definition annotations, added synonyms to 'treatment' an…

[dillerm]

…d 'prophylactic treatment', and added COB import.

[zhengj2007]

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.

[hoganwr]

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. — Reply to this email directly, view it on GitHub <#200 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJR55R3GTGRSCAQYEVVFO344H4X5AVCNFSM6AAAAACYZJ7MVSVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHM2DGNJRGM2DQNJXGM> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[dillerm]

@zhengj2007

• We do not use XXX_terms.txt files for imports because we use the custom import template.
• I replaced the OBI terms 'organism' and 'planned process' with their respective COB terms. However, OBI:0000011 (planned process) is still appearing in our OBI import file despite not being declared as an import. I am open to suggestions on how to fix this, as I am stumped.
• No action is needed here, per @hoganwr 's comment