uberon

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Question: how should unspecified anatomical terms be provided in Cellosaurus

2

Relaying a Q from Amos, before imposing my own view just putting this up for consensus, how should cellosaurus indicate in a cell line record where the anatomy is unspecified:...

cmungall

Identify all proxy merges (mappings) and make issues on external ontology trackers

8

We have a bunch of cases like: ``` Uberon:nerve --[sempav:crossSpeciesExactMatch]--> Xenopus:nerve Uberon:nerve --[sempav:crossSpeciesExactMatch]--> Xenopus:peripheral_nerve ``` This means that an external ontology considered two concepts distinct that Uberon believes are the...

matentzn

broken links on download page

2

Uberon download links are broken at https://uberon.github.io/downloads.html#core (2023.09.05-08)

zhilianghu

Addition of OBO shorthands to the RO mirror: to preserve?

1

When mirroring RO (prior to merging it into the `merged_import.owl` module), we currently give it some special treatment: ```Makefile # Probably no reason to merge them first # --add-obo-shorthand-to-properties: remove...

gouttegd

multicellular organism disjoint from organism substance #2421

8

Addresses Issue #2421 . This is in external disjoints file though the two terms are native to Uberon though.

ddooley

add compound tissue term 2

3

**Preferred term label:** Uterine endometrium caruncular **Synonyms** **Definition (free text, please give PubMed ID)** Caruncules on inner lining layer of the uterus. **Parent term (use https://www.ebi.ac.uk/ols/ontologies/uberon)** Uterine **Your nano-attribution (ORCID)**...

zhilianghu

NTRs: gross anatomical part, animal gross anatomical part

3

Add a generic GAP, as discussed in: - https://github.com/OBOFoundry/COB/issues/45 Uberon would also make a metazoan GAP See: - https://github.com/geneontology/go-ontology/issues/22994

cmungall

All equivalence axioms / logical defs must map to a pattern OR be explicitly approved

8

We need a check 1. IF there is a logical def (equiv axiom between NC and CE) 2. AND that does not map to a DP 3. AND it does...

cmungall

add compound tissue term

1

**Preferred term label:** Uterine myometrium **Synonyms** **Definition (free text, please give PubMed ID)** The muscular wall of the uterus that undergoes significant changes in size and cellular properties in specific...

zhilianghu

Restore bgee homology files

1

We used to include a TSV of all anatomical homologies. This is useful for users and also for us (e.g. to coordinate with Bgee if we plan to obsolete a...

cmungall