uberon

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Create design pattern documentation

2

I have created a new document where all design patterns can be documented. Moreover, I have included a paragraph in the Uberon editor SOP with a link to the new...

aleixpuigb

“muscle layer of X” vs “X smooth muscle”

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There are several cases in Uberon of an organ _X_ for which we have both a term like “muscle layer of _X_” and “X smooth muscle”. For example, we have...

gouttegd

The Human placenta in Uberon

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The current representation of placenta in Uberon, does not reflect the human anatomy. [The following edits have been proposed/requested to make the placenta Human aligned](https://docs.google.com/presentation/d/1HXW6nB2qzovSL6HXcvlBkiVeezvp01vn/edit?usp=sharing&ouid=104076693337416907799&rtpof=true&sd=true). The major points are: -...

aleixpuigb

Fix 'oviduct' text definition and revise subclasses

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**Uberon term** UBERON:0000993 [oviduct](https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0000993) **Suggested revision and reasons** A tube or collection of tubes in an animal that connects the ovary to the uterus. [PMID:27875265](https://joe.bioscientifica.com/view/journals/joe/232/1/R1.xml) There are some tissues that...

aleixpuigb

UBERON:0012441 endothelium of peritubular capillary : missing relationship

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UBERON:0012441 endothelium of peritubular capillary AND CL:1001033 peritubular capillary endothelial cell do not have direct relationships [Term] id: UBERON:0012441 name: endothelium of peritubular capillary namespace: uberon def: "An endothelium that...

ANiknejad

NTR: Fish Vent

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**Preferred term label:** Fish vent **Synonyms** **Definition (free text, please give PubMed ID)** The external opening which opens to the reproductive and digestive tracts of the fish. During spawning, the...

Anoosha-Sehar

Filter and reconcile the Biomappings set using sssom-cli

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This PR is a follow-up to #3141. It particularly addresses [this comment](https://github.com/obophenotype/uberon/pull/3141#discussion_r1419489287) by using the `sssom-cli` tool rather than a `sed`-based hack to filter out non-Uberon mappings. It also “reconciles”...

gouttegd

lacrimal

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**Uberon term** [lacrimal](http://purl.obolibrary.org/obo/UBERON_3010146): UBERON:3010146 and [lacrimal bone](http://purl.obolibrary.org/obo/UBERON_0001680) UBERON:0001680 **Bug description** Both terms exist in Uberon but do not seem that different. Should one be used over the other?

meghalithic

Infer all missing part-of relations using rules or the GCI-materialize approach

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Example of a problem: There should be a part-of between cingulum-of-molar and crown-of-molar (because a cingulum is part of a crown) The existing part-of (which comes from relaxation) is correct...

cmungall

Regenerated allen atlases

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Note there is a spurious diff in here - it makes it look like some IDs were deleted; just order shuffling (sorry, should have normalized ordering)

cmungall