Ray Stefancsik

Refining the Uberon Euarchontoglires subset -- part 2

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### Remaining tasks - [x] UBERON:4x series in > UBERON:4x --> mixed, I think this is a small enough subset to look over quickly and add TCs. There will be...

Update the definition of 'delaminated'

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The text definition of `PATO:0001514 delaminated` does not fit community usage. Related to https://github.com/obophenotype/upheno/pull/851

of PATO:0002175 to spatial deviation. If applied, this commit will fix #520.

Rename 'PATO:0002175 deviation' to 'spatial deviation' to make the label less ambiguous. This was requested at the [Phenotype Ontology Working Group meeting on 7/14/2022](https://docs.google.com/document/d/1WrQanAMuccS-oaoAIb9yWQAd4Rvy3R3mU01v9wHbriM/edit#heading=h.60i01y4j8hwg) in the context of [PR #854](https://github.com/obophenotype/upheno/pull/854)

Change the hierarchy of [PATO:0001509 functionality](https://www.ebi.ac.uk/ols/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0001509) to the following: * decreased functionality * insufficient non-functional ? Remove 'decreased functionality' from under functional. Add comment in patterns: 'functional' should not be...

Make 'herniated into' and 'herniated out of' the child terms of - [PATO:0000643 'herniated'](https://www.ebi.ac.uk/ols/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0000643). - [PATO:0002163 'herniated into'](https://www.ebi.ac.uk/ols/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0002163) - [PATO:0002167 'herniated out of'](https://www.ebi.ac.uk/ols/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0002167) This suggestion was made during a [Phenotype...

- [ ] create new term `prolapsed` - [ ] make it a child of [PATO:0000623 exserted](https://www.ebi.ac.uk/ols/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0000623) This term request is based on [community feedback](https://docs.google.com/document/d/1WrQanAMuccS-oaoAIb9yWQAd4Rvy3R3mU01v9wHbriM/edit#heading=h.eacsokhdqz0d) on the phenotype pattern template...

Clarify in PATO the distinction between mislocalised and dislocated

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Clarify the distinction between [mislocalised PATO:0000628](https://www.ebi.ac.uk/ols/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0000628) and [dislocated PATO:0001852](https://www.ebi.ac.uk/ols/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0001852). See [comment]((https://github.com/obophenotype/upheno/pull/829#issuecomment-1138747275) * [position PATO:0000140](https://www.ebi.ac.uk/ols/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0000140&lang=en&viewMode=PreferredRoots&siblings=false) A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to...

### Shapes, curves, spatial patterns, deviation in PATO * PATO:0000052 shape [A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points,...

Restructure density classes

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This issue is related to DOSDP phenotype pattern [Irregular density of anatomical entity](https://github.com/obophenotype/upheno/issues/797) utilising [PATO:0002141 irregular density](https://www.ebi.ac.uk/ols/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0002141). Proposals from the [Phenotype Ontology Working Group on 2022-03-10.](https://docs.google.com/document/d/1WrQanAMuccS-oaoAIb9yWQAd4Rvy3R3mU01v9wHbriM/edit#) - [ ] Split...