Nico Matentzoglu

Do not merge: Test release of Uberon with ODK 1.5.1

1

All updated files according to `make uberon`.

Fixes #369. The examples for the predicate_id slot where in the wrong slot (predicate_label), here we move them to be correct. I have also added a single example for the...

Fix capitalisation typo in increased ccc count pattern

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As we face out the use of CARO, we need to update the corresponding patterns from CARO: cellular organism to the UBERON: multicellular organism for "whole organism" patterns.

Ensure that all TOP level HPO and MP terms have corresponding uPheno classes

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Please review MP and HPO and figure out if they have corresponding uPheno classes. HP top level classes: MP top level classes: Ideally create a table in Google sheets. Ask...

Investigate why "uPheno:circulatory system phenotype" and "uPheno: integumental system phenotype" do not exist..

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... despite the existence of XPO:abnormal circulatory system. @rays22 can you check if XAO: circulatory system is mapped to Uberon:circulatory system, and if not add that mapping to Uberon? Some...

Depends on #948 @ar-ibrahim if you can keep this in your todolist and keep reminding me about it! Thanks!

Some plural labels do not work

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https://github.com/obophenotype/upheno/blob/222be547e229e2cccc2b30a50905f0a852cd8ea9/src/patterns/dosdp-dev/abnormalHasFewerPartsOfTypeAnatomicalEntity.yaml#L34 For terms like "anatomical entity", the synonym becomes "anatomical entitys" which is obviously bad. We may need to deal with that somehow.

Migrate sssom validation to new LinkML validation framework

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Blocked by: - [ ] https://github.com/linkml/linkml/issues/2115 (not imperative, but annoying - [x] https://github.com/linkml/linkml/issues/2164 (important, needs fixing) - [x] https://github.com/linkml/linkml/issues/2116 - [x] https://github.com/linkml/linkml/issues/2117 (not really fixed, see https://github.com/orgs/linkml/discussions/1975, but I implemented...

Context: The original dataclass parser catches this: ``` WARNING:sssom.parsers:One mapping in the mapping set is not well-formed, and therfore not included in the mapping set ({'subject_id': 'NANDO:2200355', 'subject_label': 'Isolated ACTH...