chore: update ontology decendant mappings #116
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Bento007
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Mar 15, 2024
## Reason for Change - #15 ## Changes - add script to generate descendant mapping. It's based off a script in [single-cell-curation](https://github.com/chanzuckerberg/single-cell-curation/blob/main/scripts/compute_mappings/compute_tissue_and_cell_type_mappings.py) - update GHA to install the local API to run generate descendant mapping. ## Testing steps - Added test cases - Compared to tissue_descendants.json and cell_type_descendant.json generating by the single-cell-curation repo. Results: - verified PR is auto generated for decendant mapping updates #116 - Add GHA run every monday at midnight, by workflow_dispatch, or if the ontology assets are updated ``` ------Comparing Ontology Guide and single-cell-curation Cell Type Descendant KEYS: In Ontology Guide not in single-cell-curation {'CL:4030031'} DESCENDANT: In Ontology Guide not in single-cell-curation CL:0000738 {'CL:2000054'} CL:0002320 {'CL:0002554'} CL:0002319 {'CL:4033051', 'CL:4033052'} CL:0000117 {'CL:4033051', 'CL:4033052'} CL:0000057 {'CL:0002554'} CL:0000540 {'CL:4033051', 'CL:4033052'} CL:0000219 {'CL:2000054'} CL:0000542 {'CL:2000054'} CL:0000988 {'CL:2000054'} KEYS: In single-cell-curation not in Ontology Guide None DESCENDANT: In single-cell-curation not in Ontology Guide ``` ## Notes for Reviewer - Terms in the locally generated cell_type_descendants.json not in cellxgene_schema/cell_type_descendants.json - `CL:4030031`: [interstitial cell](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_4030031) - `CL:0002494`: [cardiocyte](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0002494) was recently added to chanzuckerberg/single-cell-data-portal#6756 and chanzuckerberg/single-cell-curation#779. Not sure why it isn't showing up in the old version of the descendant mapping script. --------- Co-authored-by: github-actions <[email protected]>
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