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ontology guide must download and process pinned ontologies #229

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brianraymor opened this issue Oct 11, 2024 · 2 comments
Open

ontology guide must download and process pinned ontologies #229

brianraymor opened this issue Oct 11, 2024 · 2 comments
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5.3 Next minor CELLxGENE schema version after 5.2 dp Data Platform workstream

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@brianraymor
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THIS IS A TEMPLATE AND NOT READY

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The following pinned ontologies MUST be refreshed:

Ontology OBO Prefix Release Download
Cell Ontology CL 2024-08-16 cl.owl
Experimental Factor Ontology EFO 2024-08-15 EFO 3.69.0 efo.owl
Human Developmental Stages HsapDv 2024-05-28 hsapdv.owl
Mouse Developmental Stages MmusDv 2024-05-28 mmusdv.owl
Mondo Disease Ontology MONDO 2024-08-06 mondo.owl
Uberon multi-species anatomy ontology UBERON 2024-08-07 uberon.owl

The following ontologies will not be updated

Ontology OBO Prefix Release Download
Human Ancestry Ontology HANCESTRO 3.0 hancestro-base.owl
NCBI organismal classification NCBITaxon 2023-06-20 ncbitaxon.owl
Phenotype And Trait Ontology PATO 2023-05-18 pato.owl
@brianraymor brianraymor added dp Data Platform workstream 5.3 Next minor CELLxGENE schema version after 5.2 labels Oct 11, 2024
@joyceyan joyceyan self-assigned this Nov 19, 2024
@joyceyan
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@brianraymor I'm closing this out because as far as I understand, only EFO needs to be upgraded from 3.69.0 to 3.71.0. Feel free to re-open the ticket if we want to make additional updates though.

@brianraymor brianraymor reopened this Dec 12, 2024
@brianraymor
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@joyceyan - EFO had to be updated to support the Visium feature. This issue is for 5.3 in general. We always update the pinned ontologies as close to the migration date as possible because there are usually monthly releases.

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5.3 Next minor CELLxGENE schema version after 5.2 dp Data Platform workstream
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