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hubmapconsortium / ccf-ontology

CCF Ontology v2.x
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EPIC - ontology fixes for alpha20 #15

Open dosumis opened 2 years ago

dosumis commented 2 years ago
  1. Add more preferred roots for other branches (e.g. sample metadata)
  2. Cell type with temp IDs: i. Add comment to all warning that these are temporary placeholder terms based on expert recommendation and that they are not stable. Consider putting this in the definition field so that it is prominent.
    ii. --> Add to logical model? TBD
  3. Fake - CL, Uberon and FMA terms: i. Validate (is the term in UberGraph). Anita is already doing this - but we need to dump to a simple list of IRIs in a file that Josef can use. Josef will supplement this with a list of terms absent from FMA. ii. Add Robot filter step to remove terms that do not validate (are not in UberGraph) - as part of the release pipelines.
  4. Review preferred roots - should some unpopulated roots be present? TBD
  5. Update description.
    • Currently "This ontology models the common coordinate framework used in the human reference atlas."
    • Suggested: "This ontology provides a view of the Uberon anatomy ontology and the Cell Ontology based on expert reviewed content provided by the HubMap project. Cell Ontology terms are linked to sets of expert-specified cell type markers, recorded using HGNC identifiers and metadata."