Automatically pull in HuBMAP 2D images - Githubissues

obophenotype / cell-ontology

An ontology of cell types

https://obophenotype.github.io/cell-ontology/

Creative Commons Attribution 4.0 International

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Automatically pull in HuBMAP 2D images #2785

Open dosumis opened 1 week ago

dosumis commented 1 week ago

Example image here:

https://humanatlas.io/2d-ftu-illustrations?version=2.1&organ=Liver

Includes pub DOI + mapping table to Uberon and CL

Query here:

https://apps.humanatlas.io/api/grlc/#get-/hra/ftu-parts

Response ftu_digital_object,image_url,organ_iri,ftu_iri,ftu_part_iri https://purl.humanatlas.io/2d-ftu/liver-liver-lobule,https://cdn.humanatlas.io/digital-objects/2d-ftu/liver-liver-lobule/v1.2/2d-ftu-liver-liver-lobule.png,http://purl.obolibrary.org/obo/UBERON_0002107,http://purl.obolibrary.org/obo/UBERON_0004647,http://purl.obolibrary.org/obo/CL_1000398

We also need a way to get DOIs @bherr2 - can you let us know how to do this?

[ ] Write Python script to generate a ROBOT template from the output of this query - folding in DOIs.
[ ] Incorporate template into automatic build
[ ] Allow for manual addition of comments mapping annotations to cell types where annotation labels are different.

bherr2 commented 1 week ago

I've updated the ftu-parts query to pull in the FTU DOI as a column, ftu_digital_object_doi. The UI may still show the old query (caching), but the results will now include the doi. Source query is at https://github.com/hubmapconsortium/ccf-grlc/blob/main/hra/ftu-parts.rq