Add subset tag for CellxGene usage

[dosumis]

Investigate whether we can mine CxG Census to find all CL terms in use on CxG. If yes, build GA pipeline to mine CxG for a CL term list + ROBOT pipeline to tage CL terms with subset tag: cellxgene_subset. (If not possible - request functionality from CxG Census?)

@anitacaron - this is very similar to what we already do for HRA. Can you point @hkir-dev to existing pipelines?

[anitacaron]

The pipeline for HRA is in the ccf-validation-tools. It might be better to use the subset pipeline from ODK, the same as the other subsets here, e.g. eye, kidney, etc.

[anitacaron]

Or generate a component from the ROBOT template.

[hkir-dev]

I prepared an experimental project https://github.com/hkir-dev/cellxgene-cell-reporter

A nightly build GitHub action is generating

• A robot template: https://github.com/hkir-dev/cellxgene-cell-reporter/blob/main/templates/cellxgene_subset.tsv
• An ontology: https://github.com/hkir-dev/cellxgene-cell-reporter/blob/main/cellxgene_subset.owl

@anitacaron how can we integrate this to CL?

[anitacaron]

• [ ] 1. Update the cl-odk.yaml following this example: https://github.com/obophenotype/cell-ontology/blob/bf0391d3a173c552873beab5d202fb5daa95f4c1/src/ontology/cl-odk.yaml#L113-L116

The template file should be in src/templates. ODK will generate the owl file in the src/ontology/components, no need to add it.

• [ ] 2. Inside src/ontology, run sh run.sh make update_repo

• [ ] 3. Add the component URL to the catalog: example https://github.com/obophenotype/cell-ontology/blob/bf0391d3a173c552873beab5d202fb5daa95f4c1/src/ontology/catalog-v001.xml#L21

• [ ] 4. Add the component URL as an import in the cl-edit (in alphabetical order): example Import(<http://purl.obolibrary.org/obo/cl/components/kidney_upper_slim.owl>)

• [ ] 5. Add a rule to update the template in cl.Makefile: the example is downloading a component because there isn't a template, but in your case, you should download the template. (In the next ODK version, this step won't be necessary; we'll be able to just pass the link to an external template in the cl-odk.yaml file) https://github.com/obophenotype/cell-ontology/blob/bf0391d3a173c552873beab5d202fb5daa95f4c1/src/ontology/cl.Makefile#L230-L235

• [ ] 6. Inside src/ontology, run sh run.sh make components/{owl file name} to generate the owl file

Let me know if you need further help.