Move the source of truth for HubMaps HRA subset to Uberon itself

[matentzn]

We have this goal in uberon.Makefile:

HRA_SUBSET_URL="https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/UB_ASCTB_subset.owl"
$(TMPDIR)/hra_subset.owl:
	wget $(HRA_SUBSET_URL) -O $@

This creates a significant dependency of Uberon to a file totally outside of our control.. Look at this example statement. Isnt it a bit risky that some outside consortium is allowed to add taxon constraints which could potentially break the Uberon build? Also, who can tell if this subset goes stale, or moves location (since its not even linked to a PURL.

    <!-- http://purl.obolibrary.org/obo/UBERON_0000209 -->

    <Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000209">
        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
    </Class>

I vote for the source of truth of this subset to be moved to Uberon, and hubmap developers updating it here.

[matentzn]

Similar to a719af2

[anitacaron]

The subset is generated during a validation pipeline in the HuBMAP repository. It would be harder to keep the subset updated, but I can do it.

[matentzn]

Maybe before you do it, decide on a strategy with your hubmap colleagues on this.. And the rest of the Uberon team! Maybe I am overreacting here, and having an externally maintained dependency is ok.

[anitacaron]

The EBI team manages this subset, so it's Aleix and me only.

[matentzn]

So this pipeline, how complex is it? can it run in a GitHub action?

[anitacaron]

It's simple but needs to grab the terms from 30+ spreadsheet tables, etc. Everything is done in a GH Action every week now.

[matentzn]

Ok leave it as is then.. I don't want the uberon pipeline to be more complex than necessary now that it has been simplified so nicely! Lets close this issue and thanks for the explanations!

[anitacaron]

I want to add this in the odk config file, but it's not working correctly now. I need to check this later.

[anitacaron]

This is the plan. #2975