Add prefix `cellguide`

[anitacaron]

Prefix

cellguide

Name

Cell Guide

Homepage

https://cellxgene.cziscience.com/cellguide

Source Code Repository

bioregistry

Description

CellGuide is a comprehensive resource for knowledge about cell types.

License

No response

Publications

No response

Example Local Unique Identifier

CL_0002623

Regular Expression Pattern for Local Unique Identifier

No response

URI Format String

No response

Wikidata Property

No response

Contributor Name

Anita Caron

Contributor GitHub

anitacaron

Contributor ORCiD

https://orcid.org/0000-0002-6523-4866

Contributor Email

No response

Contact Name

No response

Contact ORCiD

No response

Contact GitHub

No response

Contact Email

No response

Additional Comments

The intention is to create cross-reference links in the Cell Ontology to Cell Guide pages.

[cthoyt]

@anitacaron this looks like CL identifiers? So do you want to add cellguide as a synonym for CL?

[anitacaron]

No, we want to add them as a cross-reference.

[cthoyt]

Okay, https://github.com/biopragmatics/bioregistry/issues/new?assignees=cthoyt&labels=Provider%2CNew&projects=&template=new-provider.yml&title=Add+provider+for+CL&prefix=cl might be more appropriate issue template to more directly say "cellguide is a place that resolves CL identifiers, like in https://cellxgene.cziscience.com/cellguide/CL_0001061" since cellguide is not itself a resource that mints its own identifiers

[cthoyt]

@anitacaron here's the solution I have so far:

1. I added cellguide as an alternate provider for CL. This appears on https://bioregistry.io/cl at the bottom like in
2. You can use the Bioregistry's provider support in the resolver to write links like https://bioregistry.io/cl:0000062?provider=cellguide

Is this sufficient?

[anitacaron]

@dosumis can you comment here, please?

[dosumis]

Solution makes sense to me. My main aim is to have a way to use CURIES to specify links from CL terms to CellGuide - particularly in OLS4 - which I believe uses the bioregistry as a generic way to control resolution from xrefs. @udp - could you comment on OLS4 use of bioregistry and whether it could support @cthoyt's solution?

[cthoyt]

It would be great if we could move this to the OLS tracker, since it's a pretty substantial feature request for them. I think the idea would be that for any ontology that has additional providers in the Bioregistry, that you could have some kind of configuration that tells the OLS to display an additional link on that page for the provider.

I opened a new place for discussion on https://github.com/EBISPOT/ols4/issues/601 and will close this one as complete

[dosumis]

There is a potential problem with this solution - these linkouts don't necessarily work for every term in the ontology. In the case of cellguide, only a minority of CL terms have a page (those used in annotation or superclasses of those used in annotation). For XREF based links, we've run pipelines in the past using shared linkout tables to add xrefs only where content is present on the other site. With the above solution, I think we would need a way to tag terms (a dynamic approach, testing for resolution at build time would presumably be way too slow).