griffithlab
Register CIViC Entity Prefixes
Recently, CIViC registered civic.aid and civic.eid for assertions and evidence items, respectively. @malachig is considering registering gene -> civic.gid and variant -> civic.vid.
CIViC entities in MetaKB are being revised (previously under a civic:<type><number>) to accommodate these changes.
It would be beneficial to downstream resources such as MetaKB to have a set of shared prefixes available for other CIViC entity types as needed, including:
- variant group
- source
- disease
- drug
- phenotype
- clinical trials
- variant type (currently limited to Sequence Ontology concepts)
Relevant to this discussion is the CIViC table of Entity Macros: https://civic.readthedocs.io/en/latest/using/comments.html#comment-macros
Decision from 8/19:
assertion -> civic.aid
evidence -> civic.eid
gene -> civic.gid
variant -> civic.vid
disease -> civic.did
drug -> civic.tid (forward looking to Therapeutic intervention in v2)
variant group -> undecided for now, possibly a revised structure in v2
all other above concepts have a 1:1 correspondence to an external ID
On the topic of CURIE. Here are the two registered so far: https://registry.identifiers.org/registry/civic.aid https://registry.identifiers.org/registry/civic.eid
Also want to cross link this issue with these related development issues: https://github.com/griffithlab/civic-client/issues/1353 https://github.com/griffithlab/civic-client/issues/1358
I also submitted the request for civic.vid
Currently it doesn't seem like I can request for disease or therapy/drug, because identifiers.org requires a working example URL for each entity. But I can't currently do something like:
- https://civicdb.org/links/disease/{$id}
- https://civicdb.org/links/drug/{$id}
It seems like that functionality needs to be in place and point to something real before we can register a prefix. So, this will need to wait for CIViC V2 (where disease and drug will become first class entities) to be completed?
We can set up the links right now, that's very straightforward, but yeah... they'd need something to point to and we don't have drug or disease landing pages in 1.5. I will set up the link handling in 2.0 so its ready day one though, I've already ported the rest of that logic over so it won't take long.
Added this functionality to v2 here: https://github.com/griffithlab/civic-v2/commit/a2d13732307ddc0e99c6c7f2d8370c399b6e47cc
Update on this: assertion -> civic.aid -> https://registry.identifiers.org/registry/civic.aid evidence -> civic.eid -> https://registry.identifiers.org/registry/civic.eid gene -> civic.gid -> https://registry.identifiers.org/registry/civic.gid variant -> civic.vid -> https://registry.identifiers.org/registry/civic.vid disease -> civic.did -> request submitted and pending drug -> civic.tid -> request submitted and pending source -> civic.sid -> request submitted and pending
Somehow I think the requests for did, tid and sid did not go through. Will have to reattempt.
Okay we now have requests submitted for did, tid, and sid. And this time I got confirmation emails.
Still to be done. We will also need to request one for molecular profiles and then I think that will be it.
Molecular Profile -> could be civic.pid (for "profile" id) or civic.mpid.
Variant Group -> could be civic.vgid (we decided to keep variant groups alive in CIViC)