Register CIViC Entity Prefixes

[ahwagner]

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)

[ahwagner]

Relevant to this discussion is the CIViC table of Entity Macros: https://civic.readthedocs.io/en/latest/using/comments.html#comment-macros

[ahwagner]

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

[ahwagner]

@malachig to register these

[kkrysiak]

civic.aid and civic.eid are complete

[malachig]

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:
#1353
#1358

[malachig]

Submitted request for civic.gid

[malachig]

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?

[acoffman]

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.

[acoffman]

Added this functionality to v2 here: griffithlab/civic-v2@a2d1373

[malachig]

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

[malachig]

Somehow I think the requests for did, tid and sid did not go through. Will have to reattempt.

[malachig]

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)