Rescue orphaned ontologies into ODK-backed repos: FIX, REX, VariO, MAMO

[cmungall]

fix, rex, vario, and mamo are orphaned and still depend on missing or pre-GitHub infrastructure. fix and rex recently dropped out of downstream indexing because their PURLs no longer resolved to stable artifacts.

Proposal: seed minimal ODK-backed GitHub repos for these ontologies so they remain resolvable, archivable, and usable for historical mappings and salvage work. These repos can stay clearly marked orphaned and research-only; this is preservation, not reactivation.

In scope:

• fix: orphaned, no repository
• rex: orphaned, no repository
• vario: orphaned, no public repository
• mamo: orphaned, SourceForge repository

Out of scope:

• marking any of these ontologies active
• full content modernization
• policy decisions about adoption or term transfer

fma should be handled separately. It is inactive, not orphaned, already has a Bitbucket repo, and already has an open issue: #21.

Rough plan:

1. Pick a source snapshot for each ontology.
2. Create a minimal GitHub repo for each, seeded with ODK.
3. Publish stable artifacts for indexing and inspection.
4. Update OBO metadata to point to the new repo.
5. Keep the OBO page and repo README explicit about orphaned / research-only status.

Related: #2002 #1637 #1886 #2376 #76

[jamesaoverton]

I believe that the faq/what-is-the-build-field.md doc file is related to this, and it should be revised or removed. I don't feel like I know enough about it to do the revision. @cmungall can you assign someone to update that documentation?

[cmungall]

Yes, somewhat related, though the original build pipeline was for active ontologies, whereas here I am providing homes for orphans

• Remove the build field from all yaml files and remove it from FAQ #2882

[cmungall]

Update: the rescue repos are now live and building.

• vario: https://github.com/cmungall/vario
• rex: https://github.com/cmungall/rex
• mamo: https://github.com/cmungall/mamo
• fix: https://github.com/cmungall/fix

I also checked the raw GitHub URLs that would be the obvious purl.obolibrary.org redirect targets for .owl and .obo. All 8 return HTTP 200:

• https://raw.githubusercontent.com/cmungall/vario/main/vario.owl
• https://raw.githubusercontent.com/cmungall/vario/main/vario.obo
• https://raw.githubusercontent.com/cmungall/rex/main/rex.owl
• https://raw.githubusercontent.com/cmungall/rex/main/rex.obo
• https://raw.githubusercontent.com/cmungall/mamo/main/mamo.owl
• https://raw.githubusercontent.com/cmungall/mamo/main/mamo.obo
• https://raw.githubusercontent.com/cmungall/fix/main/fix.owl
• https://raw.githubusercontent.com/cmungall/fix/main/fix.obo

Proposed next step, if OBO maintainers are in agreement:

• update OBO metadata for these ontologies so repository points to the new GitHub repos
• update OBO metadata so tracker points to the respective GitHub issue trackers
• update the OBO PURL config so purl.obolibrary.org/obo/{id}.owl and .../{id}.obo redirect to the corresponding raw GitHub URLs above

We are happy to do the metadata and PURL work; we just need agreement from OBO maintainers on this direction.

[cmungall]

in case it's not obvious I am using agents here. I usually curate responses more but I decided this is a straightforward procedural task so I just forged ahead

[matentzn]

update the OBO PURL config so purl.obolibrary.org/obo/{id}.owl and .../{id}.obo redirect to the corresponding raw GitHub URLs above

I think this should be done regardless of what anyone says:

• rex: do it because you are anyways hosting it
• fix: do it, again supposedly managed by you. I tried to find the fix file in the chebi ftp and its not there. no brainer
• mamo does not have a PURL config at all. But I am a bit unsure about this one because it clearly exists, with recent activity: https://sourceforge.net/p/mamo-ontology/code/HEAD/tree/tags/latest/
• vario: is a bit more problematic. it does have working PURLs, to a working website from 100 years ago.

So for now, I would say:

1. create PURL config for mamo but for the moment link to https://sourceforge.net/p/mamo-ontology/code/HEAD/tree/tags/latest/. I will reach out to the latest committer and see if we can get them to cede the repo to you.
2. Update rex and fix to your new repos. These dont appear problematic since you personally have anyways managed their PURLS. Post about this in #chemistry subchannel with a note that this was previously handled by Chebi and you are happy to hand it over to a CHEBI person if they so want to reclaim it. Update the md files also - the repository links are just a logical consequence of the PURL configs.
3. For Vario we do need to ask @maunov. I would leave that for later until he had a chance to way in.

[StroemPhi]

For FIX and REX @cthoyt has updated the PURL redirects in OBOFoundry/purl.obolibrary.org#1122 to point to @cmungall's repos two weeks ago, but they still don't resolve to there. Is there anything else that needs to be done to fix this?

[matentzn]

Are you sure? Both seem fine to me:

• http://purl.obolibrary.org/obo/fix.owl
• http://purl.obolibrary.org/obo/rex.owl

[StroemPhi]

Ok, now they work. They didn't this morning.