Require `repository` for new ontologies

[cthoyt]

Currently, only an issue tracker is required. I think it makes sense to also require new ontologies to provide a repository (e.g., on GitHub (highly preferred), GitLab, BitBucket, etc.)

Implicitly, this will encourage all new ontologies to use a public repository as their main place for curation.

This was motivated by the recent new ontology request for ELO (#1729), which did not include a repository. It seems to be the case that a potential submitter is not aware this is important, because it is not included in the form.

[matentzn]

Yes I agree with this. Every ontology should have a repo. Sometimes, this differs from the issue tracker, for example, if groups keep projects in separate repos but want issues in a specific community facing repo. What needs doing to achieve this? Which ontologies currently in OBO do not have a repository?

[cthoyt]

Only the following three non-obsolete, non-orphaned, non-inactive repositories are missing a repository annotation:

Prefix	Contact	Email
fma	Onard Mejino	mejino@u.washington.edu
mamo	Nicolas G	xxx@gmail.com
ogg	Yongqun Oliver He	yongqunh@med.umich.edu

1. FMA: I have recently been in contact with Onard Mejino via email to figure out what his GitHub handle is. He said he's technology illiterate and I gave him a couple options on how to move forward, but I am worried that this will be very slow. The homepage for FMA is listed as the legacy sourceforge issue sub-tracker for OBO (https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/)
2. MAMO: I have also tried to get in touch with Nicolas G regarding MAMO unsuccessfully (email sent Jan 1.). It's hosted on SourceForge at https://sourceforge.net/projects/mamo-ontology/, with the last update in 2020. I guess that could work
3. OGG: I think that https://bitbucket.org/hegroup/ogg could be used as a repository for OGG.

Given that effectively all ontologies already have this field, I think that this is a pretty sure-fire thing to promote to required.

Expand to see the code that was used to generate this table

```python from tabulate import tabulate from bioregistry.external.obofoundry import get_obofoundry def main(): rows = [] for prefix, data in get_obofoundry().items(): if data.get("inactive") or data.get("deprecated"): continue repository = data.get("repository") if repository is not None: continue rows.append(( prefix, data.get("contact.label"), data.get("contact"), f"@{data['contact.github']}" if "contact.github" in data else "", data.get("activity_status"), )) print(tabulate(rows, tablefmt="github", headers=["Prefix", "Contact", "Email", "GitHub", "Status"])) if __name__ == '__main__': main() ```

[cthoyt]

I proposed a fix for these three ontologies as well as an accompanying update to the schema in #1741. Merge on that should wait on people having a chance to comment on this, but I think it's pretty uncontroversial so maybe give it until the end of the week.

[matentzn]

I think we are good with MAMO and OGG as you suggest.

[nlharris]

Do we need to discuss this on a call?

[lschriml]

Yes

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On Jan 24, 2022, at 7:16 PM, Nomi Harris @.***> wrote:

 Do we need to discuss this on a call?

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