obsolete mirnao

[cmungall]

As per #546, we have had no working home page or download or PURL for this for a number of years

[rvita]

Pantelis Topalis replied to my request for an owner for mirnao and did not indicated that it should be obsoleted. he gave me the license info that I updated for it. I am in the process of finishing up (today, right now) the remaining metadata info that I obtained as part of the OBO services grant.

[cmungall]

If it's not obsolete then it needs to be resolvable, I am happy to help Pantelis set up a github repo

[cmungall]

This still does not resolve, it should be obsoleted

[rvita]

Pantelis Topalis topalis@imbb.forth.gr is the person who was giving me info on mirnao and agreed to be its contact person. I cannot find him on github to link to this ticket.

[matentzn]

@rvita What should be done about this PR?

[bpeters42]

If I remember correctly, we can revert the status of 'obsolete' for an ontology, in case we do so in error, without many implications. So I would go ahead an mark the ontology as obsolete to a) stop people coming in from using it if it is not maintained and b) trigger the maintainers to respond in case they disagree. - Bjoern

…

On Sun, Aug 4, 2019 at 11:49 PM Nico Matentzoglu ***@***.***> wrote: @rvita <https://github.com/rvita> What should be done about this PR? — You are receiving this because your review was requested. Reply to this email directly, view it on GitHub <#789?email_source=notifications&email_token=ADJX2ITKHDFXNHQJSTZPAKDQC7ERFA5CNFSM4GKQ54PKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3Q3LMA#issuecomment-518108592>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADJX2IQCPD2H6L6G53W2F63QC7ERFANCNFSM4GKQ54PA> .

-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

[rvita]

I still do not think it should be obsoleted if someone claimed it and is actively answering questions about it. there are still many ontologies that do not have their complete set of metadata (including many that have not yet been contacted - I am doing them in batches) and this is just one of them. Maybe we need to decide upon a time frame that each ontology must become compliant in once it has been contacted with specific missing requirements before it is deemed orphaned or obsoleted? My understanding was they would get a validation report initially? I never told Pantelis that there was a due date.

[bpeters42]

This one was not triggered due to missing metadata, but due to the fact that the ontology itself has been unavailable.

…

On Tue, Aug 6, 2019 at 7:46 AM rvita ***@***.***> wrote: I still do not think it should be obsoleted if someone claimed it and is actively answering questions about it. there are still many ontologies that do not have their complete set of metadata (including many that have not yet been contacted - I am doing them in batches) and this is just one of them. Maybe we need to decide upon a time frame that each ontology must become compliant in once it has been contacted with specific missing requirements before it is deemed orphaned or obsoleted? My understanding was they would get a validation report initially? I never told Pantelis that there was a due date. — You are receiving this because your review was requested. Reply to this email directly, view it on GitHub <#789?email_source=notifications&email_token=ADJX2IRUXMJ22UEWRMIFJ7TQDGFDNA5CNFSM4GKQ54PKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3VMEZA#issuecomment-518701668>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADJX2IXUPV3WKG64VO6YZ73QDGFDNANCNFSM4GKQ54PA> .

-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

[jamesaoverton]

I emailed topalis@imbb.forth.gr, cc @cmungall, offering to help migrate to GitHub, and asked for a reply within two weeks. If we don't hear back, we'll mark this as obsolete.

[rvita]

I emailed topalis@imbb.forth.gr In July and in Aug 2019 about this topic and he never responded. Based on his answer for IDOMAL, I think you can go ahead & obsolete. The only other contact I could find for mirnao was Vicky Dritsou who was stated to be no longer working on it byPantelis.

[jamesaoverton]

I received a reply saying that we should obsolete, so I'm going to merge this.

Do we have any interest in salvaging the OWL file and putting it somewhere?

[althonos]

I know that there is no real schema for the ontologies.yml file, but until now all ontologies had an activity_status. This PR removed it for mirnao, but for consistency it should still have activity_status; inactive (or activity_status: orphaned) I assume.

[jamesaoverton]

Thanks @althonos! I reinserted activity_status: inactive here cf47685.

This was my oversight, and the validation didn't catch it.

We do have schemas for several fields, including activity_status here util/schema/. However when is_obsolete is true we don't apply most of those schemas, see validate-metadata.py.

We have an issue for better documenting activity status and obsolete #1126, and this is the general issue for schemas #663. I'll make a note about this specific problem on #663.

[althonos]

@jamesaoverton : thanks !

I'm trying to maintain a Rust library to deserialize the ontologies.yml, and it's quite strict, so that's how I catch these kind of issues. Good to know that obsolete ontologies are not required to have all fields.