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EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI
http://www.ebi.ac.uk/ols
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PSI-MS not updated #509

Closed ypriverol closed 2 years ago

ypriverol commented 2 years ago

Dear @henrietteharmse

The following ontology PSI-MS https://www.ebi.ac.uk/ols/ontologies/ms hasn't been updated in a long time:

Version in Web: 21-11-2019 Current Version: 24:09:2021 00:00 (https://github.com/HUPO-PSI/psi-ms-CV/blob/f5edf2072ca7e6f74b747ddc268b40b2cd087f66/psi-ms.obo#L3)

The Ontology is under active update here: https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo

Best REgards Yasset

henrietteharmse commented 2 years ago

@ypriverol

The MS ontology has last been loaded on 27 Oct 2021. image

The issue is that OBO configuration states that the ontology_purl for MS is http://purl.obolibrary.org/obo/ms.owl.

See MS OBO config

If you can get that updated to point to the new URL, OLS will be able to pick it up from there.

matentzn commented 2 years ago

(FYI the MS purl was updated on the 27 October, so now it points to the hopefully right URL):

https://wheregoes.com/trace/202110247350/

henrietteharmse commented 2 years ago

@matentzn Thanks that is helpful. @ypriverol MS is in fact up to date on OLS based on the version number: 4.1.62

ypriverol commented 2 years ago

The url of the project that gets updated every week is https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo This is the formal HUPO-PSI project.

matentzn commented 2 years ago

This is not an OLS issue though, you need to take this up with the OBO foundry: for the OBO Foundry, the OWL version of the ontology is the only thing that matters, so when you update the OBO file, you need to update the OWL file as well..

ypriverol commented 2 years ago

Can you help us to make this automatically?

matentzn commented 2 years ago

Of course. This is for example how APO does it: https://github.com/obophenotype/ascomycete-phenotype-ontology/blob/master/.github/workflows/release.yml

using GitHub actions.. Whenever the OBO gets updated, the OWL gets updated automatically.

ypriverol commented 2 years ago

I will leave this open until we solve it, if that ok for you.

matentzn commented 2 years ago

You could move this to the PSI MS tracker and tag me in it, just so that @henrietteharmse don't stumble over this ticket here thinking they need to address it, I am happy to help you over there.

henrietteharmse commented 2 years ago

@ypriverol Please can you use the .owl file rather than .obo file? Currently OLS is using https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.owl.

cmungall commented 2 years ago

There is already an issue on the MS tracker: https://github.com/HUPO-PSI/psi-ms-CV/issues/26