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[bioontology-support] MI update on Bioportal?

John Zobolas john.zobolas at ntnu.no
Sat Feb 9 01:35:32 PST 2019


?Hi Pablo,


See the issue below. Maybe the .owl file that they pull is not the one with the changes?


BR, John.

________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Friday, February 8, 2019 9:45 PM
To: John Zobolas
Cc: support at bioontology.org; Vasundra Touré
Subject: Re: [bioontology-support] MI update on Bioportal?

Hello Pablo & Vasundra,

BioPortal provides functionality that gives end users the ability to enter a URL that is checked on a nightly basis for new versions of their ontology. The MI ontology entry in BioPortal is currently configured to check the following URL nightly:

http://purl.obolibrary.org/obo/mi.owl

We got this URL from your OBO Foundry page.

One thing to note here is that we are currently serving the OWL version of your ontology. The GitHub URL you provided below references the OBO version of your ontology. Is the implication here that you'd rather we be serving the OBO version, and have our system configured to pull from GitHub?

Thanks for any clarification you can provide here.

Kind regards,
Jennifer




On Feb 8, 2019, at 3:57 AM, John Zobolas <john.zobolas at ntnu.no<mailto:john.zobolas at ntnu.no>> wrote:


Hi,

The issue is that the MI ontology in the OBOfoundry page<http://obofoundry.org/ontology/mi.html> is updated but the BioPortal version?<https://bioportal.bioontology.org/ontologies/MI> in not synced yet to the current/newest version. Could you please update it?

BR, John
________________________________________
From: Pablo Porras Millan <pporras at ebi.ac.uk<mailto:pporras at ebi.ac.uk>>
Sent: Friday, February 8, 2019 12:41 PM
To: Vasundra Touré; Sandra Orchard (orchard at ebi.ac.uk<mailto:orchard at ebi.ac.uk>)
Cc: John Zobolas
Subject: Re: MI update on Bioportal?

Dear Vasundra,

I have no idea how BioPortal gets updated, but our reference github repo
is up to date and shows the latest version of the CV in OLS:
https://www.ebi.ac.uk/ols/ontologies/mi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMI_2233.
Our OBOfoundry page also seems tobe up to date
(http://obofoundry.org/ontology/mi.html).

We have never updated BioPortal manually and I am certainly not willing
to start now, so I assume they have some sort of procedure to do these
updates. Can you use an alternative source for theCV?

Cheers,

Pablo.



On 08/02/2019 08:28, Vasundra Touré wrote:
> Dear Pablo and Sandra,
>
> I have looked at the MI terms in Bioportal and it seems like they are
> not updated. (see Causal Regulatory Mechanism branch
> https://bit.ly/2DYI5VM).
>
> Isn't it suppose to be an automatic update from Bioportal? Or do you
> have to submit the changes from your side?
>
> Just wanted to point out this issue.
>
> Thanks!
>
> Best regards,
> Vasundra
>

--
------------------------------------------------------
Pablo Porras Millán, Ph.D.
Molecular Interactions Team Coordinator
European Molecular Biology Laboratory
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel:    +44 1223 494482
email:  pporras at ebi.ac.uk<mailto:pporras at ebi.ac.uk>
URLs:   www.ebi.ac.uk/about/people/pablo-porras-millan<http://www.ebi.ac.uk/about/people/pablo-porras-millan>
        www.ebi.ac.uk/intact<http://www.ebi.ac.uk/intact>
        www.ebi.ac.uk/complexportal<http://www.ebi.ac.uk/complexportal>
-------------------------------------------------------

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