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[bioontology-support] MI update on Bioportal?

Pablo Porras Millan pporras at ebi.ac.uk
Mon Feb 11 01:46:05 PST 2019


Hi John,

We do not generate the ontology as an owl file, this must be 
automatically generated from the obo file we actively maintain. If there 
is a problem ,it probaly comes from the frequency of the conversion 
between obo and owl.

In any case, I was checking through the changes in the owl file and it 
seems, as far as I cantell, to be more or less up to date. I see that 
terms such as 'indirect causal regulation' are correctly marked as 
'deprecated' or 'obsolete'. Can you please bespecific about hte changes 
you were expecting to see but are not there? Just to be sure there is 
really a synchronization problem and not an update one on our side.

Cheers,

Pablo.

On 09/02/2019 09:35, John Zobolas wrote:
>
> ​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 theOBOfoundry page 
>> <http://obofoundry.org/ontology/mi.html>is updated but theBioPortal 
>> 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>
>> -------------------------------------------------------
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu 
>> <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>

-- 
------------------------------------------------------
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
URLs:   www.ebi.ac.uk/about/people/pablo-porras-millan
	www.ebi.ac.uk/intact
	www.ebi.ac.uk/complexportal
-------------------------------------------------------

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