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[bioontology-support] MI update on Bioportal?

John Zobolas john.zobolas at ntnu.no
Mon Feb 11 02:20:16 PST 2019


Hi Jennifer and Pablo,


This issue was found by Vasundra when she saw that terms like 'indirect causal regulation' are still mentioned in the BioPortal GUI (see here<https://bioportal.bioontology.org/ontologies/MI/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMI_2246&jump_to_nav=true>).

If you ask the BioPortal API for the same term and ontology, you get the same data (you will probably need an api- key to see this): http://data.bioontology.org/search?q=indirect%20causal%20regulation&ontologies=MI. Note also that the results that are returned with this API are automatically filtered to obsolete": false,so they are not obsolete :)


In the latest version of the MI ontology<https://www.ebi.ac.uk/ols/ontologies/mi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMI_2233> though these terms are obsolete/deleted (I took the files from http://obofoundry.org/ontology/mi.html)<http://obofoundry.org/ontology/mi.html>​:


.obo file

[Term]
id: MI:2246
name: indirect causal regulation
def: "The effect of a modulator entity A on a modulated entity B that  occurs when A is not immediately upstream of B." [PMID:15845847]
subset: PSI-MI_slim
synonym: "indirect" EXACT PSI-MI-alternate []
synonym: "indirect causal regulation" EXACT PSI-MI-short []
is_obsolete: true
created_by: ppm
creation_date: 2017-01-19T15:45:44Z

.owl file:

<oboInOwl:created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ppm</oboInOwl:created_by>
        <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2017-01-19T15:45:44Z</oboInOwl:creation_date>
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">indirect</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">indirect causal regulation</oboInOwl:hasExactSynonym>
        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PSI-MI</oboInOwl:hasOBONamespace>
        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MI:2246</oboInOwl:id>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/mi#PSI-MI_slim"/>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">indirect causal regulation</rdfs:label>
        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>



Jennifer, it seems thus that there has to be a synchronization problem from your side then? (since Pablo has checked that both versions of the ontology are pretty much up to date). Or there could be another issue that does not allow you to get the latest version? Might I suggest also that you pull from the .obo version of the MI ontology since it is the one Pablo actively maintains (this is the Github link<https://github.com/HUPO-PSI/psi-mi-CV> I think you want)?

BR, John.
________________________________
From: Pablo Porras Millan <pporras at ebi.ac.uk>
Sent: Monday, February 11, 2019 10:46 AM
To: John Zobolas
Cc: support at bioontology.org; Vasundra Touré; Jennifer Leigh Vendetti; Sandra Orchard
Subject: Re: [bioontology-support] MI update on Bioportal?

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><mailto:vendetti at stanford.edu>
Sent: Friday, February 8, 2019 9:45 PM
To: John Zobolas
Cc: support at bioontology.org<mailto: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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--
------------------------------------------------------
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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