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[bioontology-support] MI update on Bioportal?

Pablo Porras Millan pporras at ebi.ac.uk
Mon Feb 11 13:47:10 PST 2019


Many thanks for your help, Jennifer. We will keep an eye on this and 
pass through any issues that our users report.

Best regards,

Pablo.

On 11/02/2019 21:20, Jennifer Leigh Vendetti wrote:
> Hi John et al.,
>
> It sounds like the OBO version of MI in GitHub is the one that’s more 
> actively maintained, so I went ahead and modified BioPortal to serve 
> that version. I also configured the MI ontology entry to check your 
> GitHub URL [1] on a nightly basis for new versions. We have a number 
> of ontologies that are configured this way, so I don’t anticipate 
> problems with pulling new versions. However, if anyone notices 
> something awry, please feel free to contact us via the support list 
> and we’ll look into it ASAP.
>
> The new upload is finished processing in BioPortal. The “indirect 
> causal regulation” class no longer appears in the tree in the 
> BioPortal user interface. Using the search functionality of our REST 
> API with the require_exact_match parameter set to true [2], there is 
> still one result returned since “indirect causal regulation” is listed 
> as a synonym for the "causal regulatory mechanism” term. I verified 
> that the synonym is declared in the OBO source file (beginning on line 
> 13,157):
>
> [Term]
> id: MI:2245
> name: causal regulatory mechanism
> def: "Type of relationship between entities involved in a causal 
> interaction. This term is to be used only to describe the effect of a 
> modulator entity A on a modulated entity B when A is not immediately 
> upstream of B." [PMID:26467481]
> synonym: "causal regulatory mechanism" EXACT PSI-MI-short []
> *synonym: "indirect causal regulation"* EXACT PSI-MI-alternate []
> is_a: MI:2233 ! causal interaction
> created_by: ppm
> creation_date: 2017-01-19T15:44:29Z
>
> Kind regards,
> Jennifer
>
> [1] https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo
> [2] 
> http://data.bioontology.org/search?q=indirect%20causal%20regulation&ontologies=MI&require_exact_match=true 
> <http://data.bioontology.org/search?q=indirect causal 
> regulation&ontologies=MI&require_exact_match=true>
>
>
>
>> On Feb 11, 2019, at 2:20 AM, John Zobolas <john.zobolas at ntnu.no 
>> <mailto:john.zobolas at ntnu.no>> wrote:
>>
>> 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:deprecatedrdf: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 <mailto:pporras at ebi.ac.uk>>
>> *Sent:*Monday, February 11, 2019 10:46 AM
>> *To:*John Zobolas
>> *Cc:*support at bioontology.org <mailto: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>
>>> *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
>> -------------------------------------------------------
>

-- 
------------------------------------------------------
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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