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[bioontology-support] [ORDO] bioportal issue

Marc Hanauer marc.hanauer at inserm.fr
Fri Aug 12 03:29:49 PDT 2016


Hi,
This is great!  Thx for your effort.
Best regards,

Envoyé de mon iPhone
-- 
Marc HANAUER
Directeur Adjoint / Deputy Director
Directeur technique / Chief technology officer
Stratégie et Innovation
Ingénieur de Recherche
marc.hanauer at inserm.fr

> Le 11 août 2016 à 19:22, Jennifer Leigh Vendetti <vendetti at stanford.edu> a écrit :
> 
> Hello Marc,
> 
> We’ve addressed the issue I mentioned below.  Version 2.2 of ORDO is parsed and available in BioPortal:
> 
> http://bioportal.bioontology.org/ontologies/ORDO
> 
> Apologies again that this one took us some time to address.
> 
> Best,
> Jennifer
> 
> 
>> On Jul 13, 2016, at 4:21 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:
>> 
>> Hi Marc,
>> 
>> I am writing with a status report regarding BioPortal’s failure to handle ORDO 2.2.
>> 
>> As you may already know, BioPortal uses the OWL API [1] internally for ontology parsing.  I wrote some Java code, independent of the BioPortal application, to make sure the OWL API handles your ontology properly.  The parsing succeeds, which indicates to me that your ontology file is valid.  When the OWL API parses your ontology file, it emits a very large number of “unparsed triple” messages (roughly 15.5K of them), e.g.:
>> 
>> [OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedProperty -> http://purl.obolibrary.org/obo/ECO_0000218
>> [OWLRDFConsumer.java:1294] Unparsed triple: _:genid120260 -> http://www.w3.org/2002/07/owl#annotatedSource -> _:genid120261
>>  
>> The size of the output from the OWL API is causing a buffer overflow / deadlock in BioPortal’s source code.  I am currently working toward fixing the issue, and hope to have something available soon.
>> 
>> Apologies that this one is taking some time for us to track down / fix.
>> 
>> Best,
>> Jennifer
>> 
>> [1] http://owlcs.github.io/owlapi/
>> 
>> 
>> 
>>> On Jun 27, 2016, at 3:18 AM, Marc Hanauer <marc.hanauer at inserm.fr> wrote:
>>> 
>>> Hello Jennifer,
>>> 
>>> I've made an update of our ontology (ORDO) last week as usual by putting the file on our own server. This time, the bioportal website seems to try the upload but with error.
>>> 
>>> The version in our own server is now "2.2" but it appears with this line on bioportal:
>>> 
>>> 2.1 (Uploaded, Error Rdf)	06/22/2016	06/22/2016	OWL | Diff
>>> 
>>> Any idea ?
>>> 
>>> Best regards,
>>> 
>>> Marc HANAUER
>>> Directeur Adjoint / Deputy Director
>>> Directeur technique / Chief technology officer
>>> Stratégie et Innovation
>>> marc.hanauer at inserm.fr
>>> 
>>> ORPHANET - INSERM US14
>>> Plateforme Maladies Rares / Rare Disease Platform
>>> 96 rue Didot
>>> 75014 PARIS
>>> FRANCE
>>>> Le 25/02/2016 à 00:41, Jennifer Leigh Vendetti a écrit :
>>>> Hello Marc,
>>>> 
>>>>> On Feb 24, 2016, at 6:45 AM, Marc Hanauer <marc.hanauer at inserm.fr> wrote:
>>>>> 
>>>>> Dear support,
>>>>> We manage the ORDO (Orphanet Rare Disease Ontology) and we have made an update recently (2 days ago).
>>>>> Usually (for the previous version), we just update the file on our own server (keeping the same URL : http://www.orphadata.org/data/ORDO/ordo_orphanet.owl ) and then the bioportal website automatically upload it.
>>>>> 
>>>>> It seems this is not the case anymore (the version in bioportal remain v2.0 instead of the new 2.1)
>>>>> 
>>>>> Do we need to perform any manual action in order to update it on bioportal ?
>>>> 
>>>> 
>>>> You don’t need to do anything manual.  We were having some performance issues with our site and temporarily disabled the cron jobs in our production environment that pull new versions of ontologies.  The cron job has been reenabled today, so the new version of your ontology should be pulled and processed overnight.
>>>> 
>>>> 
>>>>> 
>>>>> By the way, with our account, we still have trouble accessing the bioportal interface (when we sign in and try to reach the ORDO page, we obtain an error message which is not the case without login...) (see my previous msg below about this)
>>>> 
>>>> 
>>>> Sorry you’re having difficulties.  I tried reproducing this behavior here and so far haven’t had any luck.  I’ve viewed your ontology in BioPortal, both when logged in and logged out (screen shot below).  I also verified that your user account of “ORDO_Orphanet” is valid, and I don’t see any issues there.  Are you still seeing this behavior?
>>>> 
>>>> Jennifer
>>>> 
>>>> 
>>>> 
>>>> <Mail Attachment.png>
>> 
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>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
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