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[bioontology-support] [ORDO] bioportal issue

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Aug 11 10:22:26 PDT 2016


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<mailto: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<mailto: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<http://data.bioontology.org/ontologies/ORDO/submissions/9/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb> | Diff<http://data.bioontology.org/ontologies/ORDO/submissions/9/download_diff?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb>

Any idea ?

Best regards,

Marc HANAUER
Directeur Adjoint / Deputy Director
Directeur technique / Chief technology officer
Stratégie et Innovation
marc.hanauer at inserm.fr<mailto: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 <<mailto:marc.hanauer at inserm.fr>marc.hanauer at inserm.fr<mailto: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



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