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[bioontology-support] [BioPortal] Feedback from Christine Girges

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Jan 31 18:45:08 PST 2017


Hello Bernard,

The first 3 ontologies you list below are fully parsed and available in BioPortal now.

I should have the 4th one (OntoVIP) done by tomorrow.

Kind regards,
Jennifer



On Jan 31, 2017, at 4:40 AM, bernard gibaud <bernard.gibaud at univ-rennes1.fr<mailto:bernard.gibaud at univ-rennes1.fr>> wrote:

Hello Jennifer,

The problem reported below was fixed.

Is it possible to reload the following ontologies in the BioPortal:
https://bioportal.bioontology.org/ontologies/ONL-DP
https://bioportal.bioontology.org/ontologies/ONL-MSA
https://bioportal.bioontology.org/ontologies/ONL-MR-DA
https://bioportal.bioontology.org/ontologies/OntoVIP

Actually they all imported the same file 'ontoneurolog-extension-of-dolce.owl', thus leading to the same error.

Best regards,

Bernard Gibaud



Le 23/11/2016 à 08:26, bernard gibaud a écrit :
Hello Christine, Jennifer

I will try to fix this problem. Actually this problem did not cause any errors at the time the ontology was shared.

Best regards,

Bernard Gibaud

Le 22/11/2016 à 01:00, Jennifer Leigh Vendetti a écrit :
Hello Christine,

The reason for the 404 (“something has gone wrong") error is that the PURL you list below resolves to what is supposed to be the page that displays the classes for the Mental State Assessment ontology [1].  The classes page is absent because the ontology source file that was submitted to BioPortal has invalid syntax and is unable to be parsed.  This is indicated by the “Error Rdf” status listed on the ontology summary page (http://bioportal.bioontology.org/ontologies/ONL-MSA).

Normally if someone submits an ontology with syntax errors, we try our best to fix them and re-parse the ontology to make it available to end-users.  However, this particular ontology imports several other ontologies from a web URL that we don’t host here at Stanford, and the error is in one of the imports.

I’m listing the syntax error and suggested fix below, and I’ve cc’ed the ontology contact person in the event that Bernard is willing to submit a corrected version.

The error is on line 800 of the ontoneurolog-extension-of-dolce.owl ontology file (hosted at http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl).  The rdfs:comment is declared as datatype XMLLiteral, but the content of the comment doesn’t contain the required opening and closing XML tags that are expected for this particular datatype:

<rdfs:comment rdf:datatype="&rdf;XMLLiteral">[DEF] ACTION A is generated, or is produced, by ACTION B when A is done by doing B: “doing A by doing B”.
[CIT] (Pacherie, 2008, p. 198): “At least three cases [of productions] must be distinguished. The first is indeed causal generation. Doing A by doing B counts as an instance of causal generation when the production of B causes the production of A. For instance, turning the light by flipping a switch or breaking the glass by dropping it on a hard surface count as instances of causal generation. The second case is conventional generation, where doing B (in circumstances C) counts as doing A in virtue of a rule or convention that stipulates that is so counts. Thus, signalling a left turn by extending one’s left arm or voting in favour of the motion by raising one’s hand are instances of conventional generation. The third case is circumstantial generation, where doing B counts as doing A only if certain circumstances obtain. For instance, one breaks the world record for in the 100 m for men by running it in 9,77 s only in circumstances where no one has yet run this distance in 9,77 a or less.”</rdfs:comment>

Possible fixes are a) remove the XMLLiteral datatype declaration, e.g.:

<rdfs:comment>[DEF] ACTION A is generated…</rdfs:comment>

… or b) add the desired start and end tags to the comment, e.g.:

<rdfs:comment rdf:datatype="&rdf;XMLLiteral”><p>[DEF] ACTION A is generated…</p></rdfs:comment>

Kind regards,
Jennifer

[1] http://bioportal.bioontology.org/ontologies/ONL-MSA?p=classes&conceptid=root

Screen shot of the syntax error as seen in the Protege ontology editing environment:


<Mail Attachment.png>



On Nov 21, 2016, at 8:59 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Christine Girges

Email: c.girges at ucl.ac.uk<mailto:c.girges at ucl.ac.uk>

Location: https://bioportal.bioontology.org/ontologies/ONL-MSA

Feedback:

The following link does not work:

http://purl.bioontology.org/ontology/ONL-MSA

I receive this error message:

We're sorry but something has gone wrong. We have been notified of this error.

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--
Bernard Gibaud
Equipe INSERM MediCIS
Unite U1099 LTSI, Universite de Rennes 1
Faculte de Medecine
2, Avenue du Pr. Leon Bernard
CS 34317
35043 Rennes Cedex, France
France
Tel +33 (0) 2 23 23 45 90 ou +33 (0) 2 23 23 47 18 (secr)
email: bernard.gibaud at univ-rennes1.fr<mailto:bernard.gibaud at univ-rennes1.fr>
page web: https://medicis.univ-rennes1.fr/members/bernard.gibaud/index





--
Bernard Gibaud
Equipe INSERM MediCIS
Unite U1099 LTSI, Universite de Rennes 1
Faculte de Medecine
2, Avenue du Pr. Leon Bernard
CS 34317
35043 Rennes Cedex, France
France
Tel +33 (0) 2 23 23 45 90 ou +33 (0) 2 23 23 47 18 (secr)
email: bernard.gibaud at univ-rennes1.fr<mailto:bernard.gibaud at univ-rennes1.fr>
page web: https://medicis.univ-rennes1.fr/members/bernard.gibaud/index



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