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

Girges, Christine c.girges at
Wed Nov 23 01:16:02 PST 2016

Dear all,

Thank you for such a speedy response.

Bernard, would it be possible to keep me updated with regards to when the ontology is back up and running again?

Kind regards,


From: bernard gibaud <bernard.gibaud at>
Sent: 23 November 2016 07:26:45
To: Jennifer Leigh Vendetti; support at
Cc: Girges, Christine
Subject: Re: [bioontology-support] [BioPortal] Feedback from Christine Girges

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 (

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  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,


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

[cid:part4.27CAFAE6.52E441CE at]

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

Name: Christine Girges

Email: c.girges at<mailto:c.girges at>



The following link does not work:

I receive this error message:

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

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

Bernard Gibaud
Unite U1099 LTSI, Universite de Rennes 1
Faculte de Medecine
2, Avenue du Pr. Leon Bernard
CS 34317
35043 Rennes Cedex, France
Tel +33 (0) 2 23 23 45 90 ou +33 (0) 2 23 23 47 18 (secr)
email: bernard.gibaud at<mailto:bernard.gibaud at>
page web:

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