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[bioontology-support] [BioPortal] Feedback from Christine Girges
bernard.gibaud at univ-rennes1.fr
Tue Nov 22 23:26:45 PST 2016
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.
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 .
> 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
> 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
> Kind regards,
> Screen shot of the syntax error as seen in the Protege ontology
> editing environment:
>> 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
>> 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 lists.stanford.edu
>> <mailto:bioontology-support at lists.stanford.edu>
Equipe INSERM MediCIS
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email: bernard.gibaud at univ-rennes1.fr
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