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

bernard gibaud 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.

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:
>
>
>
>
>
>> 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 
>> <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.
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu 
>> <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>


-- 
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
page web: https://medicis.univ-rennes1.fr/members/bernard.gibaud/index

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