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

bernard gibaud bernard.gibaud at univ-rennes1.fr
Tue Jan 31 04:40:25 PST 2017


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:
>>
>>
>>
>>
>>
>>> 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
>


-- 
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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