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

bernard gibaud bernard.gibaud at univ-rennes1.fr
Thu Feb 2 00:12:06 PST 2017


Jennifer,

No problem, OntoVIP can be changed into ONTOVIP.

Best regards

Bernard

Le 01/02/2017 à 23:16, Jennifer Leigh Vendetti a écrit :
> Hello again Bernard,
>
> I ran into a small complication with your OntoVIP ontology.
>
> Several years ago, BioPortal’s backend code underwent a major 
> refactor.  At the time, a new constraint was added that ontology 
> acronyms must have all capital letters.  Data migration scripts were 
> run that should have cleaned up all existing acronyms with lowercase 
> letters, but it seems your ontology was missed.  Before I can re-parse 
> your ontology, I will need to change your ontology acronym to 
> something with all capital letters (instead of “OntoVIP”).
>
> Could you please confirm if you would like to use “ONTOVIP” as the new 
> acronym?  Or, something else?
>
> Best,
> Jennifer
>
>
>
>
>> On Jan 31, 2017, at 6:45 PM, Jennifer Leigh Vendetti 
>> <vendetti at stanford.edu <mailto:vendetti at stanford.edu>> wrote:
>>
>> 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.
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>
>>
>> _______________________________________________
>> 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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