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[bioontology-support] Problem retrieving classes

Carlos Oscar Sorzano coss at cnb.csic.es
Tue Jul 28 08:04:53 PDT 2020


Thank you very much, it really worked.

Kind regards, Carlos Oscar

El 28/07/2020 a las 18:13, Michael Dorf escribió:
> Hi Carlos,
>
> It looks like the ontology has loaded correctly, but it hasn’t had a 
> chance to propagate through our caching layers. I’ve cleared the 
> system caches manually, and the ontology now appears and functions 
> correctly.
>
> Let me know if you are still seeing any issues.
>
> Thank you,
>
> Michael
>
>
>
>
>> On Jul 28, 2020, at 4:25 AM, Carlos Oscar Sorzano <coss at cnb.csic.es 
>> <mailto:coss at cnb.csic.es>> wrote:
>>
>> Dear Jennifer,
>>
>> presumably I have uploaded now a true OWL file, but BioPortal cannot 
>> show yet the classes. Would you mind having a look? And thank you 
>> very much.
>>
>> Kind regards, Carlos Oscar
>>
>> On 7/24/20 8:53 PM, Jennifer Leigh Vendetti wrote:
>>> Hello Carlos Oscar,
>>>
>>> I looked at the contents of your ontology source file. You mentioned 
>>> that it’s an OWL file, but the contents appear to be in OBO format, 
>>> i.e., see the following snippet from the top of your ontology 
>>> showing OBO-style term stanzas:
>>>
>>> format-version: 1.2
>>> ontology: 
>>> http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2
>>> owl-axioms: 
>>> Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))\n\n\nAnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> 
>>> <http://purl.obolibrary.org/obo/http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2#ProtMovies> 
>>> \"ProtProcessMovies\"^^xsd:string)\n)
>>>
>>> [Term]
>>> id: Acquisition
>>> comment: Contains acquisition parameters such as magnification, 
>>> voltage, spherical aberration, amplitude contrast, dose per frame 
>>> and inital dose, optics group, and beam tilt
>>> is_a: EMObject
>>>
>>> [Term]
>>> id: AtomStruct
>>> comment: File representing an atomic structure (PDB, mmCIF, ...)
>>> is_a: EMObject
>>> property_value: hasVolume "Volume"
>>>
>>> The first line indicates that the ontology file is written in OBO 
>>> format version 1.2, however the rest of the header tags aren’t valid 
>>> according to OBO file format documentation here:
>>>
>>> https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1
>>>
>>> Could you provide more detail about how this ontology was generated? 
>>> Do you have an OBO source file that you attempted to convert to a 
>>> different format using the Protege desktop application? Also, I do 
>>> see an error message in the Protege log when opening your ontology 
>>> in the desktop version (Window -> Show log…).
>>>
>>> <Screenshot 2020-07-24 11.52.33.png>
>>>
>>> Kind regards,
>>> Jennifer
>>>
>>>
>>>> On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano 
>>>> <coss at cnb.csic.es <mailto:coss at cnb.csic.es>> wrote:
>>>>
>>>> Dear colleagues,
>>>>
>>>> I uploaded yesterday an ontology file for Cryo Electron Microscopy 
>>>> (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). 
>>>> The OWL file was generated with Protege and it does not show any 
>>>> obvious error in Protege. However, when it is read at BioPortal 
>>>> there is some problem because we see the error message "Problem 
>>>> retrieving classes" (see previous link). The file is partly parsed 
>>>> because it shows some metrics, but we must have something wrong 
>>>> with the file. Could you help us with any hint?
>>>>
>>>> Kind regards and thanks, Carlos Oscar
>>>> _______________________________________________
>>>> 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
>>>
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>
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