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[bioontology-support] Problem retrieving classes

Carlos Oscar Sorzano coss at
Sat Jul 25 01:13:41 PDT 2020

Thank you, Jennifer. I will check the configuration of Protege and see 
if I can save a truly OWL file. At least I have now something to look at.

Kind regards, Carlos Oscar

El 24/07/2020 a las 20:53, Jennifer Leigh Vendetti escribió:
> 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: 
> owl-axioms: 
> Prefix(owl:=<>)\nPrefix(rdf:=<>)\nPrefix(xml:=<>)\nPrefix(xsd:=<>)\nPrefix(rdfs:=<>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<>))\n\n\nAnnotationAssertion(<> 
> <> 
> \"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:
> 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…).
> Kind regards,
> Jennifer
>> On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano <coss at 
>> <mailto:coss at>> wrote:
>> Dear colleagues,
>> I uploaded yesterday an ontology file for Cryo Electron Microscopy 
>> ( 
>> 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 
>> <mailto:bioontology-support at>
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