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[bioontology-support] Problem retrieving classes

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Jul 24 11:53:48 PDT 2020


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…).

[cid:810EFD70-59D3-4894-8185-3BC4CF96DC3E at stanford.edu]

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
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