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[bioontology-support] Problem retrieving classes

Michael Dorf mdorf at
Tue Jul 28 09:13:09 PDT 2020

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,


On Jul 28, 2020, at 4:25 AM, Carlos Oscar Sorzano <coss at<mailto:coss at>> 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
owl-axioms: Prefix(owl:=<>)\nPrefix(rdf:=<>)\nPrefix(xml:=<>)\nPrefix(xsd:=<>)\nPrefix(rdfs:=<>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<>))\n\n\nAnnotationAssertion(<> <> \"ProtProcessMovies\"^^xsd:string)\n)

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

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…).

<Screenshot 2020-07-24 11.52.33.png>

Kind regards,

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
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