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[bioontology-support] [BioPortal] Feedback from Jay Franklin

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Apr 28 09:51:19 PDT 2020


I haven’t received a response from the ontology maintainers, so I fixed the small error in the ontology source file that was causing parsing issues and reprocessed it in our system. CMO is fully available in BioPortal now, including the ability to use with the Annotator.

Jennifer



On Apr 27, 2020, at 11:11 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi again Jay,

I found the error in the ontology source file that is causing the parsing error, and have asked the maintainers if they could repair it:

https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues/3

If I don’t get a response shortly, I’ll attempt to fix it on our end and reprocess.

Jennifer


On Apr 27, 2020, at 10:26 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Jay,

I looked at CMO in our system and it appears that the latest version (uploaded on January 7th) failed to parse. The status is showing as "Error Rdf”. This is the underlying reason that the Annotator doesn’t include results from this ontology. I’ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/164

… and am looking into the parsing errors.

Kind regards.
Jennifer



On Apr 25, 2020, at 2:19 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jay Franklin

Email: frankj7 at rpi.edu<mailto:frankj7 at rpi.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fannotator

Feedback:

Hi,

It seems as though the Clinical Measurements Ontology (CMO) is not working correctly with the Annotator tool right now. Although I can select CMO in the drop-down list of ontologies, when I input biomedical text to be annotated CMO is never returned. For example, "diastolic blood pressure" does not return its corresponding IRI "http://purl.obolibrary.org/obo/CMO_0000004".

Is this an error within the Annotator, or am I misusing the software somehow? I would like to use the Annotator with CMO, so please let me know if something can be done about this.

Thanks,
Jay Franklin
Rensselaer Polytechnic Institute

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