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[bioontology-support] [BioPortal] Feedback from Manuel T. Schrempf

John Graybeal jgraybeal at
Mon May 27 22:22:09 PDT 2019


Thank you for this report. We have entered it as, and will be examining it in more detail soon.

I note that all of the top-level classes in FMA have been defined as owl#Thing in BioPortal, so I believe this is a design decision made by the original developers of the ontology representation (that is, not a bug). If you would like to be more explicit about why you see it as wrong, that may help us assess the situation more clearly.

Thank you for your time to share this with us.


On May 25, 2019, at 4:45 AM, support at<mailto:support at> wrote:

Name: Manuel T. Schrempf

Email: e0920136 at<mailto:e0920136 at>



Hello Bioporal,
in your FMA 5.0.0 CSV file the following entry is wrong:,FMA attribute entity,,,false,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,85802,,,,,,,,,,,,,,,,,,,,,,,,fma:fma85802,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

since the parent "" does not contain a valid FMA id. I guess some other errors are in other anatomy datasets too, since my automatic parsing threw some errors. I will just exclude this anatomy from my parsing and hope future releases will have the errors fixed.

Manuel T. Schrempf

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research

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