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

Manuel T. Schrempf e0920136 at student.tuwien.ac.at
Mon May 27 23:08:13 PDT 2019


Hello John,

just that owl#Thing has no ID as (FMAxxxxxx), I parse the FMA CSV with a 
bash script and remove reduntant information, meaning everything except 
the pure integer number, since the rest is not needed for a unique 
identifacion by an ID on a database. 
"http://www.w3.org/2002/07/owl#Thing" has no FMA ID, that is why I 
reported the issue.

Best,
Manuel

On 28.05.19 07:22, John Graybeal wrote:
> Manuel,
>
> Thank you for this report. We have entered it as 
> https://github.com/ncbo/bioportal-project/issues/119, 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.
>
> John
>
>> On May 25, 2019, at 4:45 AM, support at bioontology.org 
>> <mailto:support at bioontology.org> wrote:
>>
>> Name: Manuel T. Schrempf
>>
>> Email: e0920136 at student.tuwien.ac.at 
>> <mailto:e0920136 at student.tuwien.ac.at>
>>
>> Location: http%3A%2F%2Fbioportal.bioontology.org 
>> <http://2Fbioportal.bioontology.org>%2Fontologies%2FFMA
>>
>>
>> *Feedback:*
>>
>> Hello Bioporal,
>> in your FMA 5.0.0 CSV file the following entry is wrong:
>>
>> http://purl.org/sig/ont/fma/fma85802,FMA attribute 
>> entity,,,false,,,http://www.w3.org/2002/07/owl#Thing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,85802,,,,,,,,,,,,,,,,,,,,,,,,fma:fma85802,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
>>
>> since the parent "http://www.w3.org/2002/07/owl#Thing" 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.
>>
>> Best,
>> Manuel T. Schrempf
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu 
>> <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632
>
>

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