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

Samson Tu swt at stanford.edu
Tue May 28 10:32:23 PDT 2019


Hi,

By definition, every top-level entity in an OWL ontology has owl#Thing as a parent. It’s not a design decision on the part of FMA developers. 

It’s a design decision on the part of Bioportal CSV-output developers whether to generate an entry for this definitional parent-child relationship. Given that decision, users of the CSV output have to live with the consequences either way.

With best regards,
Samson


> On May 27, 2019, at 11:08 PM, Manuel T. Schrempf <e0920136 at student.tuwien.ac.at> wrote:
> 
> 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" <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 <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 <http://purl.org/sig/ont/fma/fma85802,FMA> attribute entity,,,false,,,http://www.w3.org/2002/07/owl#Thing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,85802,,,,,,,,,,,,,,,,,,,,,,,,fma:fma85802 <http://www.w3.org/2002/07/owl#Thing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,85802,,,,,,,,,,,,,,,,,,,,,,,,fma:fma85802>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
>>> 
>>> since the parent "http://www.w3.org/2002/07/owl#Thing <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 <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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> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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