Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Manuel T. Schrempf e0920136 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. 
"" has no FMA ID, that is why I 
reported the issue.


On 28.05.19 07:22, John Graybeal wrote:
> Manuel,
> 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.
> John
>> On May 25, 2019, at 4:45 AM, support at 
>> <mailto:support at> wrote:
>> Name: Manuel T. Schrempf
>> Email: e0920136 at 
>> <mailto:e0920136 at>
>> Location: 
>> <>%2Fontologies%2FFMA
>> *Feedback:*
>> 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.
>> Best,
>> 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
> 650-736-1632

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list