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[bioontology-support] [BioPortal] Feedback from cooperl

Laurel Cooper cooperl at science.orgonstate.edu
Tue May 21 14:22:59 PDT 2013


Yes, I think it is.  Also it shows up correctly in the the Bioportal tree view
Or do you mean there is an error in the stanza?
L

Sent from my iPad

On May 21, 2013, at 1:21 PM, Trish Whetzel <whetzel at stanford.edu> wrote:

> Hi Lol, 
> 
> This looks like a bug based on the OBO stanza:
> 
> [Term]
> id: PO:0008030
> name: trichome cell
> namespace: plant_anatomy
> def: "A plant cell that is part of a trichome." [POC:curators]
> comment: A branch of a unicellular trichome is a GO sub-cellular component.
> subset: CL
> synonym: "c&#233lula del tricoma (Spanish)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo]
> synonym: "non-glandular unicellular trichome" NARROW []
> synonym: "non-secretory unicellular trichome" NARROW []
> synonym: "simple trichome" NARROW [PMID:19939948]
> synonym: "unicellular trichome" NARROW []
> synonym: "毛(毛茸、糸状体)細胞 (Japanese)" EXACT Japanese [NIG:Yukiko_Yamazaki]
> is_a: PO:0009002 ! plant cell
> relationship: develops_from PO:0004013 ! epidermal cell
> relationship: part_of PO:0000282 ! trichome
> 
> I'll submit a bug report on this. Also, note that it appears the "Get Term" web service call is also returning this incorrect is_a relationship:
> http://rest.bioontology.org/bioportal/concepts/49609?conceptid=PO%3A0008030&apikey=YourAPIKey
> 
> Trish 
> 
> 
> On May 20, 2013, at 10:11 AM, support at bioontology.org wrote:
> 
>> 
>> Name: cooperl
>> 
>> Email: cooperl at science.oregonstate.edu
>> 
>> Location: http://bioportal.bioontology.org/ontologies/49609?p=terms
>> 
>> Comment:
>> There seems to be some thing odd going on with the visualization tool.  It seems that some or all of the part_of relations are being displayed as is_a.  
>> http://bioportal.bioontology.org/ontologies/49609/?p=terms&conceptid=PO%3A0008030
>> "trichome cell" should be part_of "trichome", not is_a.  
>> Also, example from GO: root hair tip is part_of root hair, not is_a root hair.
>> http://bioportal.bioontology.org/ontologies/50270?p=terms&conceptid=GO%3A0035619&jump_to_nav=true#visualization
>> 
>> Thanks Laurel
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 


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