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[bioontology-support] duplicate relations showing in FlexoViz.html graph viewer

Trish Whetzel whetzel at stanford.edu
Tue Nov 10 12:08:38 PST 2009


Thanks Chris. It looks like the inverse relations were loaded and  
therefore are also being displayed. In the case of part_of/part of the  
arrows are also in the same direction.
I'll assign this to Pradip to check how the ontology is loaded.

Trish

On Nov 10, 2009, at 11:37 AM, Chris Callendar wrote:

> Hi Doug and Trish,
>
> I've comented on the bug report that is entered in our system (see  
> the link below), but to summarize what I said:
>
> The error is in the rest services, not in FlexViz.
> The relationship from central nervous system to motor axons  
> peripheral is "part_of", see this XML:
> http://rest.bioontology.org/bioportal/concepts/40797/ZFA%3A0000012
>
> And the relationship from motor axons peripheral to central nervous  
> system is "part of", see this XML:
> http://rest.bioontology.org/bioportal/concepts/40797/ZFA%3A0001002
>
> FlexViz will only show one relationship if they are the same type,  
> but in this case it is not smart enough to realize that there is an  
> error in the ontology and "part of" and "part_of" are actually the  
> same thing.
>
> Chris
>
>
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: November 10, 2009 6:29 AM
> To: Chris Callendar
> Cc: support at bioontology.org
> Subject: Fwd: [bioontology-support] duplicate relations showing in  
> FlexoViz.html graph viewer
>
> Hi Chris,
>
> Can you take a look at this one?
> https://bmir-gforge.stanford.edu/gf/project/bioportal_core/tracker/?action=TrackerItemEdit&tracker_item_id=1687
>
> Thanks,
> Trish
>
>
> Begin forwarded message:
>
>> From: Doug Howe <dhowe at zfin.org>
>> Date: November 9, 2009 4:47:52 PM PST
>> To: support at bioontology.org
>> Subject: [bioontology-support] duplicate relations showing in  
>> FlexoViz.html graph viewer
>>
>> Version:          v2.1.8, October 23rd, 2009
>> Operating System: Mac OS 10.5.8
>> Flash Version:    MAC 10,0,32,18
>> Flash Parameters: ontology=40580&v=2.1.8&log=true&nodeid=&server=
>> Browser URL:      http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.html#
>>
>> I'm using the FlexoViz.html to view the zebrafish anatomy  
>> ontology.   Looking at the term 'motor axons peripheral' (which has  
>> it's own problems!), the graph seems to show two 'part of'  
>> relations.  One is labeled 'part of' and one 'part_of'.  Ditto for  
>> 'develops_from' and 'develops from'.
>>
>> Is this a bug in the FlexoViz.html or maybe something strange in  
>> our ontology format?
>>
>> -Doug
>> ~~~~~~~~~~~~~~~~~~~~~~~~
>> Doug Howe, Ph.D.
>> Scientific Curator
>> Zebrafish Information Network
>> 5291 University of Oregon
>> Eugene, OR 97401-5291
>> ~~~~~~~~~~~~~~~~~~~~~~~~
>> 541-346-0120
>> dhowe at zfin.org
>> skype: doug.howe
>>
>>
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
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