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

Natasha Noy noy at stanford.edu
Tue Nov 10 12:17:27 PST 2009


Also not that the second relationship is actually "[R] part_of", not  
"part_of"

Natasha


On Nov 10, 2009, at 12:08 PM, Trish Whetzel wrote:

> 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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>
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