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

Chris Callendar chriscallendar at gmail.com
Tue Nov 10 11:37:52 PST 2009


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=T
rackerItemEdit
<https://bmir-gforge.stanford.edu/gf/project/bioportal_core/tracker/?action=
TrackerItemEdit&tracker_item_id=1687> &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




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