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[bioontology-support] Problem with multiple paths to root

Trish Whetzel whetzel at stanford.edu
Wed Aug 11 20:58:21 PDT 2010


Hi Emily,

The path to the root is based on is_a relations. The relation between  
GO:0051726 and GO:0007049 is the relation 'regulation of cell cycle'  
and therefore is not included in the rootpath. On the other hand, the  
term melanoma from the NCI Thesaurus does contain 2 is_a parents and  
both are included in the output of rootpath call, e.g. http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?email=example@example.org 
.

Do you have a need to include relations other than is_a in the  
rootpath results?

Trish



On Aug 11, 2010, at 2:59 PM, Emily Howe wrote:

> Hi Trish,
>
> How are you doing?   I just noticed a problem with GO terms having  
> multiple paths to root,  here is one example.
> GO:0051726   Here is the path returned from the annotator
>
> http://rest.bioontology.org/bioportal/virtual/rootpath/1070/GO:0051726?email=udayevani@gmail.com
>
> or with go extension
> http://rest.bioontology.org/bioportal/virtual/rootpath/1506/GO:0051726?email=udayevani@gmail.com
>
> they are the same.
>
> However  if I look up the go term in AmiGo
>
> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0051726&session_id=2460amigo1281563802
>
> You can see we are missing the path containing
> GO:0009987
> GO:0007049
>
> Am I doing something wrong?  Is this a known issue, is there a work  
> around?
>
> Thanks
> Emily




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