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[bioontology-support] trying to use rootpath service.

Ray Fergerson ray.fergerson at stanford.edu
Wed Apr 6 13:20:40 PDT 2011


Lori,

 

First let me admit up front that this is terribly confusing. I will try to
explain, but I will have to give you more information that you would
expect to have to know.

 

This functionality (get all paths to root) is implemented on top of the
annotator database rather than on top of the BioPortal ontology store
directly. The result is that it behaves quite differently from other
BioPortal methods. In particular:

(1)    Only one version of the ontology is in the annotator db so only one
version is available to query.

(2)    The version available to query is the one that was current when the
annotator db was created. Ideally this would be a week ago. Currently
though the difference is several months.

(3)    You can make the rest call with the version id rather than the
virtual id but you may not get anything back because that ontology version
is not in the db. The virtual id will always give you access to whatever
is in the db.  That is why this call is recommended in the docs.

 

You don't have to tell me that this is terrible behavior. We know. It will
eventually get fixed. 

 

The only way to get all paths to root for a particular version is to
calculate it directly from the BioPortal get term calls. The "get single
path to root" API does use the BioPortal ontology store. It only returns a
random path to root though an not all of them.

 

Ray

 

 

From: Phillips, Lori C. [mailto:LCPHILLIPS at PARTNERS.ORG] 
Sent: Wednesday, April 06, 2011 10:27 AM
To: Ray Fergerson
Subject: trying to use rootpath service.

 

Hi Ray,

 

I have been told that I can use rootpath to get all delimited paths to
root for a term:  e.g. 

 
<http://rest.bioontology.org/bioportal/virtual/rootpath/1353/9932004?delim
=\&email=example at example.org>
http://rest.bioontology.org/bioportal/virtual/rootpath/1353/9932004?delim=
\&email=example at example.org 

 

1. Does it only work with virtual ids?

2. Does it not work for views?   2021 is the id for the SNOMED Organism
view.

      

  Following  returns error that ontology id is not found

 

 
<http://rest.bioontology.org/bioportal/virtual/rootpath/1353/9932004?delim
=\&email=example at example.org>
http://rest.bioontology.org/bioportal/virtual/rootpath/2021/9932004?delim=
\&email=example at example.org 

 

Thanks

Lori



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