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[bioontology-support] trying to use rootpath service.

Ray Fergerson ray.fergerson at stanford.edu
Wed Apr 6 13:52:18 PDT 2011


Lori,

 

You are correct. If you need get all paths to root for any version of an
ontology other than the one used for annotation then currently you have to
calculate it yourself.

 

Ray

 

From: Phillips, Lori C. [mailto:LCPHILLIPS at PARTNERS.ORG] 
Sent: Wednesday, April 06, 2011 1:44 PM
To: Ray Fergerson
Subject: RE: trying to use rootpath service.

 

Trying to make sure I understand, but let me give you my situation...

 

The biggest issue I have in the NCBO extraction tool for i2b2 is building
the i2b2 fullname (paths to root) for each term.

I originally did this by making successive getTerm calls, but as you may
remember, this was discouraged because I was causing too much traffic on
your network. I was also encouraged to use views (especially in the case
of SNOMED) because it would break down the problem of trying to get all of
SNOMED at once.  Nigam suggested that I use the 'all' rest service to page
through and get all the concepts in a view and then go back and do a 'get
all paths to root'  for each term.  This latter part (get all paths to
root) is what I am attempting to do now.

 

But you are saying (I think) that this information (get all paths to root)
is not necessarily available...

 

Sounds like the only option I have that is dependable is to compute the
path myself... 

Yes? No?

 

Thanks

Lori

 

  _____  

From: Ray Fergerson [mailto:ray.fergerson at stanford.edu] 
Sent: Wednesday, April 06, 2011 4:21 PM
To: Phillips, Lori C.
Cc: support at bioontology.org
Subject: RE: trying to use rootpath service.

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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