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[bioontology-support] MeSH 2009_2009_02_13 in BioPortal via REST Services

Trish Whetzel whetzel at stanford.edu
Mon Dec 14 10:21:47 PST 2009


Hi David,

The service calls in question are not provided for every version of an  
ontology and therefore are not in synch with the ontology version id  
from the "all ontologies" call, which only lists the latest versions  
of all ontologies. In order to see which versions of the ontologies  
have been processed and accessible via the Hierarchy web services,  
this call can be used: http://rest.bioontology.org/obs/ontologies. The  
Hierarchy web services include the "parents", "children", "paths to  
root", "paths to leaves", and "siblings" call. For the "all terms"  
call I need to do a bit more checking on whether that is available for  
MeSH.

In the case of MeSH, the hierarchy information is provided from it's  
UMLS metathesaurus instantiation as compared to MeSH as a stand-alone  
terminology, i.e. with ontology version id 40401. The effect being  
that in order to use the Hierarchy web services for terminologies  
accessed from the UMLS metathesaurus the service call needs to be  
replaced with the SAB and CUI instead of the ontology version id and  
term id. For example, MSH and C0017337, resulting in: http://rest.bioontology.org/bioportal/concepts/parents/MSH/C0017337?email=example@example.org 
.  The CUI can be extracted from the results of the Term web service,  
e.g. http://rest.bioontology.org/bioportal/concepts/40401?conceptid=D005796&light=false&email=example@example.org 
. Note, there is an upcoming change in the output for the Term  
(formerly named Concept) web service: https://mailman.stanford.edu/pipermail/bioportal-announce/2009-December/000007.html


Trish


On Dec 11, 2009, at 1:36 PM, David Hummel wrote:

> Hello,
>
> For various projects, we are trying to leverage the REST services
> described here:
>
> http://www.bioontology.org/wiki/index.php/NCBO_REST_services
>
> It appears that there is a problem with many of the available calls
> (and it turns out the most potentially useful ones for us) when
> targeting the MeSH ontology.
>
> According to the "all ontologies" call:
>
> http://rest.bioontology.org/bioportal/ontologies?email=example@example.org
>
> MeSH should have ontologyId=1351 and ontologyVersionId=40401, and this
> does appear to be the case since the following calls seem to work:
>
> "term":
> http://rest.bioontology.org/bioportal/concepts/40401/D005796?email=example@example.org
> http://rest.bioontology.org/bioportal/virtual/ontology/1351/D005796?email=example@example.org
>
> "all root terms":
> http://rest.bioontology.org/bioportal/concepts/40401/root?email=example@example.org
>
> However, the following calls all return errors:
>
> "all terms":
> http://rest.bioontology.org/bioportal/concepts/40401/all?email=example@example.org
> http://rest.bioontology.org/bioportal/virtual/ontology/1351/all?email=example@example.org
>
> "parents":
> http://rest.bioontology.org/bioportal/virtual/parents/1351/D005796?email=example@example.org
> http://rest.bioontology.org/bioportal/concepts/parents/40401/D005796?email=example@example.org
>
> "children":
> http://rest.bioontology.org/bioportal/virtual/children/1351/D005796?email=example@example.org
> http://rest.bioontology.org/bioportal/concepts/children/40401/D005796?email=example@example.org
>
> "paths to roots":
> http://rest.bioontology.org/bioportal/concepts/rootpath/40401/D005796?email=example@example.org
> http://rest.bioontology.org/bioportal/virtual/rootpath/1351/D005796?email=example@example.org
>
> "paths to leaves":
> http://rest.bioontology.org/bioportal/concepts/leafpath/40401/D005796?email=example@example.org
> http://rest.bioontology.org/bioportal/virtual/leafpath/1351/D005796?email=example@example.org
>
> "siblings":
> http://rest.bioontology.org/bioportal/concepts/siblings/40401/D005796?level=1&email=example@example.org
> http://rest.bioontology.org/bioportal/virtual/siblings/1351/D005796?level=1&email=example@example.org
>
> Thanks in advance for any information you can provide.
>
> Sincerely,
>
> --
> David Hummel
> Senior Software Engineer
> Center for Biomedical Informatics
> Countway Library of Medicine
> Harvard Medical School
> 617-432-6863
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org



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