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[bioontology-support] 2 questions: scope of pubmed annotations and issues with ncit and mesh annots

Ray Fergerson ray.fergerson at
Thu Apr 11 15:19:13 PDT 2013



The problem with NCIT is probably that NCI has changed its system of
generating codes. Previously the code for the term was related to its
name. Now the code is a meaningless identifier. I suspect that the version
of NCIt used for the last RI build is incompatible with the version in
production. We are currently regenerating all RI annotations.
Unfortunately this process takes quite a while. A guess would be that it
will be out in 4 weeks.


This problem is restricted to NCIt. We cannot reproduce your problem with




From: bioontology-support-bounces at
[mailto:bioontology-support-bounces at] On Behalf Of Trish
Sent: Thursday, April 11, 2013 2:02 PM
To: Adrien Coulet
Cc: support at
Subject: Re: [bioontology-support] 2 questions: scope of pubmed
annotations and issues with ncit and mesh annots


Hi Adrien, 


1) I think it is 1 year of PubMed, perhaps for 2011. 


2) Are you still experiencing an issue searching the Resource Index (RI)
with MeSH? I was able to get results from the RI via the BioPortal Web
interface using MeSH terms "Biology", "Pharmacology", "Genetics" (each
term individually). If you are not getting results from the RI for MeSH
what search terms are you using?


For NCIt, I am getting an error and have reported this:
temEdit&tracker_item_id=4490&start=0> &tracker_item_id=4490&start=0





On Apr 10, 2013, at 9:15 AM, Adrien Coulet wrote:

Dear Trish and NCBO support, 


I am using the Resource Index annotations in my research and have two
questions about it:


1) I remember that the annotations of PubMed are not done on all of PubMed
but on a subset of it. Could you tell me what is the precise scope of this
subset? I can't find it anywhere.

2) These days, when we query the Resource Index either through the UI or
the web service for annotations made with the NCIT or MeSH we have no
result back. 

What happened? These annotations were available few weeks ago.


Thanks a lot for your consideration and your answers. 


Hope all of you at the BMIR are doing well.

Kind regards, 




Adrien Coulet

Orpailleur group, 

LORIA - INRIA Nancy - Grand Est,

University of Lorraine, France



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