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[bioontology-support] Annotator help request

Berenstein, Max (ELS-NYC) M.Berenstein at
Thu Aug 12 08:00:54 PDT 2010



We were discussing selecting four ontologies to present to users within
the app.  These are pretty standard, I believe, so the addition of new
ontologies to NCBO should not impact the app.  Now, if one of the four
we select are removed, that would cause a problem.





From: Trish Whetzel [mailto:whetzel at] 
Sent: Wednesday, August 11, 2010 11:17 PM
To: Brelsford, Jeffrey S. (LNG-DAY)
Cc: Berenstein, Max (ELS-NYC); Dunn, Andrew (LNG-DAY);
support at
Subject: Re: [bioontology-support] Annotator help request


Hi Jeff, 


Below is information on how often items can change for the Annotator Web

- The list of ontologies can change weekly if new ontologies are
uploaded to BioPortal. 


- The list of semantic types may change quarterly corresponding to new
releases of UMLS. 


- Ontologies are not generally removed from the Annotator. However there
has been the rare case in the last 1.5 years in which the ontology
authors consolidated four species specific ontologies into one ontology.
As for removing semantic types, I am not aware that semantic types are


With respect to the Resource Index Web service, I'm checking with the
development team on those questions and expect to hear back tomorrow.
However, we do announce any upcoming changes to the Web service
signature or XML output (including additions of new XML elements) and
provide a period of time to allow developers to update their code and
test it against our staging server.   


Best regards,





On Aug 10, 2010, at 9:29 AM, Brelsford, Jeffrey S. (LNG-DAY) wrote:

Hi there,


My name is Jeff Brelsford and I am working for Elsevier on an Open
Social application that will interface with two NCBO web services
(Annotator and the Resource Index).

In order to understand the feasibility of developing this application I
would like to get an idea of how dynamic the changes are for the data
supplied in your web services. We have a very limited amount of
information that we can persist from our end (mostly user preferences)
and I'd like to understand how often the following can change.


For the Annotator Web Service, how often can the following change?

*	The list of ontologies
*	The list of semantic types
*	Are ontologies or semantic types ever removed?



For the Resource Index Web Service, how often can the following change?

*	The URL format to access content from the individual resources
(these are typically the URLS built from the resourceID and the
*	The frequency of a change in the data structure in the response
concerning the <entry> and <string> elements. This is largely due to
each resource having its own unique entries (for example DrugBank may
have an indication field, but Clinical Trials will not). I'm
specifically curious about how often we can expect a change in the data
format for the following resources: Clinical Trials, DrugBank, OMIM and
Research CrossRoads.



Nigam Shah has made us aware of there's a call we can make to see
changes in formats from the response. But as I've stated earlier,
there's not a great deal that we can persist with these applications,
and it would also be difficult for us to perform ad-hoc releases to
address changes. Any type of release to address a change from the web
services would need to be scheduled on our end. In the event that a
change on your end (or from the resources themselves) is coming, is
there a period where backward compatibility is ensured?


Thank you very much for your time.



Jeff Brelsford

Science & Technology Electronic Product Services


937.865.6800 x56699

Keep your feet on the ground and keep reaching for the stars - Casey


bioontology-support mailing list
bioontology-support at


Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

whetzel at




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