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[bioontology-support] Annotator help request

Brelsford, Jeffrey S. (LNG-DAY) Jeffrey.Brelsford at
Thu Aug 12 08:11:41 PDT 2010

Hi Max,

Thanks. That's been clarified as of your updates to the CD yesterday. It appears that the ontologies we will concentrate on will be exclusively NCI Thesaurus, SNOMED CT, Gene Ontology and Human Disease Ontology.


From: Berenstein, Max (ELS-NYC)
Sent: Thursday, August 12, 2010 11:01 AM
To: Trish Whetzel; Brelsford, Jeffrey S. (LNG-DAY)
Cc: Dunn, Andrew (LNG-DAY); support at
Subject: RE: [bioontology-support] Annotator help request


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 service:
- 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 removed.

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 elementID).
  *   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 Kasem

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at<mailto:whetzel at>

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