Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Annotator help request

Trish Whetzel whetzel at
Wed Aug 11 20:16:56 PDT 2010

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

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list