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[bioontology-support] Rest Services

Trish Whetzel whetzel at stanford.edu
Thu Apr 29 17:31:43 PDT 2010


Thanks, this information helps a lot.

For the call to the Annotator, there is only 1 version of an ontology  
that is accessible via the Annotator and from time to time the  
ontology version is updated. To see which ontology versions are  
accessible, use the call:  http://rest.bioontology.org/obs/ontologies.
In addition, the UMLS ontologies such as the Medical Subject Headings,  
are now accessed directly from BioPortal so they have ontology version  
identifiers that are numeric vs. the form used previously when the  
Annotator accessed these ontologies from a separate UMLS database.   
For more documentation on the Annotator, see: http://www.bioontology.org/wiki/index.php/Annotator_User_Guide

Therefore the modifications to the call are:
http://rest.bioontology.org/obs/annotator?longestOnly=true&wholeWordOnly=true&ontologiesToExpand=42142&ontologiesToKeepInResult=42142&semanticTypes=&withDefaultStopWords=true&format=xml&levelMax=0&mappingTypes=null&textToAnnotate=Phosphorylation

For the call to rootpath, I need to do a bit more investigation.


Trish


On Apr 29, 2010, at 2:11 PM, Mathew Fleisch wrote:

> I am probably just doing something wrong, but I am pretty sure these  
> both worked a month or two ago:
>
> http://rest.bioontology.org/obs/annotator?longestOnly=true&wholeWordOnly=true&ontologiesToExpand=MSH&ontologiesToKeepInResult=MSH&semanticTypes=&withDefaultStopWords=true&format=xml&levelMax=0&mappingTypes=null&textToAnnotate=Phosphorylation
>
> http://rest.bioontology.org/bioportal/virtual/rootpath/1070/GO:0055085?email=udayevani@gmail.com
>
> Mathew Fleisch
> 415.209.2000.6735
> mfleisch at buckinstitute.org
> ________________________________________
> From: Trish Whetzel [whetzel at stanford.edu]
> Sent: Thursday, April 29, 2010 2:02 PM
> To: Mathew Fleisch
> Cc: Uday Evani; support
> Subject: Re: Rest Services
>
> Can you send an example that is not working?
>
> Thanks,
> Trish
>
>
> On Apr 29, 2010, at 1:59 PM, Mathew Fleisch wrote:
>
> hierarchy and bioportal
> I will add myself to that mailing list.
>
> Mathew Fleisch
> 415.209.2000.6735
> mfleisch at buckinstitute.org<mailto:mfleisch at buckinstitute.org>
> ________________________________________
> From: Trish Whetzel [whetzel at stanford.edu]
> Sent: Thursday, April 29, 2010 1:59 PM
> To: Mathew Fleisch
> Cc: support
> Subject: Re: Rest Services
>
> Hi Mathew,
>
> Which Web services are you using? We do announce changes to the Web  
> services prior to making changes to the production Web services and  
> announce these changes on the bioportal-announce mailing list, https://mailman.stanford.edu/pipermail/bioportal-announce 
> .
>
> Trish
>
>
> On Apr 29, 2010, at 1:39 PM, Mathew Fleisch wrote:
>
> Hello Trish,
> My name is Mathew and I am with Sean Mooney at the Buck Institute. I  
> have been developing a tool that uses rest services and my scripts  
> have stopped working... What has changed? what do I need to update?  
> Thank you in advance for your help.
>
>
> Mathew Fleisch
> 415.209.2000.6735
> mfleisch at buckinstitute.org<mailto:mfleisch at buckinstitute.org>
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> whetzel at stanford.edu<mailto:whetzel at stanford.edu>
> http://www.bioontology.org
>
>
>
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> whetzel at stanford.edu<mailto:whetzel at stanford.edu>
> http://www.bioontology.org
>
>
>

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