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[bioontology-support] looking up RIDs from labels

Trish Whetzel whetzel at stanford.edu
Sun Dec 5 08:11:33 PST 2010


Hi Daniel,

Can you provide examples of input values you would like to use? For example, are you looking for a web service that can take either the values RID6448 (concept identifier) or 61894 (FMA ID) or *.*.Precentral Gyrus.*.* (Talairach) and return information for the concept RID6448? 

Trish



On Dec 4, 2010, at 10:00 PM, Daniel Rubin wrote:

> Trish,
> As per Todd’s question below, are there any methods in biportal webservices which take both a concept identifier and property identifier in order to retrieve the values for that property on that class?
>  
> Daniel
>  
> ___________________________________
> <image001.jpg> Daniel L. Rubin, MD, MS                              <image002.jpg>
>             Assistant Professor
>             Department of Radiology | Stanford University
>             Richard M. Lucas Center | 1201 Welch Road, Office P285
>             Stanford, CA 94305-5488
>             Phone: 650-723-9495 | Fax: 650-723-5795
>             Web: http://rubin.web.stanford.edu/
>  
> From: Todd Detwiler [mailto:det at u.washington.edu] 
> Sent: Saturday, December 04, 2010 2:36 PM
> To: Daniel Rubin
> Cc: 'Neeraj Agrawal'; mejino at u.washington.edu
> Subject: Re: looking up RIDs from labels
>  
> It isn't clear to me how you would do this through the bioportal api. I've only used the bp api for accessing full ontologies (not slot values within an ontology). The problem is, there doesn't appear to be any methods which take both a concept identifier and property identifier in order to retrieve the values for that property on that class. Perhaps Natasha could provide more info. 
> Todd
> 
> On 12/3/2010 7:10 PM, Daniel Rubin wrote:
> Todd,
> Thanks. But this assumes I know the RadLex term and I want to look up theTalairach label. What if I’m starting with a Talairach string?
>  
> Daniel
>  
> ___________________________________
> <image003.jpg>Daniel L. Rubin, MD, MS                              <image002.jpg>
>             Assistant Professor
>             Department of Radiology | Stanford University
>             Richard M. Lucas Center | 1201 Welch Road, Office P285
>             Stanford, CA 94305-5488
>             Phone: 650-723-9495 | Fax: 650-723-5795
>             Web: http://rubin.web.stanford.edu/
>  
> From: Todd Detwiler [mailto:det at u.washington.edu] 
> Sent: Monday, November 29, 2010 2:12 PM
> To: Daniel Rubin
> Cc: Neeraj Agrawal; mejino at u.washington.edu
> Subject: Re: looking up RIDs from labels
>  
> OK, so let's start by talking about how things are in RadLex (native, not the owl version in bioportal). When you say "names of the slots he’d need to search in RadLex to go from an atlas label to the RadLex term", what do you mean by RadLex term? Do you want an id (i.e. RID1234) or a human readable term (i.e. precentral gyrus)? The former is attached to a class via the Protege system property :NAME. The latter is attached, for the preferred term via the Preferred name slot. But this connection is via a reified instance. Values in the Preferred name slot are instances of the RadLex term class. Each instance has a "name" slot where the actual string value resides. Similarly, terms from other terminologies are attached via reified relationships like Talairach, Freesurfer, and AAL. Values in these slots are instances of Non-RadLex term and again have a name field for retrieving the actual string values.
> 
> Now let's talk about how these things look in Bioportal. First, I don't have much in the way of example code for doing this through the bioportal web services. And, what you get back from the services doesn't look exactly like what you see in Protege. For example, here is a URL that will retrieve the concept precentral gyrus (by its RID) from the web services
> 
> http://rest.bioontology.org/bioportal/concepts/44843/RID6448
> 
> Note that the results of the above call include:
> 
>         <entry>
>           <string>Talairach</string>
> 
>           <list>
>             <string>*.*.Precentral Gyrus.*.*</string>
>           </list>
>         </entry>
> 
> I believe that you will need to parse these results (and potentially perform more service calls) to get the results you are looking for.
> 
> Todd

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