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[bioontology-support] looking up RIDs from labels

Daniel Rubin dlrubin at stanford.edu
Sun Dec 5 18:14:05 PST 2010


Thanks-we'll try that out..

DR

 

___________________________________

 Daniel L. Rubin, MD, MS                              Description:
Description: Description: Description: cid:image001.jpg at 01CB4E1D.AC3DA3D0

            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/>
http://rubin.web.stanford.edu/

 

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Sunday, December 05, 2010 4:26 PM
To: Daniel Rubin
Cc: Neeraj Agrawal; Todd Detwiler; mej >> mejino at u.washington.edu;
support at bioontology.org
Subject: Re: [bioontology-support] looking up RIDs from labels

 

The Search web service can be used to submit the value of the Talairach
property and retrieve the concept identifier. I tested these examples of
Talairach terms:  *.*.Precentral Gyrus.*.* for term RID6448 and
Inter-Hemispheric.*.Superior Frontal Gyrus.*.* for term RID6441 with our
sample code for using the Search web service and it worked fine.  

 

Documentation on the Search web service is at:
http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_BioPorta
l. Important parameters to set are ontologyids=1057 to limit the Search to
RadLex and includeproperties=1 in order to search properties other than the
preferred name and concept id. 

 

The sample code examples for the Search web service, written in Java and
Perl, are at: 

https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=b
rowse
<https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=
browse&path=%2Ftrunk%2FJava%2FBioPortalTermSearch%2Fsrc%2F>
&path=%2Ftrunk%2FJava%2FBioPortalTermSearch%2Fsrc%2F 

AND 

https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=b
rowse
<https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=
browse&path=%2Ftrunk%2FPerl%2FBioPortalTermSearch%2F>
&path=%2Ftrunk%2FPerl%2FBioPortalTermSearch%2F

 

Trish 

 

 

On Dec 5, 2010, at 3:03 PM, Trish Whetzel wrote:





Can you send a few examples of Talairach terms? 

 

Trish 

 

 

On Dec 5, 2010, at 10:36 AM, Daniel Rubin wrote:





Hi

 

Main use case is to send bioportal the Talairach term and return the RID...

Can you provide such webservice??





DR





---

Sent from my iPhone

 ..Please excuse typos..

Daniel L. Rubin, MD

Assistant Professor of Radiology

Richard M. Lucas Center

1201 Welch Road, Office P285

Stanford, CA,  94305-5488

Phone: (650) 427-0025

Fax: (650) 723-5795

Email: dlrubin at stanford.edu

Web: http://rubin.stanford.edu <http://rubin.stanford.edu/> 






On Dec 5, 2010, at 8:11 AM, Trish Whetzel <whetzel at stanford.edu> wrote:

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/>
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/>
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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