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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Here are a few:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Brodmann Area 10<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Ventral Lateral Nucleus<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Gray Matter<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Medial Dorsal Nucleus<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Lateral Globus Pallidus<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>___________________________________<o:p></o:p></span></p><div style='mso-element:para-border-div;border:none;border-top:double windowtext 1.5pt;padding:1.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'><img width=33 height=33 id="Picture_x0020_4" src="cid:image001.jpg@01CB94A7.B8AE21A0"> Daniel L. Rubin, MD, MS                              </span><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'><img width=25 height=29 id="Picture_x0020_3" src="cid:image002.jpg@01CB94A7.B8AE21A0" alt="Description: Description: Description: Description: cid:image001.jpg@01CB4E1D.AC3DA3D0"></span><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'><o:p></o:p></span></p><p class=MsoNormal style='border:none;padding:0in'><i><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'>            Assistant Professor<o:p></o:p></span></i></p><p class=MsoNormal style='border:none;padding:0in'><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'>            Department of Radiology | Stanford University<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'>            Richard M. Lucas Center</span><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'> </span><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'>| 1201 Welch Road, Office P285</span><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'>            Stanford, CA 94305-5488</span><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'>            Phone: 650-723-9495 | Fax: 650-723-5795</span><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'>            Web: </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><a href="http://rubin.web.stanford.edu/"><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif"'>http://rubin.web.stanford.edu/</span></a><o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt'><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Trish Whetzel [mailto:whetzel@stanford.edu] <br><b>Sent:</b> Sunday, December 05, 2010 3:04 PM<br><b>To:</b> Daniel Rubin<br><b>Cc:</b> Neeraj Agrawal; support@bioontology.org; mej >> mejino@u.washington.edu; Todd Detwiler<br><b>Subject:</b> Re: looking up RIDs from labels<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Can you send a few examples of Talairach terms? <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Trish <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Dec 5, 2010, at 10:36 AM, Daniel Rubin wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><div><p class=MsoNormal><span class=apple-style-span>Hi</span><o:p></o:p></p></div><div><p class=MsoNormal><br><br><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>Main use case is to send bioportal the Talairach term and return the RID...</span><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>Can you provide such webservice??</span><o:p></o:p></p></div><div><p class=MsoNormal><br><br><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>DR</span><o:p></o:p></p></div><div><p class=MsoNormal><br><br><o:p></o:p></p><div><p class=MsoNormal>---<o:p></o:p></p></div><p class=MsoNormal>Sent from my iPhone<o:p></o:p></p><div><p class=MsoNormal> ••Please<span class=apple-style-span> excuse typos••</span><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>Daniel L. Rubin, MD</span><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>Assistant Professor of Radiology</span><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>Richard M. Lucas Center</span><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>1201 Welch Road, Office P285</span><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>Stanford, CA,  94305-5488</span><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>Phone: (650) 427-0025</span><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>Fax: (650) 723-5795</span><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>Email: <a href="mailto:dlrubin@stanford.edu">dlrubin@stanford.edu</a></span><o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-style-span>Web: <a href="http://rubin.stanford.edu/">http://rubin.stanford.edu</a></span><o:p></o:p></p></div><div><p class=MsoNormal><br><br><o:p></o:p></p></div></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><br>On Dec 5, 2010, at 8:11 AM, Trish Whetzel <<a href="mailto:whetzel@stanford.edu">whetzel@stanford.edu</a>> wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><p class=MsoNormal>Hi Daniel,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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? <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Trish<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Dec 4, 2010, at 10:00 PM, Daniel Rubin wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Trish,</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>As per Todd’s question below,<span class=apple-converted-space> </span></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>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?<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Daniel<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>___________________________________</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div style='border:none;border-top:double windowtext 1.5pt;padding:1.0pt 0in 0in 0in;border-width:initial;border-color:initial'><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'><image001.jpg><span class=apple-converted-space> </span>Daniel L. Rubin, MD, MS                             <span class=apple-converted-space> </span></span><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'><image002.jpg></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'>            Assistant Professor</span></i><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'>            Department of Radiology | Stanford University</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'>            Richard M. Lucas Center</span><span class=apple-converted-space><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'> </span></span><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'>| 1201 Welch Road, Office P285</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'>            Stanford, CA 94305-5488</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'>            Phone: 650-723-9495 | Fax: 650-723-5795</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:#1F497D'>            Web:<span class=apple-converted-space> </span></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><a href="http://rubin.web.stanford.edu/"><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif"'>http://rubin.web.stanford.edu/</span></a></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div style='border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt;border-width:initial;border-color:initial'><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in;border-width:initial;border-color:initial'><div><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span class=apple-converted-space><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> </span></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Todd Detwiler [mailto:det@u.washington.edu]<span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Saturday, December 04, 2010 2:36 PM<br><b>To:</b><span class=apple-converted-space> </span>Daniel Rubin<br><b>Cc:</b><span class=apple-converted-space> </span>'Neeraj Agrawal';<span class=apple-converted-space> </span><a href="mailto:mejino@u.washington.edu">mejino@u.washington.edu</a><br><b>Subject:</b><span class=apple-converted-space> </span>Re: looking up RIDs from labels</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div></div></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>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.<span class=apple-converted-space> </span><br>Todd<br><br>On 12/3/2010 7:10 PM, Daniel Rubin wrote:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Todd,</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks. But this assumes I know the RadLex term and I want to look up the</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Talairach label. What if I’m starting with a Talairach string?<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Daniel<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>___________________________________</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div style='border:none;border-top:double windowtext 1.5pt;padding:1.0pt 0in 0in 0in;border-width:initial;border-color:initial'><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'><image003.jpg>Daniel L. Rubin, MD, MS                             <span class=apple-converted-space> </span></span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:black'><image002.jpg></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'>            Assistant Professor</span></i><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial Narrow","sans-serif";color:maroon'>            Department of Radiology | Stanford University</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:black'>            Richard M. Lucas Center | 1201 Welch Road, Office P285</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:black'>            Stanford, CA 94305-5488</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:black'>            Phone: 650-723-9495 | Fax: 650-723-5795</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:black'>            Web:<span class=apple-converted-space> </span></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><a href="http://rubin.web.stanford.edu/"><span style='font-size:10.0pt;font-family:"Arial Narrow \, sans-serif \;"'>http://rubin.web.stanford.edu/</span></a></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div style='border:none;border-left:solid windowtext 1.5pt;padding:0in 0in 0in 4.0pt;border-width:initial;border-color:initial'><div><div style='border:none;border-top:solid windowtext 1.0pt;padding:3.0pt 0in 0in 0in;border-width:initial;border-color:initial'><div><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span class=apple-converted-space><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> </span></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Todd Detwiler [<a href="mailto:det@u.washington.edu">mailto:det@u.washington.edu</a>]<span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Monday, November 29, 2010 2:12 PM<br><b>To:</b><span class=apple-converted-space> </span>Daniel Rubin<br><b>Cc:</b><span class=apple-converted-space> </span>Neeraj Agrawal;<span class=apple-converted-space> </span><a href="mailto:mejino@u.washington.edu">mejino@u.washington.edu</a><br><b>Subject:</b><span class=apple-converted-space> </span>Re: looking up RIDs from labels</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div></div></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>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.<br><br>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<br><br><a href="http://rest.bioontology.org/bioportal/concepts/44843/RID6448">http://rest.bioontology.org/bioportal/concepts/44843/RID6448</a><br><br>Note that the results of the above call include:<br><br>        <entry><br>          <string>Talairach</string><br><br>          <list><br>            <string>*.*.Precentral Gyrus.*.*</string><br>          </list><br>        </entry><br><br>I believe that you will need to parse these results (and potentially perform more service calls) to get the results you are looking for.<br><br>Todd<o:p></o:p></span></p></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></blockquote></div></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>