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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'>I just saw the announcement of Bioportal 3.8. This is really exciting! <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'>Does the new release address mapping concerns that we had previously (mentioned below) ? If we purchase a third party terminology with mappings to CUIs and import it into our local Bioportal appliance, would it possible to expand the mapping to all other terminologies in the Bioportal appliance based on the CUIs?<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'>Thanks!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Sina<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><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> Monday, February 06, 2012 3:41 PM<br><b>To:</b> Madani,Sina<br><b>Cc:</b> Paul R Alexander; Ray Fergerson; support@bioontology.org<br><b>Subject:</b> Re: [bioontology-support] mappingType<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi Sina, <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I have a few ideas to help you populate the mapping table to use this data to expand results from the Annotator. Can you send information on what ontologies you are using that you would like mapping data for and what mapping data you would like? For example, are you interested in mapping data from UMLS for SNOMED and RxNorm? <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 Feb 6, 2012, at 11:52 AM, Madani,Sina wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thank you Paul.</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'>So I guess for the time being the only component that I can use in service calls for "extended/expanded" annotation is to use  "is-a relationship" feature by setting up maxlevel parameter.</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'> </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 again for clarification</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'> </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'>Sina   </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'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><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"'>Paul R Alexander [<a href="mailto:palexander@stanford.edu">mailto:palexander@stanford.edu</a>]<span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Monday, February 06, 2012 1:45 PM<br><b>To:</b><span class=apple-converted-space> </span>Ray Fergerson<br><b>Cc:</b><span class=apple-converted-space> </span>Madani,Sina;<span class=apple-converted-space> </span><a href="mailto:support@bioontology.org">support@bioontology.org</a><br><b>Subject:</b><span class=apple-converted-space> </span>Re: [bioontology-support] mappingType</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'>Sina,<br><br>Ray is correct with one exception, putting mappings into the mappings REST service will not make them available in the Annotator. There is a table, obs_map, that needs to be populated in order for the data to be available. There is no automated process for this. If you do populate the table, then whatever value you put for the "mapping_type" column is what will be available for use on your system.<br><br>Paul R Alexander<br>Web / UI Developer<br>NCBO BioPortal<br>Stanford Center for Biomedical Informatics Research<br><br><br>On 1/31/12 3:06 PM, Ray Fergerson 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'>Sina,</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'> </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'>Unfortunately our mappings expert is out this week. He can provide a more definitive answer when he returns. My belief though is that, at some point in the past some process was run to generate lots mappings but that this process was not “productionized”. I suspect that it was a one-time effort, probably done by a graduate student. I don’t think that there is anything that we can give you that will generate these mappings. We are currently working on “productionizing” the LOOM (Lexical) mapping generation process. Eventually other automated mapping generators will be “productionized” and available with the VM. For now though I suspect that you will have to generate any mappings you want. There is a process (REST API) for getting the mapping into the system. There just is not a process to decide what should be mapped to what.</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'> </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'>Ray</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'> </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";color:black'>From:</span></b><span class=apple-converted-space><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> </span></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>Madani,Sina [<a href="mailto:AHMadani@mdanderson.org">mailto:AHMadani@mdanderson.org</a>]<span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Tuesday, January 31, 2012 2:47 PM<br><b>To:</b><span class=apple-converted-space> </span>Ray Fergerson;<span class=apple-converted-space> </span><a href="mailto:support@bioontology.org">support@bioontology.org</a><br><b>Subject:</b><span class=apple-converted-space> </span>RE: [bioontology-support] mappingType</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-s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pple-converted-space><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> </span></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'><a href="mailto:bioontology-support-bounces@lists.stanford.edu">bioontology-support-bounces@lists.stanford.edu</a>[<a href="mailto:bioontology-support-bounces@lists.stanford.edu">mailto:bioontology-support-bounces@lists.stanford.edu</a>]<span class=apple-converted-space> </span><b>On Behalf Of</b>Madani,Sina<br><b>Sent:</b><span class=apple-converted-space> </span>Tuesday, January 31, 2012 1:52 PM<br><b>To:</b><span class=apple-converted-space> </span><a href="mailto:support@bioontology.org">support@bioontology.org</a><br><b>Subject:</b><span class=apple-converted-space> </span>[bioontology-support] mappingType</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'>Hi,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>If I want to use mappingTypes parameter, like with inter-cui option, in our local Bioportal instance, do I need to perform any pre processing on the loaded terminologies?<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>I set the type to inter-cui but it doesn't seem to return any mapping for a given term "melanoma"<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'>Thanks!<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Sina<o:p></o:p></span></p></div></div></div><div><p class=MsoNormal><span style='color:black'><br><br><br><br></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><pre><span style='color:black'>_______________________________________________<o:p></o:p></span></pre><pre><span style='color:black'>bioontology-support mailing list<o:p></o:p></span></pre><pre><span style='color:black'><a href="mailto:bioontology-support@lists.stanford.edu">bioontology-support@lists.stanford.edu</a><o:p></o:p></span></pre><pre><span style='color:black'><a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</a><o:p></o:p></span></pre><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Arial","sans-serif"'>_______________________________________________<br>bioontology-support mailing list<br><a href="mailto:bioontology-support@lists.stanford.edu">bioontology-support@lists.stanford.edu</a><br><a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</a><o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>Trish Whetzel, PhD<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>Outreach Coordinator<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>The National Center for Biomedical Ontology<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>Ph: 650-721-2378<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'><a href="http://www.bioontology.org">http://www.bioontology.org</a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p></div><div><div><p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'>"Like" NCBO on Facebook: <a href="http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153">http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153</a></span></span><span style='font-size:13.5pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Arial","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;font-family:"Arial","sans-serif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