<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><pre><font class="Apple-style-span" face="Arial" size="4"><span class="Apple-style-span" style="font-size: 14px;">I checked with the developers on this item and as it turns out, the source data contains the term identifier in this form, e.g.  B7... (Full example from source ontology file: C0086692|ENG|S|L0085417|VO|S0599364|Y|A0654833||||RCD|PT|B7...|Benign tumour|3|N|256| ).  The Full Ids, e.g. <a href="http://purl.bioontology.org/ontology/RCD/B7">http://purl.bioontology.org/ontology/RCD/B7</a>...<span class="Apple-style-span" style="font-size: medium; white-space: normal; "> <span class="Apple-style-span" style="font-size: 14px; white-space: pre; "> do resolve, however I see that BioPortal is creating the hyperlink without one of the "." as part of the link.</span></span></span></font></pre><pre><font class="Apple-style-span" face="Arial" size="4"><span class="Apple-style-span" style="font-size: 14px;"><span class="Apple-style-span" style="font-size: medium; white-space: normal; "><span class="Apple-style-span" style="font-size: 14px; white-space: pre; ">Trish </span></span></span></font></pre></div><br><div><div>On Sep 28, 2010, at 4:23 PM, Trish Whetzel wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Marco,</div><div><br></div><div>Thanks for pointing this out. I was able to reproduce this error directly using the Annotator web service and will investigate further. </div><div><br></div><div>Trish </div><div><br></div><br><div><div>On Sep 28, 2010, at 3:12 PM, Marco Ocana wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; color: rgb(0, 0, 0); "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">My name is Marco Ocana and I am a software consultant. I work with Tim Clark from Harvard University/MGH.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">We are working on integrating your Annotator Web Service with a tool that we are developing.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">We encountered a problem with the results returned from the service.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Some of the URIs for the found concepts are invalid.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Below is an extract of the results. Note the ... at the end of the fullId element value. Same for localConceptId.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">We got this result from the Java/Groovy client we are creating and from your HTML web form at:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span><a target="_blank" href="http://rest.bioontology.org/test_oba.html">http://rest.bioontology.org/test_oba.html</a></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To reproduce, I just entered (without quotes):</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">"This is a test to see if we can find breast cancer or alzheimers disease"</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">The only option on the web form I changed or set was XML output.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Marco Ocana</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Balboa Systems, Inc.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><p class="p1"><span class="s1"><</span>annotationBean<span class="s1">></span></p><p class="p2">         <span class="Apple-converted-space"> </span><span class="s1"><</span><span class="s2">score</span><span class="s1">></span>7<span class="s1"></</span><span class="s2">score</span><span class="s1">></span></p><p class="p2">         <span class="Apple-converted-space"> </span><span class="s1"><</span><span class="s2">concept</span><span class="s1">></span></p><p class="p2">           <span class="Apple-converted-space"> </span><span class="s1"><</span><span class="s2">id</span><span class="s1">></span>7576609<span class="s1"></</span><span class="s2">id</span><span class="s1">></span></p><p class="p1"><span class="s3">           <span class="Apple-converted-space"> </span></span><span class="s1"><</span>localConceptId<span class="s1">></span><span class="s3">42295/B7...</span><span class="s1"></</span>localConceptId<span class="s1">></span></p><p class="p1"><span class="s3">           <span class="Apple-converted-space"> </span></span><span class="s1"><</span>localOntologyId<span class="s1">></span><span class="s3">42295</span><span class="s1"></</span>localOntologyId<span class="s1">></span></p><p class="p1"><span class="s3">           <span class="Apple-converted-space"> </span></span><span class="s1"><</span>isTopLevel<span class="s1">></span><span class="s3">0</span><span class="s1"></</span>isTopLevel<span class="s1">></span></p><p class="p2">           <span class="Apple-converted-space"> </span><span class="s1"><</span><span class="s2">fullId</span><span class="s1">></span><span><a target="_blank" href="http://purl.bioontology.org/ontology/RCD/B7">http://purl.bioontology.org/ontology/RCD/B7</a>...</span><span class="s1"></</span><span class="s2">fullId</span><span class="s1">></span></p><p class="p1"><span class="s3">           <span class="Apple-converted-space"> </span></span><span class="s1"><</span>preferredName<span class="s1">></span><span class="s3">Benign tumour</span><span class="s1"></</span>preferredName<span class="s1">></span></p><p class="p2">           <span class="Apple-converted-space"> </span><span class="s1"><</span><span class="s2">synonyms</span><span class="s1">></span></p><p class="p2">             <span class="Apple-converted-space"> </span><span class="s1"><</span><span class="s2">string</span><span class="s1">></span>Benign neoplasm<span class="s1"></</span><span class="s2">string</span><span class="s1">></span></p><p class="p2">           <span class="Apple-converted-space"> </span><span class="s1"></</span><span class="s2">synonyms</span><span class="s1">></span></p><p class="p2">           <span class="Apple-converted-space"> </span><span class="s1"><</span><span class="s2">definitions</span><span class="s1">/></span></p><p class="p1"><span class="s3">           <span class="Apple-converted-space"> </span></span><span class="s1"><</span>semanticTypes<span class="s1">></span></p><p class="p1"><span class="s3">             <span class="Apple-converted-space"> </span></span><span class="s1"><</span>semanticTypeBean<span class="s1">></span></p><p class="p2">               <span class="Apple-converted-space"> </span><span class="s1"><</span><span class="s2">id</span><span class="s1">></span>10256193<span class="s1"></</span><span class="s2">id</span><span class="s1">></span></p><p class="p1"><span class="s3">               <span class="Apple-converted-space"> </span></span><span class="s1"><</span>semanticType<span class="s1">></span><span class="s3">T191</span><span class="s1"></</span>semanticType<span class="s1">></span></p><p class="p2">               <span class="Apple-converted-space"> </span><span class="s1"><</span><span class="s2">description</span><span class="s1">></span>Neoplastic Process<span class="s1"></</span><span class="s2">description</span><span class="s1">></span></p><p class="p1"><span class="s3">             <span class="Apple-converted-space"> </span></span><span class="s1"></</span>semanticTypeBean<span class="s1">></span></p><p class="p1"><span class="s3">           <span class="Apple-converted-space"> </span></span><span class="s1"></</span>semanticTypes<span class="s1">></span></p><p class="p2">         <span class="Apple-converted-space"> </span><span class="s1"></</span><span class="s2">concept</span><span class="s1">></span></p></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; position: fixed; "></div></div>_______________________________________________<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><br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div>Trish Whetzel, PhD</div><div>Outreach Coordinator</div><div>The National Center for Biomedical Ontology</div><div>Ph: 650-721-2378</div><div><a href="mailto:whetzel@stanford.edu">whetzel@stanford.edu</a></div><div><a href="http://www.bioontology.org/">http://www.bioontology.org</a></div><div><br></div><div> </div></div></span>
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<br></div>_______________________________________________<br>bioontology-support mailing list<br><a href="mailto:bioontology-support@lists.stanford.edu">bioontology-support@lists.stanford.edu</a><br>https://mailman.stanford.edu/mailman/listinfo/bioontology-support<br></blockquote></div><br></body></html>