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<div style="direction:ltr">Yes, Samson’s suggestion is a good one. </div>
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<div style="direction:ltr">I understand your frustration about what is and isn’t included. This is an inherent ambiguity in semantic artifacts, which is deliberately exploited—but with opposing intentions—by different ontology builders, many of which intentionally
 gather terms from multiple sources in an ontology. </div>
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<div style="direction:ltr">Thinking further about what you want to achieve, you could create a View in a BioPortal ontology of just the STY terms you want to be accessed. I may reply to the list with more details, just so people know of this option.
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<div style="direction:ltr">John</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Vanderschaeghe Simon <Simon.Vanderschaeghe@uzgent.be> on behalf of redcap <redcap@uzgent.be><br>
<b>Sent:</b> Wednesday, July 11, 2018 12:09:27 AM<br>
<b>To:</b> John Graybeal<br>
<b>Cc:</b> Samson Tu; support@bioontology.org; redcap<br>
<b>Subject:</b> RE: [bioontology-support] BioPortal: Questions</font>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Hi John,</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt"><span lang="EN-US" style="font-size:11.0pt; font-family:Symbol; color:#1F497D"><span style="">·<span style="font:7.0pt "Times New Roman"">        
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">I understand that there are links between ATC & STY. However, I do not think that STY terms should ever be suggested when searching ATC. If I
 look for “Event” in the <a href="https://www.whocc.no/atc_ddd_index/">ATC index</a>, no matches are found, and I would expect the same behavior when searching ATC through BioPortal.<br>
We are using the ontologies available at BioPortal through REDCap. When users are completing a field that is validated as ATC, they can currently also search & select STY terms, which are not an inherent part of the ontology.<br>
For example, the first result of the request <a href="https://data.bioontology.org/search?q=antibiotic&ontologies=ATC&suggest=true&include=prefLabel,notation,cui&display_links=false&display_context=false&format=json&apikey=6c7cd4f4-830c-4af4-a06d-1454043f6102">
https://data.bioontology.org/search?q=antibiotic&ontologies=ATC&suggest=true&include=prefLabel,notation,cui&display_links=false&display_context=false&format=json&apikey=6c7cd4f4-830c-4af4-a06d-1454043f6102</a> is {"prefLabel":"Antibiotic","notation":"T195","@id":"http://purl.bioontology.org/ontology/STY/T195","@type":"http://www.w3.org/2002/07/owl#Class"}</span></p>
<p class="MsoListParagraph"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt"><span lang="EN-US" style="font-size:11.0pt; font-family:Symbol; color:#1F497D"><span style="">·<span style="font:7.0pt "Times New Roman"">        
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">I just finished testing again:
<a href="https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true">
https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true</a></span></p>
<p class="MsoListParagraph"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoListParagraph" style="margin-left:72.0pt; text-indent:-18.0pt"><span style="font-size:11.0pt; font-family:"Courier New"; color:#1F497D"><span style="">o<span style="font:7.0pt "Times New Roman"">  
</span></span></span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Not logged in<br>
</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"><img border="0" width="1348" height="412" id="Afbeelding_x0020_1" src="cid:image001.png@01D418F5.E61BE930"></span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"></span></p>
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<p class="MsoListParagraph" style="margin-left:72.0pt; text-indent:-18.0pt"><span style="font-size:11.0pt; font-family:"Courier New"; color:#1F497D"><span style="">o<span style="font:7.0pt "Times New Roman"">  
</span></span></span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Logged in<br>
</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"><img border="0" width="1349" height="286" id="Afbeelding_x0020_2" src="cid:image004.png@01D418F6.DE19C800"></span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"></span></p>
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<p class="MsoListParagraph" style="text-indent:-18.0pt"><span lang="EN-US" style="font-size:11.0pt; font-family:Symbol; color:#1F497D"><span style="">·<span style="font:7.0pt "Times New Roman"">        
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Regarding the missing classes in ICD10, I don’t think contacting
<a href="mailto:info@who.int">info@who.int</a> will resolve the issue. I will follow the suggestion Samson Tu made to try and contact “whoever maintains UMLS to explain or correct these missing concepts”.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Kind regards,</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Simon</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"">Van:</span></b><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""> John Graybeal [mailto:jgraybeal@stanford.edu]
<br>
<b>Verzonden:</b> dinsdag 10 juli 2018 20:26<br>
<b>Aan:</b> Vanderschaeghe Simon <Simon.Vand</span><span lang="NL" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">erschaeghe@UZGENT.be><br>
<b>CC:</b> support@bioontology.org; redcap <redcap@UZGENT.be><br>
<b>Onderwerp:</b> Re: [bioontology-support] BioPortal: Questions</span></p>
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<p class="MsoNormal">Simon, </p>
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<p class="MsoNormal">Thank you for your questions.</p>
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<p class="MsoNormal">As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?</p>
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<p class="MsoNormal">There appear to be STY terms declared and used in the ontology; I am not sure if you would argue they should be ignored. We only show the ATC terms (and not the STY terms) in the tree view because we filter the tree view to only include
 the terms that have the same root as the ontology, but the other terms are also present and can be found, as you observe. This BioPortal behavior is by design.</p>
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<p class="MsoNormal">when searching for the term “Event” and Logged in: error message “We're sorry but something has gone wrong. We have been notified of this error.”</p>
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<p class="MsoNormal">While this can be an indication there is faulty information in our index, I am not able to duplicate it. As we just finished uploading the vocabularies in UMLS 2018AA, it is quite possible that you caught the system in a temporary state.
 Can you try this again, please?</p>
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<p class="MsoNormal"> </p>
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<p class="MsoNormal">some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten
 me on the correct procedure to correct an  ontology?</p>
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<p class="MsoNormal"> </p>
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<p class="MsoNormal">We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will
 not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely
 to be a major overhaud of ICD10.</p>
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<p class="MsoNormal">To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't
 reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal
 support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.</p>
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<p class="MsoNormal">I hope these answers help,</p>
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<p class="MsoNormal">John</p>
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<p class="MsoNormal">On Jul 10, 2018, at 6:04 AM, Vanderschaeghe Simon <<a href="mailto:Simon.Vanderschaeghe@uzgent.be">Simon.Vanderschaeghe@uzgent.be</a>> wrote:</p>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"">Dear Support,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal" style="text-indent:-18.0pt"><span lang="EN-US" style="font-size:11.0pt; font-family:Symbol">·</span><span lang="EN-US" style="font-size:7.0pt">        <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">It
 seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the<span class="apple-converted-space"> </span><a href="https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root"><span style="color:#954F72">classes
 for ATC</span></a>, everything seems fine. However, when using “Jump To” in combination with any of the<span class="apple-converted-space"> </span><a href="https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root"><span style="color:#954F72">classes
 for STY</span></a>, all classes from STY can be found within ATC (e.g.<span class="apple-converted-space"> </span><a href="https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true"><span style="color:#954F72">Jump
 To: Event</span></a>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal" style="text-indent:-18.0pt"><span lang="EN-US" style="font-size:11.0pt; font-family:Symbol">·</span><span lang="EN-US" style="font-size:7.0pt">        <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">By
 looking at the aforementioned issue, I noticed that<span class="apple-converted-space"> </span><a href="https://bioportal.bioontology.org/"><span style="color:#954F72">https://bioportal.bioontology.org</span></a><span class="apple-converted-space"> </span>reacts
 differently depending on whether the user is logged in or not. For instance, when<span class="apple-converted-space"> </span><a href="https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true"><span style="color:#954F72">searching
 for the term “Event”</span></a>:</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal" style="text-indent:-18.0pt"><span lang="EN-US" style="font-size:11.0pt; font-family:"Courier New"">o</span><span lang="EN-US" style="font-size:7.0pt">  <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">Not
 logged in: expected behavior</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal" style="text-indent:-18.0pt"><span lang="EN-US" style="font-size:11.0pt; font-family:"Courier New"">o</span><span lang="EN-US" style="font-size:7.0pt">  <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">Logged
 in: error message “We're sorry but something has gone wrong. We have been notified of this error.”</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal" style="text-indent:-18.0pt"><span lang="EN-US" style="font-size:11.0pt; font-family:Symbol">·</span><span lang="EN-US" style="font-size:7.0pt">        <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">Finally,
 some time ago (2018-04-24) I added some<span class="apple-converted-space"> </span><a href="https://bioportal.bioontology.org/ontologies/ICD10/?p=notes"><span style="color:#954F72">notes to International Classification of Diseases, Version 10 (ICD10)</span></a>,
 because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">If you need any other information (e.g. screenshots), please do not hesitate to contact me.</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">Thanks in advance!</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">Kind regards,</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">Simon</span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.5pt; font-family:"Arial","sans-serif"; color:#1E64C8">SIMON VANDERSCHAEGHE</span></b><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US"><br>
</span><span lang="EN-US" style="font-size:9.5pt; font-family:"Arial","sans-serif"">Clinical Data Manager<span class="apple-converted-space"> </span><br>
Bimetra, Clinical Research Center Gent |<span class="apple-converted-space"> </span><a href="http://www.bimetra.be/"><span style="color:#954F72">www.bimetra.be</span></a></span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""><a href="https://www.uzgent.be/"><span style="font-size:12.0pt; font-family:"Times New Roman","serif"; text-decoration:none"><img border="0" width="235" height="50" id="_x0000_i1025" src="https://webresources.uzgent.be/signature/2018/logo_UZ_Gent_mailhandtekening.png" alt="UZ Gent"></span></a></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt; font-family:"Arial","sans-serif"">Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent</span><span class="apple-converted-space"> </span><br>
<span style="font-size:9.5pt; font-family:"Arial","sans-serif"">T</span><span class="apple-converted-space"> </span><span style="font-size:9.5pt; font-family:"Arial","sans-serif"">+32 9 332 09 23 | T +32 9 332 05 30 (secr.)<span class="apple-converted-space"> </span></span><br>
<b><span style="font-size:9.5pt; font-family:"Arial","sans-serif""><a href="mailto:simon.vanderschaeghe@uzgent.be"><span style="color:#1E64C8; text-decoration:none">simon.vanderschaeghe@uzgent.be</span></a></span></b><span class="apple-converted-space"> </span><br>
<span style="font-size:9.5pt; font-family:"Arial","sans-serif"">Ingang 81 | Route 812 |<span class="apple-converted-space"> </span><a href="http://www.uzgent.be/"><b><span style="color:#1E64C8; text-decoration:none">uzgent.be</span></b></a><span class="apple-converted-space"> </span>|<span class="apple-converted-space"> </span></span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""><a href="https://www.facebook.com/uzgent"><span style="font-size:9.5pt; font-family:"Arial","sans-serif"; text-decoration:none"><img border="0" width="13" height="13" id="_x0000_i1026" src="https://webresources.uzgent.be/signature/2018/fb.png" alt="Facebook UZ Gent"></span></a></span><span style="font-size:9.5pt; font-family:"Arial","sans-serif"">|<span class="apple-converted-space"> </span></span><span style="font-size:11.0pt; font-family:"Calibri","sans-serif""><a href="https://twitter.com/UZGent"><span style="font-size:9.5pt; font-family:"Arial","sans-serif"; text-decoration:none"><img border="0" width="13" height="13" id="_x0000_i1027" src="https://webresources.uzgent.be/signature/2018/tw.png" alt="Twitter UZ Gent"></span></a></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt; font-family:"Helvetica","sans-serif"">_______________________________________________<br>
bioontology-support mailing list<br>
</span><a href="mailto:bioontology-support@lists.stanford.edu"><span style="font-size:9.0pt; font-family:"Helvetica","sans-serif"; color:#954F72">bioontology-support@lists.stanford.edu</span></a><span style="font-size:9.0pt; font-family:"Helvetica","sans-serif""><br>
</span><a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support"><span style="font-size:9.0pt; font-family:"Helvetica","sans-serif"; color:#954F72">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</span></a></p>
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<p class="MsoNormal"><span style="color:black">======================== </span></p>
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<p class="MsoNormal"><span style="color:black">John Graybeal</span></p>
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<p class="MsoNormal"><span style="color:black">Technical Program Manager</span></p>
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<p class="MsoNormal"><span style="color:black">Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal</span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:black">Stanford Center for Biomedical Informatics Research<br>
650-736-1632</span></p>
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