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Vipina,
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<div class="">Thank you for this report. We have started checking in to this with our colleagues who developed this code, and will get back to you once we have more information.</div>
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<div class="">We've create ticket <a href="https://github.com/ncbo/bioportal-project/issues/142" class="">https://github.com/ncbo/bioportal-project/issues/142</a> if you want to add further input or follow our investigation.</div>
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<div class="">John<br class="">
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<div class="">On Dec 3, 2019, at 9:54 AM, Kuttichi Keloth, Vipina <<a href="mailto:vk396@njit.edu" class="">vk396@njit.edu</a>> wrote:</div>
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<div dir="ltr" class="">Hi,
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<div class="">Is there documentation available for annotator plus specifically for understanding Negation?</div>
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<div class="">I tried annotating the text "<b class="">Neck supple, no lymphadenopathy, no JVD, no edema</b>." specifying the options Match longest only, Detect Negation and using SNOMED CT as the ontology. </div>
<div class="">I am getting expected results as shown in the attached screenshot.</div>
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<div class="">But when I click on the link for reproducing these results using the corresponding
<b class="">REST API call</b></div>
<div class="">this is what I get</div>
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[{<br class="">
  "annotatedClass": {<br class="">
    "@id": "<a href="http://purl.bioontology.org/ontology/SNOMEDCT/48162006" class="">http://purl.bioontology.org/ontology/SNOMEDCT/48162006</a>",<br class="">
    "@type": "<a href="http://www.w3.org/2002/07/owl#Class" class="">http://www.w3.org/2002/07/owl#Class</a>"<br class="">
  },<br class="">
  "hierarchy": [<br class="">
    <br class="">
  ],<br class="">
  "annotations": [<br class="">
    {<br class="">
      "from": 8,<br class="">
      "to": 13,<br class="">
      "matchType": "PREF",<br class="">
      "text": "SUPPLE",<br class="">
      "negationContext": "<span style="background-color:rgb(0,255,0)" class="">AFFIRMED</span>"<br class="">
    }<br class="">
  ],<br class="">
  "mappings": [<br class="">
    <br class="">
  ]<br class="">
},{<br class="">
  "annotatedClass": {<br class="">
    "@id": "<a href="http://purl.bioontology.org/ontology/SNOMEDCT/30746006" class="">http://purl.bioontology.org/ontology/SNOMEDCT/30746006</a>",<br class="">
    "@type": "<a href="http://www.w3.org/2002/07/owl#Class" class="">http://www.w3.org/2002/07/owl#Class</a>"<br class="">
  },<br class="">
  "hierarchy": [<br class="">
    <br class="">
  ],<br class="">
  "annotations": [<br class="">
    {<br class="">
      "from": 23,<br class="">
      "to": 37,<br class="">
      "matchType": "PREF",<br class="">
      "text": "LYMPHADENOPATHY",<br class="">
      "negationContext": <span style="background-color:rgb(255,0,0)" class="">"AFFIRMED"</span><br class="">
    }<br class="">
  ],<br class="">
  "mappings": [<br class="">
    <br class="">
  ]<br class="">
},{<br class="">
  "annotatedClass": {<br class="">
    "@id": "<a href="http://purl.bioontology.org/ontology/SNOMEDCT/79654002" class="">http://purl.bioontology.org/ontology/SNOMEDCT/79654002</a>",<br class="">
    "@type": "<a href="http://www.w3.org/2002/07/owl#Class" class="">http://www.w3.org/2002/07/owl#Class</a>"<br class="">
  },<br class="">
  "hierarchy": [<br class="">
    <br class="">
  ],<br class="">
  "annotations": [<br class="">
    {<br class="">
      "from": 59,<br class="">
      "to": 63,<br class="">
      "matchType": "PREF",<br class="">
      "text": "EDEMA",<br class="">
      "negationContext": <span style="background-color:rgb(255,0,0)" class="">"AFFIRMED"</span><br class="">
    }<br class="">
  ],<br class="">
  "mappings": [<br class="">
    <br class="">
  ]<br class="">
},{<br class="">
  "annotatedClass": {<br class="">
    "@id": "<a href="http://purl.bioontology.org/ontology/SNOMEDCT/267038008" class="">http://purl.bioontology.org/ontology/SNOMEDCT/267038008</a>",<br class="">
    "@type": "<a href="http://www.w3.org/2002/07/owl#Class" class="">http://www.w3.org/2002/07/owl#Class</a>"<br class="">
  },<br class="">
  "hierarchy": [<br class="">
    <br class="">
  ],<br class="">
  "annotations": [<br class="">
    {<br class="">
      "from": 59,<br class="">
      "to": 63,<br class="">
      "matchType": "PREF",<br class="">
      "text": "EDEMA",<br class="">
      "negationContext": <span style="background-color:rgb(255,0,0)" class="">"AFFIRMED"</span><br class="">
    }<br class="">
  ],<br class="">
  "mappings": [<br class="">
    <br class="">
  ]<br class="">
}]
<div class="">**************************************************************************************</div>
<div class="">As you can see for every concept the negationContext is shown as "AFFIRMED".</div>
<div class="">I tried with different texts but I am not getting "NEGATED" in any case.</div>
<div class="">Could you please look into this and let me know what is happening in the case of API calls?</div>
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<div class="">Thank you.</div>
<div class="">Vipina</div>
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<span id="cid:f_k3q5n7ps0"><negation.png></span>_______________________________________________<br class="">
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https://mailman.stanford.edu/mailman/listinfo/bioontology-support<br class="">
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</blockquote>
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========================
<div class="">John Graybeal</div>
<div class="">Technical Program Manager</div>
<div class="">Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal</div>
<div class="">Stanford Center for Biomedical Informatics Research<br class="">
650-736-1632  | ORCID  0000-0001-6875-5360</div>
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