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[bioontology-support] Annotator Plus

Kuttichi Keloth, Vipina vk396 at njit.edu
Tue Dec 3 09:54:14 PST 2019


Hi,

Is there documentation available for annotator plus specifically for
understanding Negation?

I tried annotating the text "*Neck supple, no lymphadenopathy, no JVD, no
edema*." specifying the options Match longest only, Detect Negation and
using SNOMED CT as the ontology.
I am getting expected results as shown in the attached screenshot.

But when I click on the link for reproducing these results using the
corresponding *REST API call*
this is what I get
*****************************************************************************************
[{
  "annotatedClass": {
    "@id": "http://purl.bioontology.org/ontology/SNOMEDCT/48162006",
    "@type": "http://www.w3.org/2002/07/owl#Class"
  },
  "hierarchy": [

  ],
  "annotations": [
    {
      "from": 8,
      "to": 13,
      "matchType": "PREF",
      "text": "SUPPLE",
      "negationContext": "AFFIRMED"
    }
  ],
  "mappings": [

  ]
},{
  "annotatedClass": {
    "@id": "http://purl.bioontology.org/ontology/SNOMEDCT/30746006",
    "@type": "http://www.w3.org/2002/07/owl#Class"
  },
  "hierarchy": [

  ],
  "annotations": [
    {
      "from": 23,
      "to": 37,
      "matchType": "PREF",
      "text": "LYMPHADENOPATHY",
      "negationContext": "AFFIRMED"
    }
  ],
  "mappings": [

  ]
},{
  "annotatedClass": {
    "@id": "http://purl.bioontology.org/ontology/SNOMEDCT/79654002",
    "@type": "http://www.w3.org/2002/07/owl#Class"
  },
  "hierarchy": [

  ],
  "annotations": [
    {
      "from": 59,
      "to": 63,
      "matchType": "PREF",
      "text": "EDEMA",
      "negationContext": "AFFIRMED"
    }
  ],
  "mappings": [

  ]
},{
  "annotatedClass": {
    "@id": "http://purl.bioontology.org/ontology/SNOMEDCT/267038008",
    "@type": "http://www.w3.org/2002/07/owl#Class"
  },
  "hierarchy": [

  ],
  "annotations": [
    {
      "from": 59,
      "to": 63,
      "matchType": "PREF",
      "text": "EDEMA",
      "negationContext": "AFFIRMED"
    }
  ],
  "mappings": [

  ]
}]
**************************************************************************************
As you can see for every concept the negationContext is shown as "AFFIRMED".
I tried with different texts but I am not getting "NEGATED" in any case.
Could you please look into this and let me know what is happening in the
case of API calls?

Thank you.
Vipina
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