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[bioontology-support] Annotator Plus

John Graybeal jgraybeal at stanford.edu
Tue Dec 3 20:09:13 PST 2019


Vipina,

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.

We've create ticket https://github.com/ncbo/bioportal-project/issues/142 if you want to add further input or follow our investigation.

John

On Dec 3, 2019, at 9:54 AM, Kuttichi Keloth, Vipina <vk396 at njit.edu<mailto:vk396 at njit.edu>> wrote:

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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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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