Enrich FHIR resources with nlp-insights and QuickUMLS

The nlp-insights service supports enrichment of the following types of FHIR resources:

Condition
AllergyIntolerance

A resource is enriched by adding UMLS codes for detected concepts.

This tutorial provides examples of enrichment.

Configure nlp-insights to use QuickUMLS for NLP

If the nlp-insights service has not been configured to use QuickUMLS by default, follow the steps here.

Enrich a Condition

In this example, the nlp-insights service is sent a bundle that contains a single condition. The condition has a code with text "myocardial infarction", but no coding values. The service will add coding values to the code. This curl command is written to store the response in a file /tmp/output.json for later analysis.

curl  -w "\n%{http_code}\n" -s -o /tmp/output.json -XPOST localhost:5000/discoverInsights  -H 'Content-Type: application/json; charset=utf-8' --data-binary @- << EOF
{
    "resourceType": "Bundle",
    "id": "abc",
    "type": "transaction",
    "entry": [
        {
            "resource": {
                "id": "abcefg-1234567890",
                "code": {
                    "text": "myocardial infarction"
                },
                "subject": {
                    "reference": "Patient/97b51b8d-1d1b-497f-866c-8df5d6cc05a7"
                },
                "resourceType": "Condition"
            },
            "request": {
                "method": "POST",
                "url": "Condition"
            }
        }
    ]
}
EOF

output

200

Enriched condition

A bundle with the enriched condition is returned from the service.

cat /tmp/output.json | jq

Returned Bundle

{
  "id": "abc",
  "entry": [
    {
      "fullUrl": "urn:uuid:cac05d72-a746-4e99-83a1-5f026e18d28b",
      "request": {
        "method": "POST",
        "url": "Condition"
      },
      "resource": {
        "id": "abcefg-1234567890",
        "meta": {
          "extension": [
            {
              "extension": [
                {
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-id",
                  "valueIdentifier": {
                    "system": "urn:alvearie.io/health_patterns/services/nlp_insights/quickumls",
                    "value": "ba52d4828c166df6edbf4e53d029d7d6eaeace98cf50a434a6541147"
                  }
                },
                {
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/path",
                  "valueString": "Condition.code.coding"
                },
                {
                  "extension": [
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/reference",
                      "valueReference": {
                        "reference": "urn:uuid:cac05d72-a746-4e99-83a1-5f026e18d28b"
                      }
                    },
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/reference-path",
                      "valueString": "Condition.code.text"
                    },
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/evaluated-output",
                      "valueAttachment": {
                        "contentType": "application/json",
                        "data": "[{"cui": "C0027051", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 1.0, "snomed_ct": ["500448019", "350357012", "622062019", "37436014", "37437017", "299703017", "241792015", "395860017", "500449010", "299700019", "395861018", "241791010", "37443015", "37440017", "37441018", "37438010", "241790011", "500450010", "395863015", "1784873012", "37442013", "37439019", "500452019", "1784872019", "2747117014", "751689013"], "start": 0, "term": "myocardial infarction"}, {"cui": "C0428953", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T034"], "similarity": 1.0, "snomed_ct": ["2607355010", "108319019", "256460011", "520888012", "224368019", "224361013", "520880017", "256452010", "3300375014", "3300376010", "3300377018", "546248011", "2748878010", "546240016", "2730758010", "804656017", "2607362018", "2619221014", "2619214014", "2612497015", "2620977012", "2693159014"], "start": 0, "term": "myocardial infarction"}, {"cui": "C2926063", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T201"], "similarity": 1.0, "snomed_ct": [], "start": 0, "term": "myocardial infarction"}, {"cui": "C3810814", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T060"], "similarity": 1.0, "snomed_ct": [], "start": 0, "term": "myocardial infarction"}, {"cui": "C0027051", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.95, "snomed_ct": ["500448019", "350357012", "622062019", "37436014", "37437017", "299703017", "241792015", "395860017", "500449010", "299700019", "395861018", "241791010", "37443015", "37440017", "37441018", "37438010", "241790011", "500450010", "395863015", "1784873012", "37442013", "37439019", "500452019", "1784872019", "2747117014", "751689013"], "start": 0, "term": "myocardial infarctions"}, {"cui": "C0155668", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.8260869565217391, "snomed_ct": ["241798016", "299752018", "4031011", "535621012", "299751013", "4032016", "1221564010", "2740994017", "744868013", "578857010", "299754017", "299753011", "2748854017"], "start": 0, "term": "old myocardial infarction"}, {"cui": "C0428953", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T034"], "similarity": 0.8260869565217391, "snomed_ct": ["2607355010", "108319019", "256460011", "520888012", "224368019", "224361013", "520880017", "256452010", "3300375014", "3300376010", "3300377018", "546248011", "2748878010", "546240016", "2730758010", "804656017", "2607362018", "2619221014", "2619214014", "2612497015", "2620977012", "2693159014"], "start": 0, "term": "ecg myocardial infarction"}, {"cui": "C0489577", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T201"], "similarity": 0.8260869565217391, "snomed_ct": [], "start": 0, "term": "myocardial infarction age"}, {"cui": "C3640911", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T033"], "similarity": 0.8260869565217391, "snomed_ct": [], "start": 0, "term": "new myocardial infarction"}, {"cui": "C0027051", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.7916666666666666, "snomed_ct": ["500448019", "350357012", "622062019", "37436014", "37437017", "299703017", "241792015", "395860017", "500449010", "299700019", "395861018", "241791010", "37443015", "37440017", "37441018", "37438010", "241790011", "500450010", "395863015", "1784873012", "37442013", "37439019", "500452019", "1784872019", "2747117014", "751689013"], "start": 0, "term": "myocardial infarction (mi)"}, {"cui": "C0155668", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.7916666666666666, "snomed_ct": ["241798016", "299752018", "4031011", "535621012", "299751013", "4032016", "1221564010", "2740994017", "744868013", "578857010", "299754017", "299753011", "2748854017"], "start": 0, "term": "past myocardial infarction"}, {"cui": "C0428953", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T034"], "similarity": 0.7916666666666666, "snomed_ct": ["2607355010", "108319019", "256460011", "520888012", "224368019", "224361013", "520880017", "256452010", "3300375014", "3300376010", "3300377018", "546248011", "2748878010", "546240016", "2730758010", "804656017", "2607362018", "2619221014", "2619214014", "2612497015", "2620977012", "2693159014"], "start": 0, "term": "ecg: myocardial infarction"}, {"cui": "C0027051", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.76, "snomed_ct": ["500448019", "350357012", "622062019", "37436014", "37437017", "299703017", "241792015", "395860017", "500449010", "299700019", "395861018", "241791010", "37443015", "37440017", "37441018", "37438010", "241790011", "500450010", "395863015", "1784873012", "37442013", "37439019", "500452019", "1784872019", "2747117014", "751689013"], "start": 0, "term": "myocardial infarction, (mi)"}, {"cui": "C0155626", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.76, "snomed_ct": ["241795018", "395858019", "299702010", "94884017", "94885016", "299721019", "1231678011", "299699015", "395862013", "241793013", "241794019", "395857012", "299705012", "795634013", "578838018"], "start": 0, "term": "acute myocardial infarction"}, {"cui": "C3541950", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T033"], "similarity": 0.76, "snomed_ct": [], "start": 0, "term": "acute myocardial infarction"}, {"cui": "C0155626", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.76, "snomed_ct": ["241795018", "395858019", "299702010", "94884017", "94885016", "299721019", "1231678011", "299699015", "395862013", "241793013", "241794019", "395857012", "299705012", "795634013", "578838018"], "start": 0, "term": "myocardial infarction acute"}, {"cui": "C3829910", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T170"], "similarity": 0.76, "snomed_ct": [], "start": 0, "term": "had a myocardial infarction"}, {"cui": "C0746727", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.76, "snomed_ct": [], "start": 0, "term": "septal myocardial infarction"}, {"cui": "C2348362", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T033"], "similarity": 0.76, "snomed_ct": [], "start": 0, "term": "septal myocardial infarction"}, {"cui": "C0155668", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.7307692307692307, "snomed_ct": ["241798016", "299752018", "4031011", "535621012", "299751013", "4032016", "1221564010", "2740994017", "744868013", "578857010", "299754017", "299753011", "2748854017"], "start": 0, "term": "healed myocardial infarction"}, {"cui": "C0340324", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.7307692307692307, "snomed_ct": ["299698011", "350376014", "350377017", "622083013"], "start": 0, "term": "silent myocardial infarction"}, {"cui": "C3898652", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.7307692307692307, "snomed_ct": [], "start": 0, "term": "type 5 myocardial infarction"}, {"cui": "C3898656", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.7307692307692307, "snomed_ct": [], "start": 0, "term": "type 3 myocardial infarction"}, {"cui": "C3898657", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T170"], "similarity": 0.7307692307692307, "snomed_ct": [], "start": 0, "term": "type 2 myocardial infarction"}, {"cui": "C3898658", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T033"], "similarity": 0.7307692307692307, "snomed_ct": [], "start": 0, "term": "type 1 myocardial infarction"}, {"cui": "C2825159", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T201"], "similarity": 0.7037037037037037, "snomed_ct": [], "start": 0, "term": "date of myocardial infarction"}, {"cui": "C3845502", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.7037037037037037, "snomed_ct": [], "start": 0, "term": "myocardial infarction, stroke"}, {"cui": "C3898653", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.7037037037037037, "snomed_ct": [], "start": 0, "term": "type 4c myocardial infarction"}, {"cui": "C3898654", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.7037037037037037, "snomed_ct": [], "start": 0, "term": "type 4b myocardial infarction"}, {"cui": "C3898655", "end": 21, "ngram": "myocardial infarction", "preferred": 1, "semtypes": ["T047"], "similarity": 0.7037037037037037, "snomed_ct": [], "start": 0, "term": "type 4a myocardial infarction"}]"
                      }
                    }
                  ],
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-detail"
                }
              ],
              "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight"
            }
          ]
        },
        "code": {
          "coding": [
            {
              "extension": [
                {
                  "extension": [
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-id",
                      "valueIdentifier": {
                        "system": "urn:alvearie.io/health_patterns/services/nlp_insights/quickumls",
                        "value": "ba52d4828c166df6edbf4e53d029d7d6eaeace98cf50a434a6541147"
                      }
                    },
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/category",
                      "valueCodeableConcept": {
                        "coding": [
                          {
                            "code": "natural-language-processing",
                            "display": "NLP",
                            "system": "http://ibm.com/fhir/cdm/CodeSystem/insight-category-code-system"
                          }
                        ],
                        "text": "NLP"
                      }
                    }
                  ],
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-summary"
                }
              ],
              "code": "C0027051",
              "display": "myocardial infarction",
              "system": "http://terminology.hl7.org/CodeSystem/umls"
            }
          ],
          "text": "myocardial infarction"
        },
        "subject": {
          "reference": "Patient/97b51b8d-1d1b-497f-866c-8df5d6cc05a7"
        },
        "resourceType": "Condition"
      }
    }
  ],
  "type": "transaction",
  "resourceType": "Bundle"
}

Condition derived codes

Quick UMLS understands UMLS concept codes. As a result a code has been added to the resource.

System	Code	Display
http://terminology.hl7.org/CodeSystem/umls	C0027051	myocardial infarction

Enrich an allergy intolerance

In this example, a bundle with two allergy intolreance resources is sent to the nlp insights server. The first has a code with text "peanut", and the second resource has a code with text "amoxicillin".

Both resources contain only text and do not contain any codes for the allergy. The nlp-insights service will enrich the resources with a UMLS code for the provided text.

As in the prior example, the returned bundle is saved in a file /tmp/output.json for later analysis.

curl  -w "\n%{http_code}\n" -s -o /tmp/output.json -XPOST localhost:5000/discoverInsights  -H 'Content-Type: application/json; charset=utf-8' --data-binary @- << EOF
{
    "resourceType": "Bundle",
    "id": "abc",
    "type": "transaction",
    "entry": [
        {
            "resource": {
                "id": "wxyz-123",
                "code": {
                    "text": "peanut"
                },
                "patient": {
                    "reference": "Patient/97b51b8d-1d1b-497f-866c-8df5d6cc05a7"
                },
                "resourceType": "AllergyIntolerance"
            },
            "request": {
                "method": "POST",
                "url": "Condition"
            }
        },
        {
            "resource": {
                "id": "qrstuv-123",
                "code": {
                    "text": "amoxicillin"
                },
                "patient": {
                    "reference": "Patient/97b51b8d-1d1b-497f-866c-8df5d6cc05a7"
                },
                "resourceType": "AllergyIntolerance"
            },
            "request": {
                "method": "POST",
                "url": "Condition"
            }
        }

    ]
}
EOF

output

200

Enriched Allergy Intolerance resources

A bundle is returned that contains the enriched allergy intolerance resources. Each resource now contains the additional derived code values.

cat /tmp/output.json | jq

Returned Bundle

{
  "id": "abc",
  "entry": [
    {
      "fullUrl": "urn:uuid:001610dd-2d6d-4e18-8784-4de72ddde238",
      "request": {
        "method": "POST",
        "url": "Condition"
      },
      "resource": {
        "id": "wxyz-123",
        "meta": {
          "extension": [
            {
              "extension": [
                {
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-id",
                  "valueIdentifier": {
                    "system": "urn:alvearie.io/health_patterns/services/nlp_insights/quickumls",
                    "value": "4f6cfb8db4b6452a76cf7bcf373ef612c5b80f7dd2daeafdf07408cf"
                  }
                },
                {
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/path",
                  "valueString": "AllergyIntolerance.code.coding"
                },
                {
                  "extension": [
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/reference",
                      "valueReference": {
                        "reference": "urn:uuid:001610dd-2d6d-4e18-8784-4de72ddde238"
                      }
                    },
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/reference-path",
                      "valueString": "AllergyIntolerance.code.text"
                    },
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/evaluated-output",
                      "valueAttachment": {
                        "contentType": "application/json",
                        "data": "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"
                      }
                    }
                  ],
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-detail"
                }
              ],
              "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight"
            }
          ]
        },
        "code": {
          "coding": [
            {
              "extension": [
                {
                  "extension": [
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-id",
                      "valueIdentifier": {
                        "system": "urn:alvearie.io/health_patterns/services/nlp_insights/quickumls",
                        "value": "4f6cfb8db4b6452a76cf7bcf373ef612c5b80f7dd2daeafdf07408cf"
                      }
                    },
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/category",
                      "valueCodeableConcept": {
                        "coding": [
                          {
                            "code": "natural-language-processing",
                            "display": "NLP",
                            "system": "http://ibm.com/fhir/cdm/CodeSystem/insight-category-code-system"
                          }
                        ],
                        "text": "NLP"
                      }
                    }
                  ],
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-summary"
                }
              ],
              "code": "C0559470",
              "display": "peanut allergy",
              "system": "http://terminology.hl7.org/CodeSystem/umls"
            }
          ],
          "text": "peanut"
        },
        "patient": {
          "reference": "Patient/97b51b8d-1d1b-497f-866c-8df5d6cc05a7"
        },
        "resourceType": "AllergyIntolerance"
      }
    },
    {
      "fullUrl": "urn:uuid:52044e2f-7878-4d36-a949-717599c08f3c",
      "request": {
        "method": "POST",
        "url": "Condition"
      },
      "resource": {
        "id": "qrstuv-123",
        "meta": {
          "extension": [
            {
              "extension": [
                {
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-id",
                  "valueIdentifier": {
                    "system": "urn:alvearie.io/health_patterns/services/nlp_insights/quickumls",
                    "value": "dfc3ecbd910316a17364ce77f4e959ec627dbaa7251d051eabcfe3f6"
                  }
                },
                {
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/path",
                  "valueString": "AllergyIntolerance.code.coding"
                },
                {
                  "extension": [
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/reference",
                      "valueReference": {
                        "reference": "urn:uuid:52044e2f-7878-4d36-a949-717599c08f3c"
                      }
                    },
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/reference-path",
                      "valueString": "AllergyIntolerance.code.text"
                    },
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/evaluated-output",
                      "valueAttachment": {
                        "contentType": "application/json",
                        "data": "W3siY3VpIjogIkMwNTcxNDE3IiwgImVuZCI6IDE5LCAibmdyYW0iOiAiYW1veGljaWxsaW4gYWxsZXJneSIsICJwcmVmZXJyZWQiOiAxLCAic2VtdHlwZXMiOiBbIlQwNDciXSwgInNpbWlsYXJpdHkiOiAxLjAsICJzbm9tZWRfY3QiOiBbIjI0NzYzMDkwMTYiLCAiNDM0NzgyMDEwIiwgIjI5NTk3NTgwMTQiLCAiNjg5NTEzMDE2Il0sICJzdGFydCI6IDAsICJ0ZXJtIjogImFtb3hpY2lsbGluIGFsbGVyZ3kifV0="
                      }
                    }
                  ],
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-detail"
                }
              ],
              "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight"
            }
          ]
        },
        "code": {
          "coding": [
            {
              "extension": [
                {
                  "extension": [
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-id",
                      "valueIdentifier": {
                        "system": "urn:alvearie.io/health_patterns/services/nlp_insights/quickumls",
                        "value": "dfc3ecbd910316a17364ce77f4e959ec627dbaa7251d051eabcfe3f6"
                      }
                    },
                    {
                      "url": "http://ibm.com/fhir/cdm/StructureDefinition/category",
                      "valueCodeableConcept": {
                        "coding": [
                          {
                            "code": "natural-language-processing",
                            "display": "NLP",
                            "system": "http://ibm.com/fhir/cdm/CodeSystem/insight-category-code-system"
                          }
                        ],
                        "text": "NLP"
                      }
                    }
                  ],
                  "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-summary"
                }
              ],
              "code": "C0571417",
              "display": "amoxicillin allergy",
              "system": "http://terminology.hl7.org/CodeSystem/umls"
            }
          ],
          "text": "amoxicillin"
        },
        "patient": {
          "reference": "Patient/97b51b8d-1d1b-497f-866c-8df5d6cc05a7"
        },
        "resourceType": "AllergyIntolerance"
      }
    }
  ],
  "type": "transaction",
  "resourceType": "Bundle"
}

Allergy Intolerance derived codes

The food allergy resource has been enriched with a new code.

System	Code	Display
http://terminology.hl7.org/CodeSystem/umls	C0559470	peanut allergy

In a similar way, the medication allergy resource has been enriched with a new code.

System	Code	Display
http://terminology.hl7.org/CodeSystem/umls	C0571417	amoxicillin allergy

Evidence

nlp-insights enriches resources according to the Alvearie FHIR IG.

The nlp-insights service adds detailed information to the enriched resource to explain what caused the additional codes to be added.

Insight Summary

Each coding that has been derived by NLP contains an insight summary extension that can be examined to determine which insight derived the code.

For example consider the UMLS code C0559470 that was added to the allergy intolerance resource wxyz-123.

C0559470 coding in AllergyIntolerance wxyz-123

{
  "extension": [
    {
      "extension": [
        {
          "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-id",
          "valueIdentifier": {
            "system": "urn:alvearie.io/health_patterns/services/nlp_insights/quickumls",
            "value": "4f6cfb8db4b6452a76cf7bcf373ef612c5b80f7dd2daeafdf07408cf"
          }
        },
        {
          "url": "http://ibm.com/fhir/cdm/StructureDefinition/category",
          "valueCodeableConcept": {
            "coding": [
              {
                "code": "natural-language-processing",
                "display": "NLP",
                "system": "http://ibm.com/fhir/cdm/CodeSystem/insight-category-code-system"
              }
            ],
            "text": "NLP"
          }
        }
      ],
      "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-summary"
    }
  ],
  "code": "C0559470",
  "display": "peanut allergy",
  "system": "http://terminology.hl7.org/CodeSystem/umls"
}

The summary extension has been added to the coding. The summary has an insight id and category. The insight id has a system and identifier that together identify the insight. In this example, the system tells us that the insight was discovered using QuickUMLS. The identifier value is unique (within the system) to this insight, and may be used to find the insight extension for the insight in the resource meta.

When nlp-insights derives codes, it will create one insight for all derived codes that are created from the same text. It is common for all summary extensions to refer to the same insight id.

The category tells us that the coding was derived using Natural Language Processing.

Insight Extension in Resource Meta

The insight identified by the summary extension has an insight extension in the resource's meta. The insight extension contains lots of details about what the insight applies to and why it was created.

Insight extension in the meta for AllergyIntolerance wxyz-123

{
  "extension": [
    {
      "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-id",
      "valueIdentifier": {
        "system": "urn:alvearie.io/health_patterns/services/nlp_insights/quickumls",
        "value": "4f6cfb8db4b6452a76cf7bcf373ef612c5b80f7dd2daeafdf07408cf"
      }
    },
    {
      "url": "http://ibm.com/fhir/cdm/StructureDefinition/path",
      "valueString": "AllergyIntolerance.code.coding"
    },
    {
      "extension": [
        {
          "url": "http://ibm.com/fhir/cdm/StructureDefinition/reference",
          "valueReference": {
            "reference": "urn:uuid:001610dd-2d6d-4e18-8784-4de72ddde238"
          }
        },
        {
          "url": "http://ibm.com/fhir/cdm/StructureDefinition/reference-path",
          "valueString": "AllergyIntolerance.code.text"
        },
        {
          "url": "http://ibm.com/fhir/cdm/StructureDefinition/evaluated-output",
          "valueAttachment": {
            "contentType": "application/json",
            "data": "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"
          }
        }
      ],
      "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight-detail"
    }
  ],
  "url": "http://ibm.com/fhir/cdm/StructureDefinition/insight"
}

The extensions of interest within the insight extension are:

extension	purpose
insight-id	identifier for the insight.
path	HL7 FHIR Path to the part of this resource that the insight applies to. This is the location where derived codes have been added.
insight-detail	Detailed supporting evidence for the insight.

Insight detail

The insight detail extension provides information about why the insight got created:

Extension	Purpose
reference	The resource that contained the text that was used to create the insight. For enrichment, this will always be the enriched resource, the insight is derived from the same resource that the insight pertains to.
reference-path	HL7 FHIR Path that describes the location of the text used to create the insight (within reference)
evaluated-output	base64 response from the ACD Service