Merge pull request #97 from FHIR/terminologyUtility

Terminology utility

app/api_spec.yml

@@ -1280,6 +1280,7 @@ paths:
             type: string
             pattern: '^\s*[Nn][Pp]_\d{4,10}(\.)?(\d{1,2})?\s*$'
           example: "NP_000005.3"
+
   /utilities/find-the-gene:
     get:
       description: |-
@@ -1305,6 +1306,41 @@ paths:
             pattern: '^\s*[Nn][Cc]_\d{4,10}(\.)(\d{1,2}):\d{1,10}-\d{1,10}\s*$'
             example: "NC_000001.11:11794399-11794400"
 
+  /utilities/terminology-translation:
+    get:
+      description: |-
+        This utility demonstrates terminology translations SNOMED to MedGen and DiseaseOntology; ICD10 to MedGen and DiseaseOntology; RxNorm to NCIt.
+      summary: "Translate from one code system to another"
+      operationId: "app.utilities_endpoints.translate_terminology"
+      tags:
+        - "Operations Utilities (not part of balloted HL7 Operations)"
+      responses:
+        '200':
+          description: "Returns matching codes in target code system(s)."
+          content:
+            application/json:
+              schema:
+                type: object
+      parameters:
+        - name: codeSystem
+          in: query
+          required: true
+          description: Code system for code to be translated.
+          schema:
+            type: string
+            enum:
+              - "http://www.nlm.nih.gov/research/umls/rxnorm"
+              - "http://snomed.info/sct"
+              - "http://hl7.org/fhir/sid/icd-10"
+            example: "http://snomed.info/sct"
+        - name: code
+          in: query
+          schema:
+            type: string
+            example: '126949007'
+          required: true
+          description: The code to be translated.
+
 tags:
   - name: Subject Genotype Operations
   - name: Subject Phenotype Operations

app/utilities_endpoints.py

@@ -1,6 +1,13 @@
 from flask import abort, jsonify
 from collections import OrderedDict
 from app import common
+import requests
+
+
+def fetch_concept_map(mapID):
+    url = f"http://hapi.fhir.org/baseR4/ConceptMap/{mapID}"
+    headers = {'Accept': 'application/json'}
+    return requests.get(url, headers=headers)
 
 
 def get_feature_coordinates(
@@ -189,3 +196,97 @@ def find_the_gene(range=None):
         output.append(ord_dict)
 
     return (jsonify(output))
+
+
+def translate_terminology(codeSystem, code):
+    # validate input parameters
+    if codeSystem not in ['http://www.nlm.nih.gov/research/umls/rxnorm', 'http://snomed.info/sct', 'http://hl7.org/fhir/sid/icd-10']:
+        return "unrecognized code system"
+    response = [{}]
+
+    # process rxnorm input
+    if codeSystem == 'http://www.nlm.nih.gov/research/umls/rxnorm':
+        MapRxNorm = fetch_concept_map(44872525)
+        if MapRxNorm.status_code == 200:
+            MapRxNorm = MapRxNorm.json()
+            for element in MapRxNorm["group"][0]["element"]:
+                if element["code"] == code:
+                    response[0]["outcome"] = 'match found'
+                    response[0]["code"] = element["target"][0]["code"]
+                    response[0]["system"] = 'https://ncithesaurus.nci.nih.gov/'
+                    response[0]["display"] = element["target"][0]["display"]
+                    return response
+            response[0]["outcome"] = 'no match found'
+            response[0]["system"] = 'https://ncithesaurus.nci.nih.gov/'
+            return response
+        else:
+            abort(500, "HAPI server error")
+
+    # process snomed input, return disease ontology code AND medgen
+    if codeSystem == 'http://snomed.info/sct':
+        Mapsnomed = fetch_concept_map(44947014)
+        if Mapsnomed.status_code == 200:
+            Mapsnomed = Mapsnomed.json()
+            for element in Mapsnomed["group"][0]["element"]:
+                if element["code"] == code:
+                    response[0]["outcome"] = 'match found'
+                    response[0]["code"] = element["target"][0]["code"]
+                    response[0]["system"] = 'https://disease-ontology.org/'
+                    response[0]["display"] = element["target"][0]["display"]
+                    break
+                response[0]["outcome"] = 'no match found'
+                response[0]["system"] = 'https://disease-ontology.org/'
+        else:
+            abort(500, "HAPI server error")
+
+        Mapsnomed = fetch_concept_map(44872524)
+        if Mapsnomed.status_code == 200:
+            Mapsnomed = Mapsnomed.json()
+            response.append({})
+            for element in Mapsnomed["group"][0]["element"]:
+                if element["code"] == code:
+                    response[1]["outcome"] = 'match found'
+                    response[1]["code"] = element["target"][0]["code"]
+                    response[1]["system"] = 'https://www.ncbi.nlm.nih.gov/medgen/'
+                    response[1]["display"] = element["target"][0]["display"]
+                    break
+                response[1]["outcome"] = 'no match found'
+                response[1]["system"] = 'https://www.ncbi.nlm.nih.gov/medgen/'
+        else:
+            abort(500, "HAPI server error")
+        return response
+
+    # process ICD10 input, return disease ontology AND medgen codes
+    if codeSystem == 'http://hl7.org/fhir/sid/icd-10':
+        code = code.upper().replace(".", "")
+        MapICD10 = fetch_concept_map(44872527)
+        if MapICD10.status_code == 200:
+            MapICD10 = MapICD10.json()
+            for element in MapICD10["group"][0]["element"]:
+                if element["code"] == code:
+                    response[0]["outcome"] = 'match found'
+                    response[0]["code"] = element["target"][0]["code"]
+                    response[0]["system"] = 'https://disease-ontology.org/'
+                    response[0]["display"] = element["target"][0]["display"]
+                    break
+                response[0]["outcome"] = 'no match found'
+                response[0]["system"] = 'https://disease-ontology.org/'
+        else:
+            abort(500, "HAPI server error")
+
+        MapICD10 = fetch_concept_map(44872523)
+        if MapICD10.status_code == 200:
+            MapICD10 = MapICD10.json()
+            response.append({})
+            for element in MapICD10["group"][0]["element"]:
+                if element["code"] == code:
+                    response[1]["outcome"] = "match found"
+                    response[1]["code"] = element["target"][0]["code"]
+                    response[1]["system"] = "https://www.ncbi.nlm.nih.gov/medgen/"
+                    response[1]["display"] = element["target"][0]["display"]
+                    break
+                response[1]["outcome"] = "no match found"
+                response[1]["system"] = "https://www.ncbi.nlm.nih.gov/medgen/"
+        else:
+            abort(500, "HAPI server error")
+        return response