From 61b10d7483fc474d0d1d10d697fb61a8821e9f56 Mon Sep 17 00:00:00 2001
From: Javier Rodriguez Vidal <jvrodrivi@gmail.com>
Date: Fri, 19 Feb 2021 11:12:00 +0000
Subject: [PATCH] Script que permite componer los conceptos de las anotaciones
 BERT (B, B+I)

---
 UMLS_Extractor/ConceptExtractor.py | 59 ++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 UMLS_Extractor/ConceptExtractor.py

diff --git a/UMLS_Extractor/ConceptExtractor.py b/UMLS_Extractor/ConceptExtractor.py
new file mode 100644
index 0000000..49fa246
--- /dev/null
+++ b/UMLS_Extractor/ConceptExtractor.py
@@ -0,0 +1,59 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Jan 27 10:26:48 2021
+Library
+"""
+
+# Extract the B or B+Is concepts and their entities, starts and ends.
+# Input: list of list of dictionaries where each dictionary: 
+# {'word' : '', 'score' : '', entity : '', index : '', start : '', end : ''}
+# Output: List of tuples with four elements. [(concept, entity, start, end)]
+def extractionOfConcepts(annotations):
+    
+    #VARIABLES
+    entities = []
+
+    complete_word = '' 
+    start = 0
+    end = 0
+    entity = ''
+    i=0
+
+    for document in annotations:   
+        i = i+1
+        for word in document:
+            #B
+            if word.get('entity')[0] == 'B':   
+                
+                #If there was a previous concept started, finish it
+                if len(complete_word) > 0:
+                    entities.append((complete_word, entity, start, end))
+                    complete_word = ''
+                    start = 0
+                    end = 0
+                    entity = ''
+                    
+                #Strat a new concept
+                complete_word = word.get('word')
+                start = word.get('start')
+                end = word.get('end')
+                entity = word.get('entity')[2:]
+                
+            #I
+            elif word.get('entity')[0] == 'I':
+                #if there isnt a B before, ignore
+                if len(complete_word) > 0:
+                    complete_word = complete_word + ' ' + word.get('word')
+                    #Update end
+                    end = word.get('end')
+                
+            #O
+            elif word.get('entity')[0] == 'O':
+                #If there was a previous concept started, finish it
+                if len(complete_word) > 0:
+                    entities.append((complete_word, entity, start, end))
+                    complete_word = ''
+                    start = 0
+                    end = 0
+                    entity = ''
+    return entities
-- 
2.24.1