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README.md

@@ -1,84 +1,69 @@
 ---
 dataset_info:
   features:
-    - name: text
-      dtype: string
-    - name: tokens
-      sequence: string
-    - name: tokens_offsets
-      sequence:
-        sequence: int32
-    - name: clinical_entity_tags
-      sequence:
-        class_label:
-          names:
-            "0": O
-            "1": B-CLINENTITY
-            "2": I-CLINENTITY
-    - name: temporal_information_tags
-      sequence:
-        class_label:
-          names:
-            "0": O
-            "1": B-EVENT
-            "2": B-ACTOR
-            "3": B-BODYPART
-            "4": B-TIMEX3
-            "5": B-RML
-            "6": I-EVENT
-            "7": I-ACTOR
-            "8": I-BODYPART
-            "9": I-TIMEX3
-            "10": I-RML
+  - name: text
+    dtype: string
+  - name: tokens
+    sequence: string
+  - name: tokens_offsets
+    sequence:
+      sequence: int32
+  - name: clinical_entity_tags
+    sequence:
+      class_label:
+        names:
+          '0': O
+          '1': B-CLINENTITY
+          '2': I-CLINENTITY
+  - name: temporal_information_tags
+    sequence:
+      class_label:
+        names:
+          '0': O
+          '1': B-EVENT
+          '2': B-ACTOR
+          '3': B-BODYPART
+          '4': B-TIMEX3
+          '5': B-RML
+          '6': I-EVENT
+          '7': I-ACTOR
+          '8': I-BODYPART
+          '9': I-TIMEX3
+          '10': I-RML
   config_name: e3c
   splits:
-    - name: en.layer1
-      num_bytes: 1280534
-      num_examples: 1520
-    - name: en.layer2
-      num_bytes: 2566638
-      num_examples: 2873
-    - name: en.layer2.validation
-      num_bytes: 290490
-      num_examples: 334
-    - name: es.layer1
-      num_bytes: 1262006
-      num_examples: 1134
-    - name: es.layer2
-      num_bytes: 2524461
-      num_examples: 2347
-    - name: es.layer2.validation
-      num_bytes: 278045
-      num_examples: 261
-    - name: eu.layer1
-      num_bytes: 1537670
-      num_examples: 3126
-    - name: eu.layer2
-      num_bytes: 853766
-      num_examples: 1594
-    - name: eu.layer2.validation
-      num_bytes: 227044
-      num_examples: 468
-    - name: fr.layer1
-      num_bytes: 1275362
-      num_examples: 1109
-    - name: fr.layer2
-      num_bytes: 2581993
-      num_examples: 2389
-    - name: fr.layer2.validation
-      num_bytes: 275163
-      num_examples: 293
-    - name: it.layer1
-      num_bytes: 1299388
-      num_examples: 1146
-    - name: it.layer2
-      num_bytes: 2697483
-      num_examples: 2436
-    - name: it.layer2.validation
-      num_bytes: 291866
-      num_examples: 275
+  - name: en.layer1
+    num_bytes: 1273610
+    num_examples: 1520
+  - name: en.layer2
+    num_bytes: 2550153
+    num_examples: 2873
+  - name: es.layer1
+    num_bytes: 1252571
+    num_examples: 1134
+  - name: es.layer2
+    num_bytes: 2498266
+    num_examples: 2347
+  - name: eu.layer1
+    num_bytes: 1519021
+    num_examples: 3126
+  - name: eu.layer2
+    num_bytes: 839955
+    num_examples: 1594
+  - name: fr.layer1
+    num_bytes: 1258738
+    num_examples: 1109
+  - name: fr.layer2
+    num_bytes: 2628628
+    num_examples: 2389
+  - name: it.layer1
+    num_bytes: 1276534
+    num_examples: 1146
+  - name: it.layer2
+    num_bytes: 2641257
+    num_examples: 2436
   download_size: 230213492
-  dataset_size: 19241909
+  dataset_size: 17738733
 ---
 
 # Dataset Card for E3C
@@ -107,4 +92,4 @@ information about clinical entities based on medical taxonomies, to be used for
     url = {https://uts.nlm.nih.gov/uts/umls/home},
     year = {2021},
 }
-```
+```

e3c.py

@@ -4,6 +4,10 @@ from typing import Iterator
 import datasets
 from bs4 import BeautifulSoup, ResultSet
 from datasets import DownloadManager
+from syntok.tokenizer import Tokenizer
+
+tok = Tokenizer()
+
 
 _CITATION = """\
 @report{Magnini2021,
@@ -132,17 +136,6 @@ class E3C(datasets.GeneratorBasedBuilder):
                     ),
                 },
             ),
-            datasets.SplitGenerator(
-                name="en.layer2.validation",
-                gen_kwargs={
-                    "filepath": os.path.join(
-                        data_dir,
-                        "E3C-Corpus-2.0.0/data_validation",
-                        "English",
-                        "layer2",
-                    ),
-                },
-            ),
             datasets.SplitGenerator(
                 name="es.layer1",
                 gen_kwargs={
@@ -165,17 +158,6 @@ class E3C(datasets.GeneratorBasedBuilder):
                     ),
                 },
             ),
-            datasets.SplitGenerator(
-                name="es.layer2.validation",
-                gen_kwargs={
-                    "filepath": os.path.join(
-                        data_dir,
-                        "E3C-Corpus-2.0.0/data_validation",
-                        "Spanish",
-                        "layer2",
-                    ),
-                },
-            ),
             datasets.SplitGenerator(
                 name="eu.layer1",
                 gen_kwargs={
@@ -198,17 +180,6 @@ class E3C(datasets.GeneratorBasedBuilder):
                     ),
                 },
             ),
-            datasets.SplitGenerator(
-                name="eu.layer2.validation",
-                gen_kwargs={
-                    "filepath": os.path.join(
-                        data_dir,
-                        "E3C-Corpus-2.0.0/data_validation",
-                        "Basque",
-                        "layer2",
-                    ),
-                },
-            ),
             datasets.SplitGenerator(
                 name="fr.layer1",
                 gen_kwargs={
@@ -231,17 +202,6 @@ class E3C(datasets.GeneratorBasedBuilder):
                     ),
                 },
             ),
-            datasets.SplitGenerator(
-                name="fr.layer2.validation",
-                gen_kwargs={
-                    "filepath": os.path.join(
-                        data_dir,
-                        "E3C-Corpus-2.0.0/data_validation",
-                        "French",
-                        "layer2",
-                    ),
-                },
-            ),
             datasets.SplitGenerator(
                 name="it.layer1",
                 gen_kwargs={
@@ -264,17 +224,6 @@ class E3C(datasets.GeneratorBasedBuilder):
                     ),
                 },
             ),
-            datasets.SplitGenerator(
-                name="it.layer2.validation",
-                gen_kwargs={
-                    "filepath": os.path.join(
-                        data_dir,
-                        "E3C-Corpus-2.0.0/data_validation",
-                        "Italian",
-                        "layer2",
-                    ),
-                },
-            ),
         ]
 
     @staticmethod
@@ -339,10 +288,16 @@ class E3C(datasets.GeneratorBasedBuilder):
         guid = 0
         for content in self.get_parsed_data(filepath):
             for sentence in content["SENTENCE"]:
+                tokens = [
+                    (token.offset + sentence[0], token.offset + sentence[0] + len(token.value),
+                     token.value)
+                    for token in list(tok.tokenize(sentence[-1]))
+                ]
+
                 filtered_tokens = list(
                     filter(
                         lambda token: token[0] >= sentence[0] and token[1] <= sentence[1],
-                        content["TOKENS"],
+                        tokens,
                     )
                 )
                 tokens_offsets = [