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- *.7z filter=lfs diff=lfs merge=lfs -text
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- *.arrow filter=lfs diff=lfs merge=lfs -text
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- *.bin filter=lfs diff=lfs merge=lfs -text
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- *.bz2 filter=lfs diff=lfs merge=lfs -text
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- *.ckpt filter=lfs diff=lfs merge=lfs -text
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- *.ftz filter=lfs diff=lfs merge=lfs -text
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- *.gz filter=lfs diff=lfs merge=lfs -text
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- *.h5 filter=lfs diff=lfs merge=lfs -text
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- *.joblib filter=lfs diff=lfs merge=lfs -text
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- *.lfs.* filter=lfs diff=lfs merge=lfs -text
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- *.lz4 filter=lfs diff=lfs merge=lfs -text
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- *.mlmodel filter=lfs diff=lfs merge=lfs -text
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- *.model filter=lfs diff=lfs merge=lfs -text
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- *.msgpack filter=lfs diff=lfs merge=lfs -text
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- *.npy filter=lfs diff=lfs merge=lfs -text
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- *.npz filter=lfs diff=lfs merge=lfs -text
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- *.onnx filter=lfs diff=lfs merge=lfs -text
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- *.ot filter=lfs diff=lfs merge=lfs -text
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- *.parquet filter=lfs diff=lfs merge=lfs -text
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- *.pb filter=lfs diff=lfs merge=lfs -text
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- *.pickle filter=lfs diff=lfs merge=lfs -text
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- *.pkl filter=lfs diff=lfs merge=lfs -text
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- *.pt filter=lfs diff=lfs merge=lfs -text
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- *.pth filter=lfs diff=lfs merge=lfs -text
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- *.rar filter=lfs diff=lfs merge=lfs -text
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- *.safetensors filter=lfs diff=lfs merge=lfs -text
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- saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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- *.tar.* filter=lfs diff=lfs merge=lfs -text
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- *.tflite filter=lfs diff=lfs merge=lfs -text
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- *.tgz filter=lfs diff=lfs merge=lfs -text
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- *.wasm filter=lfs diff=lfs merge=lfs -text
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- *.xz filter=lfs diff=lfs merge=lfs -text
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- *.zip filter=lfs diff=lfs merge=lfs -text
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- *.zst filter=lfs diff=lfs merge=lfs -text
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- *tfevents* filter=lfs diff=lfs merge=lfs -text
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- # Audio files - uncompressed
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- *.pcm filter=lfs diff=lfs merge=lfs -text
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- *.sam filter=lfs diff=lfs merge=lfs -text
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- *.raw filter=lfs diff=lfs merge=lfs -text
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- # Audio files - compressed
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- *.aac filter=lfs diff=lfs merge=lfs -text
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- *.flac filter=lfs diff=lfs merge=lfs -text
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- *.mp3 filter=lfs diff=lfs merge=lfs -text
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- *.ogg filter=lfs diff=lfs merge=lfs -text
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- *.wav filter=lfs diff=lfs merge=lfs -text
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- # Image files - uncompressed
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- *.bmp filter=lfs diff=lfs merge=lfs -text
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- *.gif filter=lfs diff=lfs merge=lfs -text
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- *.png filter=lfs diff=lfs merge=lfs -text
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- *.tiff filter=lfs diff=lfs merge=lfs -text
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- # Image files - compressed
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- *.jpg filter=lfs diff=lfs merge=lfs -text
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- *.jpeg filter=lfs diff=lfs merge=lfs -text
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- *.webp filter=lfs diff=lfs merge=lfs -text
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
bigbiohub.py DELETED
@@ -1,556 +0,0 @@
1
- from collections import defaultdict
2
- from dataclasses import dataclass
3
- from enum import Enum
4
- import logging
5
- from pathlib import Path
6
- from types import SimpleNamespace
7
- from typing import TYPE_CHECKING, Dict, Iterable, List, Tuple
8
-
9
- import datasets
10
-
11
- if TYPE_CHECKING:
12
- import bioc
13
-
14
- logger = logging.getLogger(__name__)
15
-
16
-
17
- BigBioValues = SimpleNamespace(NULL="<BB_NULL_STR>")
18
-
19
-
20
- @dataclass
21
- class BigBioConfig(datasets.BuilderConfig):
22
- """BuilderConfig for BigBio."""
23
-
24
- name: str = None
25
- version: datasets.Version = None
26
- description: str = None
27
- schema: str = None
28
- subset_id: str = None
29
-
30
-
31
- class Tasks(Enum):
32
- NAMED_ENTITY_RECOGNITION = "NER"
33
- NAMED_ENTITY_DISAMBIGUATION = "NED"
34
- EVENT_EXTRACTION = "EE"
35
- RELATION_EXTRACTION = "RE"
36
- COREFERENCE_RESOLUTION = "COREF"
37
- QUESTION_ANSWERING = "QA"
38
- TEXTUAL_ENTAILMENT = "TE"
39
- SEMANTIC_SIMILARITY = "STS"
40
- TEXT_PAIRS_CLASSIFICATION = "TXT2CLASS"
41
- PARAPHRASING = "PARA"
42
- TRANSLATION = "TRANSL"
43
- SUMMARIZATION = "SUM"
44
- TEXT_CLASSIFICATION = "TXTCLASS"
45
-
46
-
47
- entailment_features = datasets.Features(
48
- {
49
- "id": datasets.Value("string"),
50
- "premise": datasets.Value("string"),
51
- "hypothesis": datasets.Value("string"),
52
- "label": datasets.Value("string"),
53
- }
54
- )
55
-
56
- pairs_features = datasets.Features(
57
- {
58
- "id": datasets.Value("string"),
59
- "document_id": datasets.Value("string"),
60
- "text_1": datasets.Value("string"),
61
- "text_2": datasets.Value("string"),
62
- "label": datasets.Value("string"),
63
- }
64
- )
65
-
66
- qa_features = datasets.Features(
67
- {
68
- "id": datasets.Value("string"),
69
- "question_id": datasets.Value("string"),
70
- "document_id": datasets.Value("string"),
71
- "question": datasets.Value("string"),
72
- "type": datasets.Value("string"),
73
- "choices": [datasets.Value("string")],
74
- "context": datasets.Value("string"),
75
- "answer": datasets.Sequence(datasets.Value("string")),
76
- }
77
- )
78
-
79
- text_features = datasets.Features(
80
- {
81
- "id": datasets.Value("string"),
82
- "document_id": datasets.Value("string"),
83
- "text": datasets.Value("string"),
84
- "labels": [datasets.Value("string")],
85
- }
86
- )
87
-
88
- text2text_features = datasets.Features(
89
- {
90
- "id": datasets.Value("string"),
91
- "document_id": datasets.Value("string"),
92
- "text_1": datasets.Value("string"),
93
- "text_2": datasets.Value("string"),
94
- "text_1_name": datasets.Value("string"),
95
- "text_2_name": datasets.Value("string"),
96
- }
97
- )
98
-
99
- kb_features = datasets.Features(
100
- {
101
- "id": datasets.Value("string"),
102
- "document_id": datasets.Value("string"),
103
- "passages": [
104
- {
105
- "id": datasets.Value("string"),
106
- "type": datasets.Value("string"),
107
- "text": datasets.Sequence(datasets.Value("string")),
108
- "offsets": datasets.Sequence([datasets.Value("int32")]),
109
- }
110
- ],
111
- "entities": [
112
- {
113
- "id": datasets.Value("string"),
114
- "type": datasets.Value("string"),
115
- "text": datasets.Sequence(datasets.Value("string")),
116
- "offsets": datasets.Sequence([datasets.Value("int32")]),
117
- "normalized": [
118
- {
119
- "db_name": datasets.Value("string"),
120
- "db_id": datasets.Value("string"),
121
- }
122
- ],
123
- }
124
- ],
125
- "events": [
126
- {
127
- "id": datasets.Value("string"),
128
- "type": datasets.Value("string"),
129
- # refers to the text_bound_annotation of the trigger
130
- "trigger": {
131
- "text": datasets.Sequence(datasets.Value("string")),
132
- "offsets": datasets.Sequence([datasets.Value("int32")]),
133
- },
134
- "arguments": [
135
- {
136
- "role": datasets.Value("string"),
137
- "ref_id": datasets.Value("string"),
138
- }
139
- ],
140
- }
141
- ],
142
- "coreferences": [
143
- {
144
- "id": datasets.Value("string"),
145
- "entity_ids": datasets.Sequence(datasets.Value("string")),
146
- }
147
- ],
148
- "relations": [
149
- {
150
- "id": datasets.Value("string"),
151
- "type": datasets.Value("string"),
152
- "arg1_id": datasets.Value("string"),
153
- "arg2_id": datasets.Value("string"),
154
- "normalized": [
155
- {
156
- "db_name": datasets.Value("string"),
157
- "db_id": datasets.Value("string"),
158
- }
159
- ],
160
- }
161
- ],
162
- }
163
- )
164
-
165
-
166
- def get_texts_and_offsets_from_bioc_ann(ann: "bioc.BioCAnnotation") -> Tuple:
167
-
168
- offsets = [(loc.offset, loc.offset + loc.length) for loc in ann.locations]
169
-
170
- text = ann.text
171
-
172
- if len(offsets) > 1:
173
- i = 0
174
- texts = []
175
- for start, end in offsets:
176
- chunk_len = end - start
177
- texts.append(text[i : chunk_len + i])
178
- i += chunk_len
179
- while i < len(text) and text[i] == " ":
180
- i += 1
181
- else:
182
- texts = [text]
183
-
184
- return offsets, texts
185
-
186
-
187
- def remove_prefix(a: str, prefix: str) -> str:
188
- if a.startswith(prefix):
189
- a = a[len(prefix) :]
190
- return a
191
-
192
-
193
- def parse_brat_file(
194
- txt_file: Path,
195
- annotation_file_suffixes: List[str] = None,
196
- parse_notes: bool = False,
197
- ) -> Dict:
198
- """
199
- Parse a brat file into the schema defined below.
200
- `txt_file` should be the path to the brat '.txt' file you want to parse, e.g. 'data/1234.txt'
201
- Assumes that the annotations are contained in one or more of the corresponding '.a1', '.a2' or '.ann' files,
202
- e.g. 'data/1234.ann' or 'data/1234.a1' and 'data/1234.a2'.
203
- Will include annotator notes, when `parse_notes == True`.
204
- brat_features = datasets.Features(
205
- {
206
- "id": datasets.Value("string"),
207
- "document_id": datasets.Value("string"),
208
- "text": datasets.Value("string"),
209
- "text_bound_annotations": [ # T line in brat, e.g. type or event trigger
210
- {
211
- "offsets": datasets.Sequence([datasets.Value("int32")]),
212
- "text": datasets.Sequence(datasets.Value("string")),
213
- "type": datasets.Value("string"),
214
- "id": datasets.Value("string"),
215
- }
216
- ],
217
- "events": [ # E line in brat
218
- {
219
- "trigger": datasets.Value(
220
- "string"
221
- ), # refers to the text_bound_annotation of the trigger,
222
- "id": datasets.Value("string"),
223
- "type": datasets.Value("string"),
224
- "arguments": datasets.Sequence(
225
- {
226
- "role": datasets.Value("string"),
227
- "ref_id": datasets.Value("string"),
228
- }
229
- ),
230
- }
231
- ],
232
- "relations": [ # R line in brat
233
- {
234
- "id": datasets.Value("string"),
235
- "head": {
236
- "ref_id": datasets.Value("string"),
237
- "role": datasets.Value("string"),
238
- },
239
- "tail": {
240
- "ref_id": datasets.Value("string"),
241
- "role": datasets.Value("string"),
242
- },
243
- "type": datasets.Value("string"),
244
- }
245
- ],
246
- "equivalences": [ # Equiv line in brat
247
- {
248
- "id": datasets.Value("string"),
249
- "ref_ids": datasets.Sequence(datasets.Value("string")),
250
- }
251
- ],
252
- "attributes": [ # M or A lines in brat
253
- {
254
- "id": datasets.Value("string"),
255
- "type": datasets.Value("string"),
256
- "ref_id": datasets.Value("string"),
257
- "value": datasets.Value("string"),
258
- }
259
- ],
260
- "normalizations": [ # N lines in brat
261
- {
262
- "id": datasets.Value("string"),
263
- "type": datasets.Value("string"),
264
- "ref_id": datasets.Value("string"),
265
- "resource_name": datasets.Value(
266
- "string"
267
- ), # Name of the resource, e.g. "Wikipedia"
268
- "cuid": datasets.Value(
269
- "string"
270
- ), # ID in the resource, e.g. 534366
271
- "text": datasets.Value(
272
- "string"
273
- ), # Human readable description/name of the entity, e.g. "Barack Obama"
274
- }
275
- ],
276
- ### OPTIONAL: Only included when `parse_notes == True`
277
- "notes": [ # # lines in brat
278
- {
279
- "id": datasets.Value("string"),
280
- "type": datasets.Value("string"),
281
- "ref_id": datasets.Value("string"),
282
- "text": datasets.Value("string"),
283
- }
284
- ],
285
- },
286
- )
287
- """
288
-
289
- example = {}
290
- example["document_id"] = txt_file.with_suffix("").name
291
- with txt_file.open() as f:
292
- example["text"] = f.read()
293
-
294
- # If no specific suffixes of the to-be-read annotation files are given - take standard suffixes
295
- # for event extraction
296
- if annotation_file_suffixes is None:
297
- annotation_file_suffixes = [".a1", ".a2", ".ann"]
298
-
299
- if len(annotation_file_suffixes) == 0:
300
- raise AssertionError(
301
- "At least one suffix for the to-be-read annotation files should be given!"
302
- )
303
-
304
- ann_lines = []
305
- for suffix in annotation_file_suffixes:
306
- annotation_file = txt_file.with_suffix(suffix)
307
- if annotation_file.exists():
308
- with annotation_file.open() as f:
309
- ann_lines.extend(f.readlines())
310
-
311
- example["text_bound_annotations"] = []
312
- example["events"] = []
313
- example["relations"] = []
314
- example["equivalences"] = []
315
- example["attributes"] = []
316
- example["normalizations"] = []
317
-
318
- if parse_notes:
319
- example["notes"] = []
320
-
321
- for line in ann_lines:
322
- line = line.strip()
323
- if not line:
324
- continue
325
-
326
- if line.startswith("T"): # Text bound
327
- ann = {}
328
- fields = line.split("\t")
329
-
330
- ann["id"] = fields[0]
331
- ann["type"] = fields[1].split()[0]
332
- ann["offsets"] = []
333
- span_str = remove_prefix(fields[1], (ann["type"] + " "))
334
- text = fields[2]
335
- for span in span_str.split(";"):
336
- start, end = span.split()
337
- ann["offsets"].append([int(start), int(end)])
338
-
339
- # Heuristically split text of discontiguous entities into chunks
340
- ann["text"] = []
341
- if len(ann["offsets"]) > 1:
342
- i = 0
343
- for start, end in ann["offsets"]:
344
- chunk_len = end - start
345
- ann["text"].append(text[i : chunk_len + i])
346
- i += chunk_len
347
- while i < len(text) and text[i] == " ":
348
- i += 1
349
- else:
350
- ann["text"] = [text]
351
-
352
- example["text_bound_annotations"].append(ann)
353
-
354
- elif line.startswith("E"):
355
- ann = {}
356
- fields = line.split("\t")
357
-
358
- ann["id"] = fields[0]
359
-
360
- ann["type"], ann["trigger"] = fields[1].split()[0].split(":")
361
-
362
- ann["arguments"] = []
363
- for role_ref_id in fields[1].split()[1:]:
364
- argument = {
365
- "role": (role_ref_id.split(":"))[0],
366
- "ref_id": (role_ref_id.split(":"))[1],
367
- }
368
- ann["arguments"].append(argument)
369
-
370
- example["events"].append(ann)
371
-
372
- elif line.startswith("R"):
373
- ann = {}
374
- fields = line.split("\t")
375
-
376
- ann["id"] = fields[0]
377
- ann["type"] = fields[1].split()[0]
378
-
379
- ann["head"] = {
380
- "role": fields[1].split()[1].split(":")[0],
381
- "ref_id": fields[1].split()[1].split(":")[1],
382
- }
383
- ann["tail"] = {
384
- "role": fields[1].split()[2].split(":")[0],
385
- "ref_id": fields[1].split()[2].split(":")[1],
386
- }
387
-
388
- example["relations"].append(ann)
389
-
390
- # '*' seems to be the legacy way to mark equivalences,
391
- # but I couldn't find any info on the current way
392
- # this might have to be adapted dependent on the brat version
393
- # of the annotation
394
- elif line.startswith("*"):
395
- ann = {}
396
- fields = line.split("\t")
397
-
398
- ann["id"] = fields[0]
399
- ann["ref_ids"] = fields[1].split()[1:]
400
-
401
- example["equivalences"].append(ann)
402
-
403
- elif line.startswith("A") or line.startswith("M"):
404
- ann = {}
405
- fields = line.split("\t")
406
-
407
- ann["id"] = fields[0]
408
-
409
- info = fields[1].split()
410
- ann["type"] = info[0]
411
- ann["ref_id"] = info[1]
412
-
413
- if len(info) > 2:
414
- ann["value"] = info[2]
415
- else:
416
- ann["value"] = ""
417
-
418
- example["attributes"].append(ann)
419
-
420
- elif line.startswith("N"):
421
- ann = {}
422
- fields = line.split("\t")
423
-
424
- ann["id"] = fields[0]
425
- ann["text"] = fields[2]
426
-
427
- info = fields[1].split()
428
-
429
- ann["type"] = info[0]
430
- ann["ref_id"] = info[1]
431
- ann["resource_name"] = info[2].split(":")[0]
432
- ann["cuid"] = info[2].split(":")[1]
433
- example["normalizations"].append(ann)
434
-
435
- elif parse_notes and line.startswith("#"):
436
- ann = {}
437
- fields = line.split("\t")
438
-
439
- ann["id"] = fields[0]
440
- ann["text"] = fields[2] if len(fields) == 3 else BigBioValues.NULL
441
-
442
- info = fields[1].split()
443
-
444
- ann["type"] = info[0]
445
- ann["ref_id"] = info[1]
446
- example["notes"].append(ann)
447
-
448
- return example
449
-
450
-
451
- def brat_parse_to_bigbio_kb(brat_parse: Dict) -> Dict:
452
- """
453
- Transform a brat parse (conforming to the standard brat schema) obtained with
454
- `parse_brat_file` into a dictionary conforming to the `bigbio-kb` schema (as defined in ../schemas/kb.py)
455
- :param brat_parse:
456
- """
457
-
458
- unified_example = {}
459
-
460
- # Prefix all ids with document id to ensure global uniqueness,
461
- # because brat ids are only unique within their document
462
- id_prefix = brat_parse["document_id"] + "_"
463
-
464
- # identical
465
- unified_example["document_id"] = brat_parse["document_id"]
466
- unified_example["passages"] = [
467
- {
468
- "id": id_prefix + "_text",
469
- "type": "abstract",
470
- "text": [brat_parse["text"]],
471
- "offsets": [[0, len(brat_parse["text"])]],
472
- }
473
- ]
474
-
475
- # get normalizations
476
- ref_id_to_normalizations = defaultdict(list)
477
- for normalization in brat_parse["normalizations"]:
478
- ref_id_to_normalizations[normalization["ref_id"]].append(
479
- {
480
- "db_name": normalization["resource_name"],
481
- "db_id": normalization["cuid"],
482
- }
483
- )
484
-
485
- # separate entities and event triggers
486
- unified_example["events"] = []
487
- non_event_ann = brat_parse["text_bound_annotations"].copy()
488
- for event in brat_parse["events"]:
489
- event = event.copy()
490
- event["id"] = id_prefix + event["id"]
491
- trigger = next(
492
- tr
493
- for tr in brat_parse["text_bound_annotations"]
494
- if tr["id"] == event["trigger"]
495
- )
496
- if trigger in non_event_ann:
497
- non_event_ann.remove(trigger)
498
- event["trigger"] = {
499
- "text": trigger["text"].copy(),
500
- "offsets": trigger["offsets"].copy(),
501
- }
502
- for argument in event["arguments"]:
503
- argument["ref_id"] = id_prefix + argument["ref_id"]
504
-
505
- unified_example["events"].append(event)
506
-
507
- unified_example["entities"] = []
508
- anno_ids = [ref_id["id"] for ref_id in non_event_ann]
509
- for ann in non_event_ann:
510
- entity_ann = ann.copy()
511
- entity_ann["id"] = id_prefix + entity_ann["id"]
512
- entity_ann["normalized"] = ref_id_to_normalizations[ann["id"]]
513
- unified_example["entities"].append(entity_ann)
514
-
515
- # massage relations
516
- unified_example["relations"] = []
517
- skipped_relations = set()
518
- for ann in brat_parse["relations"]:
519
- if (
520
- ann["head"]["ref_id"] not in anno_ids
521
- or ann["tail"]["ref_id"] not in anno_ids
522
- ):
523
- skipped_relations.add(ann["id"])
524
- continue
525
- unified_example["relations"].append(
526
- {
527
- "arg1_id": id_prefix + ann["head"]["ref_id"],
528
- "arg2_id": id_prefix + ann["tail"]["ref_id"],
529
- "id": id_prefix + ann["id"],
530
- "type": ann["type"],
531
- "normalized": [],
532
- }
533
- )
534
- if len(skipped_relations) > 0:
535
- example_id = brat_parse["document_id"]
536
- logger.info(
537
- f"Example:{example_id}: The `bigbio_kb` schema allows `relations` only between entities."
538
- f" Skip (for now): "
539
- f"{list(skipped_relations)}"
540
- )
541
-
542
- # get coreferences
543
- unified_example["coreferences"] = []
544
- for i, ann in enumerate(brat_parse["equivalences"], start=1):
545
- is_entity_cluster = True
546
- for ref_id in ann["ref_ids"]:
547
- if not ref_id.startswith("T"): # not textbound -> no entity
548
- is_entity_cluster = False
549
- elif ref_id not in anno_ids: # event trigger -> no entity
550
- is_entity_cluster = False
551
- if is_entity_cluster:
552
- entity_ids = [id_prefix + i for i in ann["ref_ids"]]
553
- unified_example["coreferences"].append(
554
- {"id": id_prefix + str(i), "entity_ids": entity_ids}
555
- )
556
- return unified_example
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
muchmore.py DELETED
@@ -1,739 +0,0 @@
1
- # coding=utf-8
2
- # Copyright 2022 The HuggingFace Datasets Authors and the current dataset script contributor.
3
- #
4
- # Licensed under the Apache License, Version 2.0 (the "License");
5
- # you may not use this file except in compliance with the License.
6
- # You may obtain a copy of the License at
7
- #
8
- # http://www.apache.org/licenses/LICENSE-2.0
9
- #
10
- # Unless required by applicable law or agreed to in writing, software
11
- # distributed under the License is distributed on an "AS IS" BASIS,
12
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13
- # See the License for the specific language governing permissions and
14
- # limitations under the License.
15
-
16
- """
17
- A dataset loader for the MuchMore Springer Bilingual Corpus
18
-
19
- homepage
20
-
21
- * https://muchmore.dfki.de/resources1.htm
22
-
23
- description of annotation format
24
-
25
- * https://muchmore.dfki.de/pubs/D4.1.pdf
26
-
27
- Four files are distributed
28
-
29
- * springer_english_train_plain.tar.gz (english plain text of abstracts)
30
- * springer_german_train_plain.tar.gz (german plain text of abstracts)
31
- * springer_english_train_V4.2.tar.gz (annotated xml in english)
32
- * springer_german_train_V4.2.tar.gz (annotated xml in german)
33
-
34
- Each tar file has one member file per abstract.
35
- There are keys to join the english and german files
36
- but there is not a 1-1 mapping between them (i.e. some
37
- english files have no german counterpart and some german
38
- files have no english counterpart). However, there is a 1-1
39
- mapping between plain text and annotations for a given language
40
- (i.e. an abstract in springer_english_train_plain.tar.gz will
41
- also be found in springer_english_train_V4.2.tar.gz)
42
-
43
- Counts,
44
-
45
- * 15,631 total abstracts
46
- * 7,823 english abstracts
47
- * 7,808 german abstracts
48
- * 6,374 matched (en/de) abstracts
49
- * 1,449 english abstracts with no german
50
- * 1,434 german abstracts with no english
51
-
52
- Notes
53
-
54
- * Arthroskopie.00130237.eng.abstr.chunkmorph.annotated.xml seems to be empty
55
-
56
-
57
- * entity spans can overlap. an example from the first sample:
58
-
59
- {'id': 'Arthroskopie.00130003.eng.abstr-s1-t1',
60
- 'type': 'umlsterm',
61
- 'text': ['posterior'],
62
- 'offsets': [[4, 13]],
63
- 'normalized': [{'db_name': 'UMLS', 'db_id': 'C0032009'}]},
64
- {'id': 'Arthroskopie.00130003.eng.abstr-s1-t8',
65
- 'type': 'umlsterm',
66
- 'text': ['posterior cruciate ligament'],
67
- 'offsets': [[4, 31]],
68
- 'normalized': [{'db_name': 'UMLS', 'db_id': 'C0080039'}]},
69
- {'id': 'Arthroskopie.00130003.eng.abstr-s1-t2',
70
- 'type': 'umlsterm',
71
- 'text': ['ligament'],
72
- 'offsets': [[23, 31]],
73
- 'normalized': [{'db_name': 'UMLS', 'db_id': 'C0023685'},
74
- {'db_name': 'UMLS', 'db_id': 'C0023686'}]},
75
-
76
-
77
- * semantic relations are defined beween concepts but entities can
78
- have multiple concpets associated with them. in the bigbio
79
- schema we skip relations between multiple concept of the
80
- same entity. an example of a relation that is kept from the
81
- source schema is below,
82
-
83
- In [35]: dsd['train'][0]['sentences'][0]['tokens']
84
- Out[35]:
85
- [{'id': 'w1', 'pos': 'DT', 'lemma': 'the', 'text': 'The'},
86
- {'id': 'w2', 'pos': 'JJ', 'lemma': 'posterior', 'text': 'posterior'},
87
- {'id': 'w3', 'pos': 'JJ', 'lemma': 'cruciate', 'text': 'cruciate'},
88
- {'id': 'w4', 'pos': 'NN', 'lemma': 'ligament', 'text': 'ligament'},
89
- {'id': 'w5', 'pos': 'PUNCT', 'lemma': None, 'text': '('},
90
- {'id': 'w6', 'pos': 'NN', 'lemma': None, 'text': 'PCL'},
91
- {'id': 'w7', 'pos': 'PUNCT', 'lemma': None, 'text': ')'},
92
- {'id': 'w8', 'pos': 'VBZ', 'lemma': 'be', 'text': 'is'},
93
- {'id': 'w9', 'pos': 'DT', 'lemma': 'the', 'text': 'the'},
94
- {'id': 'w10', 'pos': 'JJS', 'lemma': 'strong', 'text': 'strongest'},
95
- {'id': 'w11', 'pos': 'NN', 'lemma': 'ligament', 'text': 'ligament'},
96
- {'id': 'w12', 'pos': 'IN', 'lemma': 'of', 'text': 'of'},
97
- {'id': 'w13', 'pos': 'DT', 'lemma': 'the', 'text': 'the'},
98
- {'id': 'w14', 'pos': 'JJ', 'lemma': 'human', 'text': 'human'},
99
- {'id': 'w15', 'pos': 'NN', 'lemma': 'knee', 'text': 'knee'},
100
- {'id': 'w16', 'pos': 'JJ', 'lemma': 'joint', 'text': 'joint'},
101
- {'id': 'w17', 'pos': 'PUNCT', 'lemma': None, 'text': '.'}]
102
-
103
-
104
- In [36]: dsd['train'][0]['sentences'][0]['semrels'][0]
105
- Out[36]: {'id': 'r1', 'term1': 't3.1', 'term2': 't6.1', 'reltype': 'surrounds'}
106
-
107
- In [37]: dsd['train'][0]['sentences'][0]['umlsterms'][2]
108
- Out[37]:
109
- {'id': 't3',
110
- 'from': 'w11',
111
- 'to': 'w11',
112
- 'concepts': [{'id': 't3.1',
113
- 'cui': 'C0023685',
114
- 'preferred': 'Ligaments',
115
- 'tui': 'T024',
116
- 'mshs': [{'code': 'A2.513'}]},
117
- {'id': 't3.2',
118
- 'cui': 'C0023686',
119
- 'preferred': 'Articular ligaments',
120
- 'tui': 'T023',
121
- 'mshs': [{'code': 'A2.513.514'}, {'code': 'A2.835.583.512'}]}]}
122
-
123
- In [38]: dsd['train'][0]['sentences'][0]['umlsterms'][5]
124
- Out[38]:
125
- {'id': 't6',
126
- 'from': 'w16',
127
- 'to': 'w16',
128
- 'concepts': [{'id': 't6.1',
129
- 'cui': 'C0022417',
130
- 'preferred': 'Joints',
131
- 'tui': 'T030',
132
- 'mshs': [{'code': 'A2.835.583'}]}]}
133
-
134
- """
135
-
136
- import itertools
137
- import os
138
- import re
139
- import tarfile
140
- import xml.etree.ElementTree as ET
141
- from collections import defaultdict
142
- from typing import Dict, List
143
- from xml.etree.ElementTree import Element
144
-
145
- import datasets
146
- from datasets import Features, Value
147
-
148
- # TODO: home page has a list of publications but its not clear which to choose
149
- # https://muchmore.dfki.de/papers1.htm
150
- # to start, chose the one below.
151
- # Buitelaar, Paul / Declerck, Thierry / Sacaleanu, Bogdan / Vintar, Spela / Raileanu, Diana / Crispi, Claudia: A Multi-Layered, XML-Based Approach to the Integration of Linguistic and Semantic Annotations. In: Proceedings of EACL 2003 Workshop on Language Technology and the Semantic Web (NLPXML’03), Budapest, Hungary, April 2003.
152
- from .bigbiohub import kb_features
153
- from .bigbiohub import text2text_features
154
- from .bigbiohub import BigBioConfig
155
- from .bigbiohub import Tasks
156
-
157
- _LANGUAGES = ['English', 'German']
158
- _PUBMED = True
159
- _LOCAL = False
160
- _CITATION = """\
161
- @inproceedings{buitelaar2003multi,
162
- title={A multi-layered, xml-based approach to the integration of linguistic and semantic annotations},
163
- author={Buitelaar, Paul and Declerck, Thierry and Sacaleanu, Bogdan and Vintar, {\v{S}}pela and Raileanu, Diana and Crispi, Claudia},
164
- booktitle={Proceedings of EACL 2003 Workshop on Language Technology and the Semantic Web (NLPXML'03), Budapest, Hungary},
165
- year={2003}
166
- }
167
- """
168
-
169
- _DESCRIPTION = """\
170
- The corpus used in the MuchMore project is a parallel corpus of English-German scientific
171
- medical abstracts obtained from the Springer Link web site. The corpus consists
172
- approximately of 1 million tokens for each language. Abstracts are from 41 medical
173
- journals, each of which constitutes a relatively homogeneous medical sub-domain (e.g.
174
- Neurology, Radiology, etc.). The corpus of downloaded HTML documents is normalized in
175
- various ways, in order to produce a clean, plain text version, consisting of a title, abstract
176
- and keywords. Additionally, the corpus was aligned on the sentence level.
177
-
178
- Automatic (!) annotation includes: Part-of-Speech; Morphology (inflection and
179
- decomposition); Chunks; Semantic Classes (UMLS: Unified Medical Language System,
180
- MeSH: Medical Subject Headings, EuroWordNet); Semantic Relations from UMLS.
181
- """
182
-
183
- _DATASETNAME = "muchmore"
184
- _DISPLAYNAME = "MuchMore"
185
-
186
- _HOMEPAGE = "https://muchmore.dfki.de/resources1.htm"
187
-
188
- # TODO: website says the following, but don't see a specific license
189
- # TODO: add to FAQs about what to do in this situation.
190
-
191
- # "The cross-lingual information access prototype system for the medical domain
192
- # will be made publicly accessible through the internet. It provides access to
193
- # multilingual information on the basis of a domain ontology and classification.
194
- # For the main task of multilingual domain modelling, the project will focus
195
- # on German and English. "
196
- _LICENSE = 'License information unavailable'
197
- _URLs = {
198
- "muchmore_source": [
199
- "https://muchmore.dfki.de/pubs/springer_english_train_plain.tar.gz",
200
- "https://muchmore.dfki.de/pubs/springer_english_train_V4.2.tar.gz",
201
- "https://muchmore.dfki.de/pubs/springer_german_train_plain.tar.gz",
202
- "https://muchmore.dfki.de/pubs/springer_german_train_V4.2.tar.gz",
203
- ],
204
- "muchmore_bigbio_kb": [
205
- "https://muchmore.dfki.de/pubs/springer_english_train_V4.2.tar.gz",
206
- "https://muchmore.dfki.de/pubs/springer_german_train_V4.2.tar.gz",
207
- ],
208
- "muchmore_en_bigbio_kb": "https://muchmore.dfki.de/pubs/springer_english_train_V4.2.tar.gz",
209
- "muchmore_de_bigbio_kb": "https://muchmore.dfki.de/pubs/springer_german_train_V4.2.tar.gz",
210
- "plain": [
211
- "https://muchmore.dfki.de/pubs/springer_english_train_plain.tar.gz",
212
- "https://muchmore.dfki.de/pubs/springer_german_train_plain.tar.gz",
213
- ],
214
- "plain_en": "https://muchmore.dfki.de/pubs/springer_english_train_plain.tar.gz",
215
- "plain_de": "https://muchmore.dfki.de/pubs/springer_german_train_plain.tar.gz",
216
- "muchmore_bigbio_t2t": [
217
- "https://muchmore.dfki.de/pubs/springer_english_train_plain.tar.gz",
218
- "https://muchmore.dfki.de/pubs/springer_german_train_plain.tar.gz",
219
- ],
220
- }
221
-
222
- # took version from annotated file names
223
- _SOURCE_VERSION = "4.2.0"
224
- _BIGBIO_VERSION = "1.0.0"
225
- _SUPPORTED_TASKS = [
226
- Tasks.TRANSLATION,
227
- Tasks.NAMED_ENTITY_RECOGNITION,
228
- Tasks.NAMED_ENTITY_DISAMBIGUATION,
229
- Tasks.RELATION_EXTRACTION,
230
- ]
231
-
232
- NATIVE_ENCODING = "ISO-8859-1"
233
- FILE_NAME_PATTERN = r"^(.+?)\.(eng|ger)\.abstr(\.chunkmorph\.annotated\.xml)?$"
234
- LANG_MAP = {"eng": "en", "ger": "de"}
235
-
236
-
237
- class MuchMoreDataset(datasets.GeneratorBasedBuilder):
238
- """MuchMore Springer Bilingual Corpus"""
239
-
240
- DEFAULT_CONFIG_NAME = "muchmore_source"
241
- SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
242
- BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)
243
-
244
- BUILDER_CONFIGS = [
245
- BigBioConfig(
246
- name="muchmore_source",
247
- version=SOURCE_VERSION,
248
- description="MuchMore source schema",
249
- schema="source",
250
- subset_id="muchmore",
251
- ),
252
- BigBioConfig(
253
- name="muchmore_bigbio_kb",
254
- version=BIGBIO_VERSION,
255
- description="MuchMore simplified BigBio kb schema",
256
- schema="bigbio_kb",
257
- subset_id="muchmore",
258
- ),
259
- BigBioConfig(
260
- name="muchmore_en_bigbio_kb",
261
- version=BIGBIO_VERSION,
262
- description="MuchMore simplified BigBio kb schema",
263
- schema="bigbio_kb",
264
- subset_id="muchmore_en",
265
- ),
266
- BigBioConfig(
267
- name="muchmore_de_bigbio_kb",
268
- version=BIGBIO_VERSION,
269
- description="MuchMore simplified BigBio kb schema",
270
- schema="bigbio_kb",
271
- subset_id="muchmore_de",
272
- ),
273
- BigBioConfig(
274
- name="muchmore_bigbio_t2t",
275
- version=BIGBIO_VERSION,
276
- description="MuchMore simplified BigBio translation schema",
277
- schema="bigbio_t2t",
278
- subset_id="muchmore",
279
- ),
280
- ]
281
-
282
- # default config produces english annotations at the moment
283
- def _info(self):
284
-
285
- if self.config.schema == "source":
286
- features = Features(
287
- {
288
- "sample_id": Value("string"),
289
- "corresp": Value("string"),
290
- "language": Value("string"),
291
- "abstract": Value("string"),
292
- "sentences": [
293
- {
294
- "id": Value("string"),
295
- "corresp": Value("string"),
296
- "umlsterms": [
297
- {
298
- "id": Value("string"),
299
- "from": Value("string"),
300
- "to": Value("string"),
301
- "concepts": [
302
- {
303
- "id": Value("string"),
304
- "cui": Value("string"),
305
- "preferred": Value("string"),
306
- "tui": Value("string"),
307
- "mshs": [
308
- {
309
- "code": Value("string"),
310
- }
311
- ],
312
- }
313
- ],
314
- }
315
- ],
316
- "ewnterms": [
317
- {
318
- "id": Value("string"),
319
- "to": Value("string"),
320
- "from": Value("string"),
321
- "senses": [
322
- {
323
- "offset": Value("string"),
324
- }
325
- ],
326
- }
327
- ],
328
- "semrels": [
329
- {
330
- "id": Value("string"),
331
- "term1": Value("string"),
332
- "term2": Value("string"),
333
- "reltype": Value("string"),
334
- }
335
- ],
336
- "chunks": [
337
- {
338
- "id": Value("string"),
339
- "to": Value("string"),
340
- "from": Value("string"),
341
- "type": Value("string"),
342
- }
343
- ],
344
- "tokens": [
345
- {
346
- "id": Value("string"),
347
- "pos": Value("string"),
348
- "lemma": Value("string"),
349
- "text": Value("string"),
350
- }
351
- ],
352
- }
353
- ],
354
- }
355
- )
356
-
357
- elif self.config.schema == "bigbio_kb":
358
- features = kb_features
359
-
360
- elif self.config.name in ("plain", "plain_en", "plain_de"):
361
- features = Features(
362
- {
363
- "sample_id": Value("string"),
364
- "sample_id_prefix": Value("string"),
365
- "language": Value("string"),
366
- "abstract": Value("string"),
367
- }
368
- )
369
-
370
- elif self.config.schema == "bigbio_t2t":
371
- features = text2text_features
372
-
373
- return datasets.DatasetInfo(
374
- description=_DESCRIPTION,
375
- features=features,
376
- supervised_keys=None,
377
- homepage=_HOMEPAGE,
378
- license=str(_LICENSE),
379
- citation=_CITATION,
380
- )
381
-
382
- def _split_generators(self, dl_manager):
383
- """Returns SplitGenerators."""
384
- my_urls = _URLs[self.config.name]
385
- data_dirs = dl_manager.download(my_urls)
386
- # ensure that data_dirs is always a list of string paths
387
- if isinstance(data_dirs, str):
388
- data_dirs = [data_dirs]
389
-
390
- return [
391
- datasets.SplitGenerator(
392
- name=datasets.Split.TRAIN,
393
- gen_kwargs={
394
- "file_names_and_pointers": itertools.chain(
395
- *[dl_manager.iter_archive(data_dir) for data_dir in data_dirs]
396
- ),
397
- "split": "train",
398
- },
399
- ),
400
- ]
401
-
402
- @staticmethod
403
- def _get_umlsterms_from_xsent(xsent: Element) -> List:
404
- xumlsterms = xsent.find("./umlsterms")
405
-
406
- umlsterms = []
407
- for xumlsterm in xumlsterms.findall("./umlsterm"):
408
-
409
- concepts = []
410
- for xconcept in xumlsterm.findall("./concept"):
411
-
412
- mshs = [
413
- {"code": xmsh.get("code")} for xmsh in xconcept.findall("./msh")
414
- ]
415
-
416
- concept = {
417
- "id": xconcept.get("id"),
418
- "cui": xconcept.get("cui"),
419
- "preferred": xconcept.get("preferred"),
420
- "tui": xconcept.get("tui"),
421
- "mshs": mshs,
422
- }
423
- concepts.append(concept)
424
-
425
- umlsterm = {
426
- "id": xumlsterm.get("id"),
427
- "from": xumlsterm.get("from"),
428
- "to": xumlsterm.get("to"),
429
- "concepts": concepts,
430
- }
431
- umlsterms.append(umlsterm)
432
-
433
- return umlsterms
434
-
435
- @staticmethod
436
- def _get_ewnterms_from_xsent(xsent: Element) -> List:
437
- xewnterms = xsent.find("./ewnterms")
438
-
439
- ewnterms = []
440
- for xewnterm in xewnterms.findall("./ewnterm"):
441
-
442
- senses = [
443
- {"offset": xsense.get("offset")}
444
- for xsense in xewnterm.findall("./sense")
445
- ]
446
-
447
- ewnterm = {
448
- "id": xewnterm.get("id"),
449
- "from": xewnterm.get("from"),
450
- "to": xewnterm.get("to"),
451
- "senses": senses,
452
- }
453
- ewnterms.append(ewnterm)
454
-
455
- return ewnterms
456
-
457
- @staticmethod
458
- def _get_semrels_from_xsent(xsent: Element) -> List[Dict[str, str]]:
459
- xsemrels = xsent.find("./semrels")
460
- return [
461
- {
462
- "id": xsemrel.get("id"),
463
- "term1": xsemrel.get("term1"),
464
- "term2": xsemrel.get("term2"),
465
- "reltype": xsemrel.get("reltype"),
466
- }
467
- for xsemrel in xsemrels.findall("./semrel")
468
- ]
469
-
470
- @staticmethod
471
- def _get_chunks_from_xsent(xsent: Element) -> List[Dict[str, str]]:
472
- xchunks = xsent.find("./chunks")
473
- return [
474
- {
475
- "id": xchunk.get("id"),
476
- "to": xchunk.get("to"),
477
- "from": xchunk.get("from"),
478
- "type": xchunk.get("type"),
479
- }
480
- for xchunk in xchunks.findall("./chunk")
481
- ]
482
-
483
- @staticmethod
484
- def _get_tokens_from_xsent(xsent: Element) -> List[Dict[str, str]]:
485
- xtext = xsent.find("./text")
486
- return [
487
- {
488
- "id": xtoken.get("id"),
489
- "pos": xtoken.get("pos"),
490
- "lemma": xtoken.get("lemma"),
491
- "text": xtoken.text,
492
- }
493
- for xtoken in xtext.findall("./token")
494
- ]
495
-
496
- def _generate_original_examples(self, file_names_and_pointers):
497
- """Generate something close to the original dataset.
498
-
499
- This will yield one sample per abstract with the plaintext
500
- and the annotations combined into one object. If an abstract
501
- is available in both english and german each language version
502
- will be a distinct example.
503
- """
504
- abstracts = {}
505
- samples = {}
506
- for file_name, fp in file_names_and_pointers:
507
-
508
- if file_name.endswith(".abstr"):
509
- sample_id = file_name
510
- abstracts[sample_id] = fp.read().decode(NATIVE_ENCODING)
511
-
512
- elif file_name.endswith(".abstr.chunkmorph.annotated.xml"):
513
- content_bytes = fp.read()
514
- content_str = content_bytes.decode(NATIVE_ENCODING)
515
- if content_str == "":
516
- continue
517
-
518
- xroot = ET.fromstring(content_str)
519
-
520
- sentences = []
521
- for xsent in xroot.findall("./"):
522
- sentence = {
523
- "id": xsent.get("id"),
524
- "corresp": xsent.get("corresp"),
525
- "umlsterms": self._get_umlsterms_from_xsent(xsent),
526
- "ewnterms": self._get_ewnterms_from_xsent(xsent),
527
- "semrels": self._get_semrels_from_xsent(xsent),
528
- "chunks": self._get_chunks_from_xsent(xsent),
529
- "tokens": self._get_tokens_from_xsent(xsent),
530
- }
531
- sentences.append(sentence)
532
-
533
- sample_id = xroot.get("id")
534
- samples[sample_id] = {
535
- "sample_id": sample_id,
536
- "corresp": xroot.get("corresp"),
537
- "language": xroot.get("lang"),
538
- "sentences": sentences,
539
- }
540
-
541
- for _id, (sample_id, sample) in enumerate(samples.items()):
542
- sample["abstract"] = abstracts[sample_id]
543
- yield _id, sample
544
-
545
- def _generate_bigbio_kb_examples(self, file_names_and_pointers):
546
- """Generate big science biomedical kb examples."""
547
-
548
- def snippets_tokens_from_sents(sentences):
549
- snippets = []
550
- for sentence in sentences:
551
- snippet = [el["text"] for el in sentence["tokens"]]
552
- snippets.append(snippet)
553
- return snippets
554
-
555
- def sid_to_text_off(sid, snip_txts_lens):
556
- ii_sid = int(sid[1:])
557
- start = sum(snip_txts_lens[: ii_sid - 1]) + (ii_sid - 1)
558
- end = start + snip_txts_lens[ii_sid - 1]
559
- return start, end
560
-
561
- def sid_wid_to_text_off(sid, wid, snip_txts_lens, snip_toks_lens):
562
- s_start, s_end = sid_to_text_off(sid, snip_txts_lens)
563
- ii_sid = int(sid[1:])
564
- ii_wid = int(wid[1:])
565
- w_start = sum(snip_toks_lens[ii_sid - 1][: ii_wid - 1]) + (ii_wid - 1)
566
- start = s_start + w_start
567
- end = start + snip_toks_lens[ii_sid - 1][ii_wid - 1]
568
- return start, end
569
-
570
- for _id, (file_name, fp) in enumerate(file_names_and_pointers):
571
-
572
- content_bytes = fp.read()
573
- content_str = content_bytes.decode(NATIVE_ENCODING)
574
- if content_str == "":
575
- continue
576
-
577
- xroot = ET.fromstring(content_str)
578
-
579
- sentences = []
580
- for xsent in xroot.findall("./"):
581
- sentence = {
582
- "id": xsent.get("id"),
583
- "corresp": xsent.get("corresp"),
584
- "umlsterms": self._get_umlsterms_from_xsent(xsent),
585
- "ewnterms": self._get_ewnterms_from_xsent(xsent),
586
- "semrels": self._get_semrels_from_xsent(xsent),
587
- "chunks": self._get_chunks_from_xsent(xsent),
588
- "tokens": self._get_tokens_from_xsent(xsent),
589
- }
590
- sentences.append(sentence)
591
-
592
- snip_toks = snippets_tokens_from_sents(sentences)
593
- snip_txts = [" ".join(snip_tok) for snip_tok in snip_toks]
594
- snip_txts_lens = [len(el) for el in snip_txts]
595
- snip_toks_lens = [[len(tok) for tok in snip] for snip in snip_toks]
596
- text = " ".join(snip_txts)
597
- passages = [
598
- {
599
- "id": "{}-passage-0".format(xroot.get("id")),
600
- "type": "abstract",
601
- "text": [text],
602
- "offsets": [(0, len(text))],
603
- }
604
- ]
605
-
606
- entities = []
607
- rel_map = {}
608
- for sentence in sentences:
609
- sid = sentence["id"]
610
- ii_sid = int(sid[1:])
611
-
612
- for umlsterm in sentence["umlsterms"]:
613
- umlsterm_id = umlsterm["id"]
614
- entity_id = f"{sid}-{umlsterm_id}"
615
- wid_from = umlsterm["from"]
616
- wid_to = umlsterm["to"]
617
- ii_wid_from = int(wid_from[1:])
618
- ii_wid_to = int(wid_to[1:])
619
-
620
- tok_text = " ".join(
621
- snip_toks[ii_sid - 1][ii_wid_from - 1 : ii_wid_to]
622
- )
623
- w_from_start, w_from_end = sid_wid_to_text_off(
624
- sid, wid_from, snip_txts_lens, snip_toks_lens
625
- )
626
- w_to_start, w_to_end = sid_wid_to_text_off(
627
- sid, wid_to, snip_txts_lens, snip_toks_lens
628
- )
629
-
630
- offsets = [(w_from_start, w_to_end)]
631
- main_text = text[w_from_start:w_to_end]
632
- umls_cuis = [el["cui"] for el in umlsterm["concepts"]]
633
- for concept in umlsterm["concepts"]:
634
- rel_map[concept["id"]] = entity_id
635
-
636
- entity = {
637
- "id": "{}-{}".format(xroot.get("id"), entity_id),
638
- "offsets": offsets,
639
- "text": [tok_text],
640
- "type": "umlsterm",
641
- "normalized": [
642
- {"db_name": "UMLS", "db_id": cui} for cui in umls_cuis
643
- ],
644
- }
645
- entities.append(entity)
646
-
647
- relations = []
648
- for sentence in sentences:
649
- sid = sentence["id"]
650
- for semrel in sentence["semrels"]:
651
- semrel_id = semrel["id"]
652
- rel_id = "{}-{}-{}-{}".format(
653
- sid, semrel_id, semrel["term1"], semrel["term2"],
654
- )
655
- arg1_id = "{}-{}".format(xroot.get("id"), rel_map[semrel["term1"]])
656
- arg2_id = "{}-{}".format(xroot.get("id"), rel_map[semrel["term2"]])
657
- # some semrels are between multiple normalizations of
658
- # a single entity. we skip these. see docstring at top
659
- # of module for more complete description
660
- if arg1_id == arg2_id:
661
- continue
662
- relation = {
663
- "id": "{}-{}".format(xroot.get("id"), rel_id),
664
- "type": semrel["reltype"],
665
- "arg1_id": arg1_id,
666
- "arg2_id": arg2_id,
667
- "normalized": []
668
- }
669
- relations.append(relation)
670
-
671
- yield _id, {
672
- "id": xroot.get("id"),
673
- "document_id": xroot.get("id"),
674
- "passages": passages,
675
- "entities": entities,
676
- "coreferences": [],
677
- "events": [],
678
- "relations": relations,
679
- }
680
-
681
- def _generate_plain_examples(self, file_names_and_pointers):
682
- """Generate plain text abstract examples."""
683
- for _id, (file_name, fp) in enumerate(file_names_and_pointers):
684
- match = re.match(FILE_NAME_PATTERN, file_name)
685
- yield _id, {
686
- "sample_id_prefix": match.group(1),
687
- "sample_id": file_name,
688
- "language": LANG_MAP[match.group(2)],
689
- "abstract": fp.read().decode(NATIVE_ENCODING),
690
- }
691
-
692
- def _generate_translation_examples(self, file_names_and_pointers):
693
- sample_map = defaultdict(list)
694
- for file_name, fp in file_names_and_pointers:
695
- if file_name.endswith("eng.abstr"):
696
- language = "en"
697
- elif file_name.endswith("ger.abstr"):
698
- language = "de"
699
- else:
700
- raise ValueError()
701
- sample_id_prefix = re.sub(".(eng|ger).abstr$", "", file_name)
702
- sample_id = file_name
703
- abstract = fp.read().decode(NATIVE_ENCODING)
704
- sample_map[sample_id_prefix].append(
705
- {"language": language, "sample_id": sample_id, "abstract": abstract}
706
- )
707
-
708
- _id = 0
709
- for sample_id_prefix, sample_pair in sample_map.items():
710
- if len(sample_pair) != 2:
711
- continue
712
- en_idx = 0 if sample_pair[0]["language"] == "en" else 1
713
- de_idx = 0 if en_idx == 1 else 1
714
- yield _id, {
715
- "id": sample_id_prefix,
716
- "document_id": sample_id_prefix,
717
- "text_1": sample_pair[en_idx]["abstract"],
718
- "text_2": sample_pair[de_idx]["abstract"],
719
- "text_1_name": "en",
720
- "text_2_name": "de",
721
- }
722
- _id += 1
723
-
724
- def _generate_examples(self, file_names_and_pointers, split):
725
-
726
- if self.config.schema == "source":
727
- genny = self._generate_original_examples(file_names_and_pointers)
728
-
729
- elif self.config.schema == "bigbio_kb":
730
- genny = self._generate_bigbio_kb_examples(file_names_and_pointers)
731
-
732
- elif self.config.name in ("plain", "plain_en", "plain_de"):
733
- genny = self._generate_plain_examples(file_names_and_pointers)
734
-
735
- elif self.config.schema == "bigbio_t2t":
736
- genny = self._generate_translation_examples(file_names_and_pointers)
737
-
738
- for _id, sample in genny:
739
- yield _id, sample
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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