init

README.md

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+---
+language:
+- en
+license:
+- other
+multilinguality:
+- monolingual
+size_categories:
+- 10K<n<100K
+task_categories:
+- token-classification
+task_ids:
+- named-entity-recognition
+pretty_name: BioNLP2004
+---
+
+# Dataset Card for "tner/bionlp2004"
+
+## Dataset Description
+
+- **Repository:** [T-NER](https://github.com/asahi417/tner)
+- **Paper:** [https://aclanthology.org/U15-1010.pdf](https://aclanthology.org/U15-1010.pdf)
+- **Dataset:** BioNLP2004
+- **Domain:** Biochemical
+- **Number of Entity:** 4
+
+### Dataset Summary
+BioNLP2004 NER dataset formatted in a part of [TNER](https://github.com/asahi417/tner) project.
+Original BioNLP2004 dataset contains training and test.
+We take a half amount of test instances randomly from the training set and create a validation set with it.
+
+- Entity Types:`ORG`, `LOC`, `PER`, `MISC`
+
+## Dataset Structure
+
+### Data Instances
+An example of `train` looks as follows.
+
+```
+{
+    "tags": [0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+    "tokens": ["1", ".", "1", ".", "4", "Borrower", "engages", "in", "criminal", "conduct", "or", "is", "involved", "in", "criminal", "activities", ";"]
+}
+```
+
+### Label ID
+The label2id dictionary can be found at [here](https://huggingface.co/datasets/tner/fin/raw/main/dataset/label.json).
+```python
+{
+    "O": 0,
+    "I-ORG": 1,
+    "I-LOC": 2,
+    "I-PER": 3,
+    "I-MISC": 4
+}
+```
+
+### Data Splits
+
+|  name   |train|validation|test|
+|---------|----:|---------:|---:|
+|fin      |861  |       303| 303|
+
+### Citation Information
+
+```
+@inproceedings{collier-kim-2004-introduction,
+    title = "Introduction to the Bio-entity Recognition Task at {JNLPBA}",
+    author = "Collier, Nigel  and
+      Kim, Jin-Dong",
+    booktitle = "Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications ({NLPBA}/{B}io{NLP})",
+    month = aug # " 28th and 29th",
+    year = "2004",
+    address = "Geneva, Switzerland",
+    publisher = "COLING",
+    url = "https://aclanthology.org/W04-1213",
+    pages = "73--78",
+}
+```

bionlp2004.py

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+""" NER dataset compiled by T-NER library https://github.com/asahi417/tner/tree/master/tner """
+import json
+from itertools import chain
+import datasets
+
+logger = datasets.logging.get_logger(__name__)
+_DESCRIPTION = """[BioNLP2004 NER dataset](https://aclanthology.org/W04-1213.pdf)"""
+_NAME = "bionlp2004"
+_VERSION = "1.0.0"
+_CITATION = """
+@inproceedings{collier-kim-2004-introduction,
+    title = "Introduction to the Bio-entity Recognition Task at {JNLPBA}",
+    author = "Collier, Nigel  and
+      Kim, Jin-Dong",
+    booktitle = "Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications ({NLPBA}/{B}io{NLP})",
+    month = aug # " 28th and 29th",
+    year = "2004",
+    address = "Geneva, Switzerland",
+    publisher = "COLING",
+    url = "https://aclanthology.org/W04-1213",
+    pages = "73--78",
+}
+"""
+
+_HOME_PAGE = "https://github.com/asahi417/tner"
+_URL = f'https://huggingface.co/datasets/tner/{_NAME}/raw/main/dataset'
+_URLS = {
+    str(datasets.Split.TEST): [f'{_URL}/test.json'],
+    str(datasets.Split.TRAIN): [f'{_URL}/train.json'],
+    str(datasets.Split.VALIDATION): [f'{_URL}/valid.json'],
+}
+
+
+class BioNLP2004Config(datasets.BuilderConfig):
+    """BuilderConfig"""
+
+    def __init__(self, **kwargs):
+        """BuilderConfig.
+
+        Args:
+          **kwargs: keyword arguments forwarded to super.
+        """
+        super(BioNLP2004Config, self).__init__(**kwargs)
+
+
+class BioNLP2004(datasets.GeneratorBasedBuilder):
+    """Dataset."""
+
+    BUILDER_CONFIGS = [
+        BioNLP2004Config(name=_NAME, version=datasets.Version(_VERSION), description=_DESCRIPTION),
+    ]
+
+    def _split_generators(self, dl_manager):
+        downloaded_file = dl_manager.download_and_extract(_URLS)
+        return [datasets.SplitGenerator(name=i, gen_kwargs={"filepaths": downloaded_file[str(i)]})
+                for i in [datasets.Split.TRAIN, datasets.Split.VALIDATION, datasets.Split.TEST]]
+
+    def _generate_examples(self, filepaths):
+        _key = 0
+        for filepath in filepaths:
+            logger.info(f"generating examples from = {filepath}")
+            with open(filepath, encoding="utf-8") as f:
+                _list = [i for i in f.read().split('\n') if len(i) > 0]
+                for i in _list:
+                    data = json.loads(i)
+                    yield _key, data
+                    _key += 1
+
+    def _info(self):
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=datasets.Features(
+                {
+                    "tokens": datasets.Sequence(datasets.Value("string")),
+                    "tags": datasets.Sequence(datasets.Value("int32")),
+                }
+            ),
+            supervised_keys=None,
+            homepage=_HOME_PAGE,
+            citation=_CITATION,
+        )

dataset/label.json

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+{"O": 0, "B-DNA": 1, "I-DNA": 2, "B-protein": 3, "I-protein": 4, "B-cell_type": 5, "I-cell_type": 6, "B-cell_line": 7, "I-cell_line": 8, "B-RNA": 9, "I-RNA": 10}