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Cannot load the dataset split (in streaming mode) to extract the first rows.
Error code:   StreamingRowsError
Exception:    NotImplementedError
Message:      Extraction protocol for TAR archives like 'http://www.nactem.ac.uk/GENIA/current/Shared-tasks/JNLPBA/Train/Genia4ERtraining.tar.gz' is not implemented in streaming mode. Please use `dl_manager.iter_archive` instead.

Example usage:

	url = dl_manager.download(url)
	tar_archive_iterator = dl_manager.iter_archive(url)

	for filename, file in tar_archive_iterator:
		...
Traceback:    Traceback (most recent call last):
                File "/src/workers/datasets_based/src/datasets_based/workers/first_rows.py", line 485, in compute_first_rows_response
                  rows = get_rows(
                File "/src/workers/datasets_based/src/datasets_based/workers/first_rows.py", line 120, in decorator
                  return func(*args, **kwargs)
                File "/src/workers/datasets_based/src/datasets_based/workers/first_rows.py", line 164, in get_rows
                  ds = load_dataset(
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/load.py", line 1751, in load_dataset
                  return builder_instance.as_streaming_dataset(split=split)
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1206, in as_streaming_dataset
                  splits_generators = {sg.name: sg for sg in self._split_generators(dl_manager)}
                File "/tmp/modules-cache/datasets_modules/datasets/jnlpba/3062f220823930cffde7976b694aa67bac3b06c322a02ced92d3761519810ce4/jnlpba.py", line 103, in _split_generators
                  train_files = dl_manager.download_and_extract(TRAIN_URL)
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/download/streaming_download_manager.py", line 1074, in download_and_extract
                  return self.extract(self.download(url_or_urls))
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/download/streaming_download_manager.py", line 1026, in extract
                  urlpaths = map_nested(self._extract, url_or_urls, map_tuple=True)
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/utils/py_utils.py", line 436, in map_nested
                  return function(data_struct)
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/download/streaming_download_manager.py", line 1036, in _extract
                  raise NotImplementedError(
              NotImplementedError: Extraction protocol for TAR archives like 'http://www.nactem.ac.uk/GENIA/current/Shared-tasks/JNLPBA/Train/Genia4ERtraining.tar.gz' is not implemented in streaming mode. Please use `dl_manager.iter_archive` instead.
              
              Example usage:
              
              	url = dl_manager.download(url)
              	tar_archive_iterator = dl_manager.iter_archive(url)
              
              	for filename, file in tar_archive_iterator:
              		...

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Dataset Card for JNLPBA

Dataset Summary

The data came from the GENIA version 3.02 corpus (Kim et al., 2003). This was formed from a controlled search on MEDLINE using the MeSH terms human, blood cells and transcription factors. From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus.

Supported Tasks and Leaderboards

NER

Languages

English

Dataset Structure

Data Instances

{ 'id': '1', 'tokens': ['IL-2', 'gene', 'expression', 'and', 'NF-kappa', 'B', 'activation', 'through', 'CD28', 'requires', 'reactive', 'oxygen', 'production', 'by', '5-lipoxygenase', '.'], 'ner_tags': [1, 2, 0, 0, 9, 10, 0, 0, 9, 0, 0, 0, 0, 0, 9, 0], }

Data Fields

  • id: Sentence identifier.
  • tokens: Array of tokens composing a sentence.
  • ner_tags: Array of tags, where 0 indicates no bio-entity mentioned, 1 signals the first token of a bio-entity and 2 the subsequent bio-entity tokens.

Data Splits

Train samples: 37094 Validation samples: 7714

Dataset Creation

Curation Rationale

[Needs More Information]

Source Data

Initial Data Collection and Normalization

[Needs More Information]

Who are the source language producers?

[Needs More Information]

Annotations

Annotation process

[Needs More Information]

Who are the annotators?

[Needs More Information]

Personal and Sensitive Information

[Needs More Information]

Considerations for Using the Data

Social Impact of Dataset

[Needs More Information]

Discussion of Biases

[Needs More Information]

Other Known Limitations

[Needs More Information]

Additional Information

Dataset Curators

[Needs More Information]

Licensing Information

[Needs More Information]

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", }

Contributions

Thanks to @edugp for adding this dataset.

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