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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, where0
indicates no bio-entity mentioned,1
signals the first token of a bio-entity and2
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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