Datasets:
linnaeus

Tasks:

Token Classification

Sub-tasks: named-entity-recognition

Languages: English

Multilinguality: monolingual

Size Categories: 10K<n<100K

Language Creators: expert-generated

Annotations Creators: expert-generated

Source Datasets: original

License: unknown

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Cannot load the dataset split (in streaming mode) to extract the first rows.

Error code:   StreamingRowsError
Exception:    IndexError
Message:      list index out of range
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/linnaeus/1fff4a2230967ab65f5b5caade70ec149cfb87c979b1a3cdfbededbff0097de5/linnaeus.py", line 98, in _split_generators
                  downloaded_files = dl_manager.download_and_extract(urls_to_download)
                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 444, in map_nested
                  mapped = [
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/utils/py_utils.py", line 445, in <listcomp>
                  _single_map_nested((function, obj, types, None, True, None))
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/utils/py_utils.py", line 346, in _single_map_nested
                  return function(data_struct)
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/download/streaming_download_manager.py", line 1031, in _extract
                  protocol = _get_extraction_protocol(urlpath, use_auth_token=self.download_config.use_auth_token)
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/download/streaming_download_manager.py", line 433, in _get_extraction_protocol
                  with fsspec.open(urlpath, **kwargs) as f:
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/fsspec/core.py", line 419, in open
                  return open_files(
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/fsspec/core.py", line 194, in __getitem__
                  out = super().__getitem__(item)
              IndexError: list index out of range

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Dataset Card for [Dataset Name]

Dataset Summary

LINNAEUS is a general-purpose dictionary matching software, capable of processing multiple types of document formats in the biomedical domain (MEDLINE, PMC, BMC, OTMI, text, etc.). It can produce multiple types of output (XML, HTML, tab-separated-value file, or save to a database). It also contains methods for acting as a server (including load balancing across several servers), allowing clients to request matching over a network. A package with files for recognizing and identifying species names is available for LINNAEUS, showing 94% recall and 97% precision compared to LINNAEUS-species-corpus.

Supported Tasks and Leaderboards

This dataset is used for species Named Entity Recognition.

Languages

The dataset is in English.

Dataset Structure

Data Instances

An example from the dataset is:

{'id': '2',
'tokens': ['Scp160p', 'is', 'a', '160', 'kDa', 'protein', 'in', 'the', 'yeast', 'Saccharomyces', 'cerevisiae', 'that', 'contains', '14', 'repeats', 'of', 'the', 'hnRNP', 'K', '-', 'homology', '(', 'KH', ')', 'domain', ',', 'and', 'demonstrates', 'significant', 'sequence', 'homology', 'to', 'a', 'family', 'of', 'proteins', 'collectively', 'known', 'as', 'vigilins', '.'],
'ner_tags': [0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]}

Data Fields

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

Data Splits

name	train	validation	test
linnaeus	11936	4079	7143

Dataset Creation

Curation Rationale

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Source Data

Initial Data Collection and Normalization

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Who are the source language producers?

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Annotations

Annotation process

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Who are the annotators?

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Personal and Sensitive Information

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Considerations for Using the Data

Social Impact of Dataset

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Discussion of Biases

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Other Known Limitations

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Additional Information

Dataset Curators

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Licensing Information

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Citation Information

@article{Gerner2010,
abstract = {The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles.},
author = {Gerner, Martin and Nenadic, Goran and Bergman, Casey M},
doi = {10.1186/1471-2105-11-85},
issn = {1471-2105},
journal = {BMC Bioinformatics},
number = {1},
pages = {85},
title = {{LINNAEUS: A species name identification system for biomedical literature}},
url = {https://doi.org/10.1186/1471-2105-11-85},
volume = {11},
year = {2010}
}

Contributions

Thanks to @edugp for adding this dataset.

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