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The dataset preview is not available for this split.
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/", line 485, in compute_first_rows_response
                  rows = get_rows(
                File "/src/workers/datasets_based/src/datasets_based/workers/", line 120, in decorator
                  return func(*args, **kwargs)
                File "/src/workers/datasets_based/src/datasets_based/workers/", line 164, in get_rows
                  ds = load_dataset(
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/", 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/", line 1206, in as_streaming_dataset
                  splits_generators = { sg for sg in self._split_generators(dl_manager)}
                File "/tmp/modules-cache/datasets_modules/datasets/linnaeus/1fff4a2230967ab65f5b5caade70ec149cfb87c979b1a3cdfbededbff0097de5/", 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/", line 1074, in download_and_extract
                  return self.extract(
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/download/", 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/", line 444, in map_nested
                  mapped = [
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/utils/", 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/", line 346, in _single_map_nested
                  return function(data_struct)
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/datasets/download/", 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/", line 433, in _get_extraction_protocol
                  with, **kwargs) as f:
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/fsspec/", line 419, in open
                  return open_files(
                File "/src/workers/datasets_based/.venv/lib/python3.9/site-packages/fsspec/", line 194, in __getitem__
                  out = super().__getitem__(item)
              IndexError: list index out of range

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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.


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

[More Information Needed]

Source Data

Initial Data Collection and Normalization

[More Information Needed]

Who are the source language producers?

[More Information Needed]


Annotation process

[More Information Needed]

Who are the annotators?

[More Information Needed]

Personal and Sensitive Information

[More Information Needed]

Considerations for Using the Data

Social Impact of Dataset

[More Information Needed]

Discussion of Biases

[More Information Needed]

Other Known Limitations

[More Information Needed]

Additional Information

Dataset Curators

[More Information Needed]

Licensing Information

[More Information Needed]

Citation Information

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 = {},
volume = {11},
year = {2010}


Thanks to @edugp for adding this dataset.

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