Datasets:
linnaeus

	---
	annotations_creators:
	- expert-generated
	language_creators:
	- expert-generated
	language:
	- en
	license:
	- cc-by-4.0
	multilinguality:
	- monolingual
	size_categories:
	- 10K<n<100K
	source_datasets:
	- original
	task_categories:
	- token-classification
	task_ids:
	- named-entity-recognition
	paperswithcode_id: linnaeus
	pretty_name: LINNAEUS
	dataset_info:
	features:
	- name: id
	dtype: string
	- name: tokens
	sequence: string
	- name: ner_tags
	sequence:
	class_label:
	names:
	'0': O
	'1': B
	'2': I
	config_name: linnaeus
	splits:
	- name: train
	num_bytes: 4772417
	num_examples: 11936
	- name: validation
	num_bytes: 1592823
	num_examples: 4079
	- name: test
	num_bytes: 2802877
	num_examples: 7143
	download_size: 18204624
	dataset_size: 9168117
	---

	# Dataset Card for [Dataset Name]

	## Table of Contents
	- [Dataset Description](#dataset-description)
	- [Dataset Summary](#dataset-summary)
	- [Supported Tasks and Leaderboards](#supported-tasks-and-leaderboards)
	- [Languages](#languages)
	- [Dataset Structure](#dataset-structure)
	- [Data Instances](#data-instances)
	- [Data Fields](#data-fields)
	- [Data Splits](#data-splits)
	- [Dataset Creation](#dataset-creation)
	- [Curation Rationale](#curation-rationale)
	- [Source Data](#source-data)
	- [Annotations](#annotations)
	- [Personal and Sensitive Information](#personal-and-sensitive-information)
	- [Considerations for Using the Data](#considerations-for-using-the-data)
	- [Social Impact of Dataset](#social-impact-of-dataset)
	- [Discussion of Biases](#discussion-of-biases)
	- [Other Known Limitations](#other-known-limitations)
	- [Additional Information](#additional-information)
	- [Dataset Curators](#dataset-curators)
	- [Licensing Information](#licensing-information)
	- [Citation Information](#citation-information)
	- [Contributions](#contributions)

	## Dataset Description

	- Homepage: [linnaeus](http://linnaeus.sourceforge.net/)
	- Repository: https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/linnaeus-IOB
	- Paper: [BMC Bioinformatics](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-85)
	- Leaderboard:
	- Point of Contact:

	### Dataset Summary

	The LINNAEUS corpus consists of 100 full-text documents from the PMCOA
	document set which were randomly selected. All mentions of species terms were manually
	annotated and normalized to the NCBI taxonomy IDs of the intended species.

	The original LINNAEUS corpus is available in a TAB-separated standoff format. The resource does not define training,
	development or test subsets.

	We converted the corpus into BioNLP shared task standoff format using a custom script, split it into 50-, 17-, and 33-
	document training, development and test sets, and then converted these into the CoNLL format using standoff2conll.

	As a full-text corpus, LINNAEUS contains comparatively frequent
	non-ASCII characters, which were mapped to ASCII using the
	standoff2conll -a option.
	The conversion was highly accurate, but due to sentence-splitting errors within entity mentions,
	the number of annotations in the converted data was larger by four (100.09%) than that
	in the source data. 99.77% of names in the original annotation matched names in the converted
	data.

	### 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

	[More Information Needed]

	### Source Data

	#### Initial Data Collection and Normalization

	[More Information Needed]

	#### Who are the source language producers?

	[More Information Needed]

	### Annotations

	#### 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

	This version of the dataset is licensed under [Creative Commons Attribution 4.0 International](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/blob/master/LICENSE.md).

	### Citation Information

	```bibtex
	@article{crichton2017neural,
	title={A neural network multi-task learning approach to biomedical named entity recognition},
	author={Crichton, Gamal and Pyysalo, Sampo and Chiu, Billy and Korhonen, Anna},
	journal={BMC Bioinformatics},
	volume={18},
	number={1},
	pages={368},
	year={2017},
	publisher={BioMed Central}
	doi = {10.1186/s12859-017-1776-8},
	issn = {1471-2105},
	url = {https://doi.org/10.1186/s12859-017-1776-8},
	}
	@article{Gerner2010,
	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](https://github.com/edugp) for adding this dataset.