Datasets:

cambridgeltl
/

linnaeus

	---
	annotations_creators:
	- expert-generated
	language_creators:
	- expert-generated
	language:
	- en
	license:
	- unknown
	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:
	- Paper: [BMC Bioinformatics](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-85)
	- Leaderboard:
	- Point of Contact:

	### 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

	[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

	[More Information Needed]

	### Citation Information

	```bibtex
	@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](https://github.com/edugp) for adding this dataset.