Datasets:
Tasks:
Token Classification
Sub-tasks:
named-entity-recognition
Languages:
English
Size:
10K<n<100K
License:
| 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. |