README.md

metadata

language:
  - en
  - fr
  - gal
  - it
  - pt
  - ro
  - cat
multilinguality:
  - multilingual
license: cc-by-4.0
task_categories:
  - token-classification
pretty_name: LivingNER
config_names:
  - en
  - fr
  - gal
  - it
  - pt
  - to
  - cat
  - combined
dataset_info:
  - config_name: en
    splits:
      - name: train
        num_bytes: 14699476
        num_examples: 1000
      - name: validation
        num_bytes: 6764942
        num_examples: 500
  - config_name: fr
    splits:
      - name: train
        num_bytes: 14699476
        num_examples: 1000
      - name: validation
        num_bytes: 6764942
        num_examples: 500
  - config_name: gal
    splits:
      - name: train
        num_bytes: 14699476
        num_examples: 1000
      - name: validation
        num_bytes: 6764942
        num_examples: 500
  - config_name: it
    splits:
      - name: train
        num_bytes: 14699476
        num_examples: 1000
      - name: validation
        num_bytes: 6764942
        num_examples: 500
  - config_name: pt
    splits:
      - name: train
        num_bytes: 14699476
        num_examples: 1000
      - name: validation
        num_bytes: 6764942
        num_examples: 500
  - config_name: ro
    splits:
      - name: train
        num_bytes: 14699476
        num_examples: 1000
      - name: validation
        num_bytes: 6764942
        num_examples: 500
  - config_name: cat
    splits:
      - name: train
        num_bytes: 14699476
        num_examples: 1000
      - name: validation
        num_bytes: 6764942
        num_examples: 500
  - config_name: combined
    splits:
      - name: train
        num_bytes: 108745150,
        num_examples: 7000
      - name: validation
        num_bytes: 50100231
        num_examples: 3500
configs:
  - config_name: default
    data_files:
      - split: train
        path: en/train/data-*
      - split: validation
        path: en/validation/data-*
  - config_name: en
    data_files:
      - split: train
        path: en/train/data-*
      - split: validation
        path: en/validation/data-*
  - config_name: fr
    data_files:
      - split: train
        path: fr/train/data-*
      - split: validation
        path: fr/validation/data-*
  - config_name: gal
    data_files:
      - split: train
        path: gal/train/data-*
      - split: validation
        path: gal/validation/data-*
  - config_name: it
    data_files:
      - split: train
        path: it/train/data-*
      - split: validation
        path: it/validation/data-*
  - config_name: pt
    data_files:
      - split: train
        path: pt/train/data-*
      - split: validation
        path: pt/validation/data-*
  - config_name: ro
    data_files:
      - split: train
        path: ro/train/data-*
      - split: validation
        path: ro/validation/data-*
  - config_name: cat
    data_files:
      - split: train
        path: cat/train/data-*
      - split: validation
        path: cat/validation/data-*
  - config_name: combined
    data_files:
      - split: train
        path: combined/train/data-*
      - split: validation
        path: combined/validation/data-*

LivingNER: Named entity recognition, normalization & classification of species, pathogens and food

Dataset Summary

The LivingNER Gold Standard corpus is a collection of 2000 clinical case reports covering a broad range of medical specialities, i.e. infectious diseases (including Covid-19 cases), cardiology, neurology, oncology, dentistry, pediatrics, endocrinology, primary care, allergology, radiology, psychiatry, ophthalmology, urology, internal medicine, emergency and intensive care medicine, tropical medicine, and dermatology annotated with species [SPECIES] (including living organisms and microorganisms) and infectious diseases [ENFERMEDAD] mentions. Species mentions include many pathogens and infectious agents, but also food, allergens, pets or other species, taxonomic groups and organisms of clinical relevance.

The LivingNER corpus has also annotations of mentions of humans (tag HUMAN), including the patients itself, family members, healhcare professionals or other persons mentioned in the case reports. Thus it can be useful to extract family history information of patients or information about the social and healthcare personal environment and interactions.

All mentions have been exhaustively manually mapped by experts to their corresponding (NCBI Taxonomy)[https://www.ncbi.nlm.nih.gov/taxonomy] identifiers.

It was used for the (LivingNER)[https://temu.bsc.es/livingner/] Shared Task on pathogens and living beings detection and normalization in Spanish medical documents, which was celebrated as part of IberLEF 2022.

Dataset Description

• Languages:
  • en
  • fr
  • gal
  • it
  • pt
  • ro
  • combined
• Training Set Size: 1000
• Test Set Size: 500
• Features:
  • text: Original text
  • language: Language identifier
  • tokens: Tokenized text
  • ner_tags: Named entity tags in BIO format
  • entity_mentions: Detailed entity information

Usage

from datasets import load_dataset

# Load the dataset
dataset = load_dataset('path/to/dataset', '{lang}')

# Access splits
train_data = dataset['train']
test_data = dataset['test']

Labels

The following entity types are annotated in this dataset: ['O', 'B-HUMAN', 'I-HUMAN', 'B-SPECIES', 'I-SPECIES']

Citation Information

@article{amiranda2022nlp,
  title={Mention detection, normalization \& classification of species, pathogens, humans and food in clinical documents: Overview of LivingNER shared task and resources},
  author={Miranda-Escalada, Antonio and Farr{\'e}-Maduell, Eul{`a}lia and Lima-L{\'o}pez, Salvador and Estrada, Darryl and Gasc{\'o}, Luis and Krallinger, Martin},
  journal = {Procesamiento del Lenguaje Natural}, year={2022}
}

@dataset{miranda_escalada_2022_7684093,
  author       = {Miranda-Escalada, Antonio and
                  Farré-Maduell, Eulàlia and
                  Lima-López, Salvador and
                  González Gacio, Gloria and
                  Krallinger, Martin},
  title        = {LivingNER corpus: Named entity recognition,
                   normalization \& classification of species,
                   pathogens and food
                  },
  month        = jun,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {6.3.1},
  doi          = {10.5281/zenodo.7684093},
  url          = {https://doi.org/10.5281/zenodo.7684093},
}