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

This guide describes the annotation and standardization process of the LivingNER corpus, a collection of 2,000 clinical cases in Spanish from more than 10 medical specialties (infectious diseases, tropical and travel medicine clinic, internal medicine, COVID-19, allergology, pediatrics, oncology and urology, among others) annotated with species (including living organisms and microorganisms) and infectious disease citations. Each of the mentions in the corpus has been standardized using NCBI Taxonomy terminology. Finally, the species mentions have been classified into classes of clinical interest to improve their usability (companion animals, animal attacks, food, nosocomial entities and antibiotic-resistant bacteria).

Please cite if you use this resource:

A. Miranda-Escalada, E. Farré-Maduell, S. Lima-López, D. Estrada, L. Gascó, M. Krallinger, Mention detection, normalization & classification of species, pathogens, humans and food in clinical documents: Overview of livingner shared task and resources, Procesamiento del Lenguaje Natural (2022)

@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}
}

Resources

• Web
• Training and validation set
• Evaluation library
• LivingNER terminology

For more information visit https://temu.bsc.es/livingner/ or email us at encargo-pln-life@bsc.es