CFP LivingNER shared task: Named entity recognition, normalization & classification of species, pathogens and food
Martin Krallinger
Call for Participation LivingNER Shared Task (IberLEF2022)
Named entity recognition, normalization & classification of species, pathogens and food
https://temu.bsc.es/livingner/
LivingNER is the first track focusing specifically on the automatic detection of species mentions (humans, plants, animals, insects, pathogens), as well as their normalization to species taxonomy concepts (NCBI Taxonomy @https://www.ncbi.nlm.nih.gov/taxonomy).
The detection, grounding, and classification of species mentions from documents is highly relevant for a diversity of real-world applications in medicine, biology, biodiversity, nutrition, and pharmacology. For instance, it represents a key component for text mining applied to:
Pathogens and tropical diseases (and their mode of transmission)
animal caused injuries, bites, etc. on humans
pets and farm animals (incl. health-related issues related to them)
microorganisms, antibiotic resistance, microbiome
hospital-acquired or nosocomial infections
allergies and food (incl. diets, intoxications, certain toxic habits, drug-food interactions)
epidemiology and family history (incl. close contacts, cohabitants, and relatives)
etc.
The LivingNER track organizers will also release multilingual resources to stress the clear potential for multilingual adaptation of participating systems including and beyond English content (due to the use of universal scientific species nomenclatures).
Following the success of previously organized shared tasks (i.e. CANTEMIST, PharmaCoNER, or MEDDOCAN), we are now launching the LivingNER shared task as part of the IberLEF 2022 evaluation initiative (co-located with SEPLN 2022), with the following three sub-tracks:
LivingNER-Clinical NER: automatic detection of mentions of species (both human and non-human).
LivingNER-Species Norm: finding mentions of species and mapping them to their corresponding NCBI taxonomy concept identifiers.
LivingNER-Clinical IMPACT: classifying documents according to 4 axes of clinical relevance (pets/farm animals, animal causing injuries, food, and nosocomial) and retrieving the evidence supporting the classification.
Key information:
Annotation guidelines: https://doi.org/10.5281/zenodo.6385162
Registration: https://temu.bsc.es/livingner/registration/
LivingNER vocabulary: https://doi.org/10.5281/zenodo.6390506
Machine Translated Data (for multilingual purposes): https://doi.org/10.5281/zenodo.6376662
Schedule
Test set release (start of evaluation period): April 22nd, 2022
End of the evaluation period (system submissions): May 22nd, 2022
Working papers submission: June 17th, 2022
Notification of acceptance (peer-reviews): June 26th, 2022
Camera-ready system descriptions: July 3rd, 2022
IberLEF @ SEPLN 2022: September 2022
Publications and IBERLEF/SEPLN2022 workshop
Teams participating in LivingNER will be invited to contribute a systems description paper for the IberLEF (SEPLN 2022) Working Notes proceedings and a short presentation of their approach at the IberLEF 2022 workshop.
Main Organizers
Martin Krallinger, Barcelona Supercomputing Center, Spain
Eulàlia Farré, Barcelona Supercomputing Center, Spain
Salvador Lima, Barcelona Supercomputing Center, Spain
Antonio Miranda-Escalada, Barcelona Supercomputing Center, Spain
Martin Krallinger, Dr.
Head of Biological Text Mining Unit
Barcelona Supercomputing Center (BSC-CNS)
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