Named entity recognition, normalization & classification of species, pathogens and food: LivingNER Shared Task (IberLEF2022)

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21 Apr 2022
Groups audience: 

I am happy to share the call for participation of our new named entity recognition/text mining track on the detection/normalization of species (including humans, pathogens like virus, bacteria, parasites, as well as pets/farming animals and food, among others) in medical content.

CFP: LivingNER Shared Task (IberLEF2022)
Named entity recognition, normalization & classification of species, pathogens and food

Key information:
·     Web:
·     Data:
·     Guidelines:
·     Registration:
·     LivingNER vocabulary:
·     Machine Translated Data (for multilingual purposes):
LivingNER is the first track focusing on the automatic detection of species mentions (humans, plants, animals, insects, pathogens), as well as their normalization to species taxonomy concepts (NCBI Taxonomy).

The detection, grounding & classification of species mentions from documents is relevant for a diversity of applications in medicine, biology, biodiversity or nutrition. It represents a key component for text mining applied to:

· Pathogens, tropical diseases (and their mode of transmission)
· Animal caused injuries, bites, etc. on humans
· Pets, farm animals (incl. health-related issues related to them)
· Microorganisms, antibiotic resistance, microbiome 
· Hospital-acquired nosocomial infections 
· Allergies, food (incl. diets, intoxications, certain toxic habits, drug-food interactions)
· Epidemiology, family history (incl. contacts, cohabitants, and relatives) etc.

The LivingNER organizers will release multilingual resources to stress the potential for multilingual adaptation of participating systems (due to the use of universal scientific species nomenclatures).

Following previous tasks (CANTEMIST, PharmaCoNER, or MEDDOCAN), we launch the LivingNER task, with the following sub-tracks:

1. LivingNER-Clinical NER: automatic detection of mentions of species (both human and non-human).
2. LivingNER-Species Norm: finding mentions of species and mapping them to their corresponding NCBI taxonomy concept identifiers.
3. LivingNER-Clinical IMPACT: classifying documents according to 4 axes of clinical relevance (pets/farm animals, animals causing injuries, food, and nosocomial pathogens).

· Test set release: April 22nd, 2022
· End of evaluation: May 22nd, 2022
· Working papers: June 17th, 2022
· Notification of acceptance: June 26th, 2022
· Camera-ready papers: July 3rd, 2022
· IberLEF @ SEPLN 2022: September 202

Participants will be invited to contribute a systems description paper for the IberLEF (SEPLN 2022) Working Notes and a short presentation of their approach at the IberLEF workshop.

Martin Krallinger, BSC
Eulàlia Farré, BSC
Salvador Lima, BSC
Antonio Miranda-Escalada, BSC


Scientific Committee:

  • Tome Eftimov, Jožef Stefan Institute, Ljubljana, Slovenia
  • Irena Spasic, School of Computer Science & Informatics, co-Director of the Data Innovation Research Institute, Cardiff University, UK
  • Kirk Roberts, School of Biomedical Informatics, University of Texas Health Science Center, USA
  • Felipe Bravo, Assistant Professor, University of Chile, Chile
  • Karin Verspoor, School of Computing and Information Systems, Health and Biomedical Informatics Centre, University of Melbourne, Australia
  • Tristan Naumann, Microsoft Research Healthcare NExT, USA
  • Claire Nédellec, University Paris-Saclay, INRAE, France
  • Enea Parimbelli, Assistant Professor at University of Pavia, Italy
  • Casimiro Pio Carrino, Research Engineer at Barcelona Supercomputing Center, Spain
  • Zhiyong Lu, Deputy Director for Literature Search, National Center for Biotechnology Information (NCBI), USA
  • Ashish Tendulkar, Google Research
  • Rosa Estopà Bagot, Universitat Pompeu Fabra, Spain
  • Carlos Luis Parra Calderón, Head of Technological Innovation, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, Spain
  • Thierry Declerck, Senior Consultant at DFKI GmbH, Germany
  • Ernestina Menasalvas, Universidad Politécnica de Madrid, Spain
  • Koldo Gojenola, University of the Basque Country, Spain
  • Aurélie Névéol, LIMSI-CNRS, Université Paris-Sud, France
  • Giorgio Maria Di Nunzio, University of Padua, Italy
  • Anália Lourenço, Universidade de Vigo, Spain
  • Frank Emmert-Streib, Tampere University, Finland
  • Pablo Serrano, Planning Director at Hospital 12 de Octubre, Spain