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

  • Creator
  • #99603

    Martin Krallinger

    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

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