[Call for Participation] BioASQ 2025: BioNNE-L (Biomedical Nested Named Entity Linking) Shared Task

[Elena Tutubalina]

[Apologies for cross-posting]

Dear Researchers,

We are pleased to announce the BioNNE-L (Biomedical Nested Named Entity Linking) Shared Task which will take place during the BioASQ 2025 Workshop co-located with CLEF 2025 hosted at Madrid, Spain, 9-12 September 2025. BioASQ is a major workshop on biomedical Natural Language Processing (NLP) with a main focus on information extraction and question answering tasks. CLEF is a longstanding conference series devoted to the systematic evaluation of information access systems, primarily through experimentation on shared tasks. 

🎯 Task Type: Biomedical Concept Normalization (Entity Linking).

📝 Task Specification: Given a biomedical entity's mention, retrieve a matching vocabulary concept from the Unified Medical Language System (UMLS), the largest biomedical meta-thesaurus. Participants are invited to develop monolingual entity linking systems for Russian and English, as well as a single multilingual model that supports both languages.

📄 Data: Annotated entities extracted from scientific paper abstracts in biology and medicine.

Shared Task-specific challenges:

🪆 High Nestedness: Shorter entities can be nested within longer entities, creating a multi-level hierarchy.

❓ Incompleteness of Russian Terminology: Some Russian mentions are linked to UMLS concepts with no Russian name, but do have an English name.

See the details in our GitHub: https://github.com/nerel-ds/NEREL-BIO/tree/master/BioNNE-L_Shared_Task

In order to download annotations, please register at the BioASQ website: http://participants-area.bioasq.org/#

To submit your results you need to register on the Codalab Competition page: https://codalab.lisn.upsaclay.fr/competitions/21568

Dates:

Training data release: 5 February 2025

Test data release, evaluation phase starts: 25 April 2025

Test set predictions due: 6 May 2025

Submission of participant papers: 31 May 2025

Acceptance notification for participant papers: 24 June 2025

Camera-ready working notes papers: 8 July 2025

BioASQ Workshop at  CLEF 2024, Grenoble, France: 9-12 September 2025

Contact    

Andrey Sakhovskiy, KFU, email: andrey.s...@gmail.com

Elena Tutubalina, AIRI, email: tutuba...@gmail.com