Call for Participation: BioASQ 2025: BioNNE-L (Biomedical Nested Named Entity Linking) Shared Task
[Apologies if you receive multiple copies of this email.]
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: GitHub Repository
In order to download annotations, please register at the BioASQ website: BioASQ Registration
To submit your results you need to register on the Codalab Competition page: Codalab Competition
Important 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.sakhovskiy@gmail.com
Elena Tutubalina, AIRI, email: tutubalinaev@gmail.com