lasigeBioTM: A Lean Biomedical QA System Empowered by Structured Knowledge

This repository contains the code used for our participation at the BioASQ2025 Task13 b Biomedical Semantic QA

The paper describing our participation is available here.

Systems:

• lasigeBioTM-baseline: GCD/lasigeBioTM-baseline.py
• lasigeBioTM-onto: OntoRag/lasigeBioTm-onto.py
• lasigeBioTM-onto-trie: GCD/lasigeBioTM-onto-trie.py
• sp_lasigeBioTM: GCD/GCR/qa_mistral_bent.py

NER & NEL

• BENT annotation tool

Project Structure

BioASQ13_2025/
├── data/		                # Contains used annotation files
│   └── ...
├── ElasticSearch/	            # Scripts for indexing and searching with ElasticSearch
│   └── ...
├── Evaluate/
│   └── ...
├── GCD/		                # Scripts with Graph Constrained Decoding
│   ├── extract_docs.py
│   ├── lasigeBioTM-baseline.py
│   ├── lasigeBioTM-onto-trie.py
│   ├── snippets_mistral_base.py
│   ├── ...
│   └── GCR/
│       ├── qa_mistral_bent.py
│       └── ...
├── OntoRag/		            # Scripts with RAG using ontologies
│   ├── lasigeBioTm-onto.py
│   ├── ontology_info.py
│   └── obo_files/
├── PhaseA/
│   └── ...
└── UTILS/		                # Utility scripts and helper functions
│   └── ...
├── bioasq_env.yml	            # Dependencies