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Active learning for biomedical relation extraction, the oligogenic use case

par Nachtegael, Charlotte
Président du jury Bontempi, Gianluca
Promoteur Lenaerts, Tom
Publication Non publié, 2024-06-28

Thèse de doctorat

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Résumé :

In a context where technological advancements have enabled increased availability of genetic data through high-throughput sequencing technologies, the complexity of genetic diseases has become increasingly apparent. Oligogenic diseases, characterised by a combination of genetic variants in two or more genes, have emerged as a crucial research area, challenging the traditional model of "one genotype, one phenotype". Thus, understanding the underlying mechanisms and genetic interactions of oligogenic diseases has become a major priority in biomedical research. This context underlines the importance of developing dedicated tools to study these complex diseases.Our first major contribution, OLIDA, is an innovative database designed to collect data on variant combinations responsible for these diseases, filling significant gaps in the current knowledge, focused up until now on the digenic diseases. This resource, accessible via a web platform, adheres to FAIR principles and represents a significant advancement over its predecessor, DIDA, in terms of data curation and quality assessment.Furthermore, to support the biocuration of oligogenic diseases, we used active learning to construct DUVEL, a biomedical corpus focused on digenic variant combinations. To achieve this, we first investigated how to optimise these methods across numerous biomedical relation extraction datasets and developed a web-based platform, ALAMBIC, for text annotation using active learning. Our results and the quality of the corpus obtained demonstrate the effectiveness of active learning methods in biomedical relation annotation tasks.By establishing a curation pipeline for oligogenic diseases, as well as a standards for integrating active learning methods into biocuration, our work represents a significant advancement in the field of biomedical natural language processing and the understanding of oligogenic diseases.