completed · group research project · 2023
Biological knowledge-graph construction
Amsterdam University College research project using transformer-assisted relation extraction on PubMed abstracts.
This group research project investigated whether transformer-based relationship extraction could turn a large corpus of PubMed abstracts into useful biological knowledge graphs. We retrieved and processed approximately 15,000 abstracts, extracted subject–relation–object triples, filtered and normalised biological entities and assembled the resulting relationships as graphs.
The work combined Biopython and Entrez for corpus collection, transformer-based relationship and keyword extraction, biomedical language processing, NetworkX visualisation and graph-embedding evaluation. It was completed with Boray Kasap and Eliott Mattei during my exchange year at Amsterdam University College.