2020/11/10 by Jupinder Parmar, Parmar, Jupinder, William C. Koehler +7
Biochemistry, Genetics and Molecular Biology · Computer Science · #Biomedical Text Mining and Ontologies #Computation and Language (cs.CL) #FOS: Computer and information sciences #Machine Learning (cs.LG) #Semantic Web and Ontologies #Topic Modeling
paper · pdf · doi:10.48550/arxiv.2011.05188
openalex publication_date 2020/11/10 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
We introduce a biomedical information extraction (IE) pipeline that extracts biological relationships from text and demonstrate that its components, such as named entity recognition (NER) and relation extraction (RE), outperform state-of-the-art in BioNLP. We apply it to tens of millions of PubMed abstracts to extract protein-protein interactions (PPIs) and augment these extractions to a biomedical knowledge graph that already contains PPIs extracted from STRING, the leading structured PPI database. We show that, despite already containing PPIs from an established structured source, augmenting our own IE-based extractions to the graph allows us to predict novel disease-gene associations with a 20% relative increase in hit@30, an important step towards developing drug targets for uncured diseases.