A web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph
Antonio Di Maria, Lorenzo Bellomo, Fabrizio Billeci, Alfio Cardillo, Salvatore Alaimo, Paolo Ferragina, Alfredo Ferro, Alfredo Pulvirenti- Computational Mathematics
- Computational Theory and Mathematics
- Computer Science Applications
- Molecular Biology
- Biochemistry
- Statistics and Probability
Abstract
Motivation
The rapid increase of bio-medical literature makes it harder and harder for scientists to keep pace with the discoveries on which they build their studies. Therefore, computational tools have become more widespread, among which network analysis plays a crucial role in several life-science contexts. Nevertheless, building correct and complete networks about some user-defined biomedical topics on top of the available literature is still challenging.
Results
We introduce NetMe 2.0, a web-based platform that automatically extracts relevant biomedical entities and their relations from a set of input texts—i.e., in the form of full-text or abstract of PubMed Central’s papers, free texts, or PDFs uploaded by users—and models them as a BioMedical Knowledge Graph (BKG). NetMe 2.0 also implements an innovative Retrieval Augmented Generation module (Graph-RAG) that works on top of the relationships modeled by the BKG and allows the distilling of well-formed sentences that explain their content. The experimental results show that NetMe 2.0 can infer comprehensive and reliable biological networks with significant Precision-Recall metrics when compared to state-of-the-art approaches.
Availability
https://netme.click/
Supplementary information
Supplementary data are available at Bioinformatics