NETME: On-the-Fly Knowledge Network Construction from Biomedical Literature

Abstract

Background:The rapidly increasing biological literature is a key resource to automatically extract and gain knowledge concerning biological elements and their relations. Knowledge Networks are helpful tools in the context of biological knowledge discovery and modeling. Results:We introduce a novel system called NETME, which, starting from a set of full-texts obtained from PubMed, through an easy-to-use web interface, interactively extracts biological elements from ontological databases and then synthesizes a network inferring relations among such elements. The results clearly show that our tool is capable of inferring comprehensive and reliable biological networks.

tRFUniverse: A comprehensive resource for the interactive analyses of tRNA-derived ncRNAs in human cancer

“…As a final fragment-specific analysis, in tRFUniverse , we allow users to build a knowledge graph based on the information available about the selected tRNA-derived ncRNA from the literature. Such a function is powered by NetME, 64 , 65 a novel text-mining software that, starting from a set of full texts obtained from PubMed, can extract biological elements from ontological databases and then synthesize a network inferring relations among such elements. In this case, tRFUniverse creates a query to NetME using as a biological element the tRNA-derived ncRNA selected from the user with all its potential aliases reported in other databases.…”