Lit-OTAR Framework for Extracting Biological Evidences from Literature

Abstract

The lit-OTAR framework, developed through a collaboration between Europe PMC and Open Targets, leverages deep learning to revolutionise drug discovery by extracting evidence from scientific literature for drug target identification and validation. This novel framework combines Named Entity Recognition (NER) for identifying genes/proteins, diseases, organisms, and chemicals/drugs within scientific texts, and entity normalisation to map these entities to databases like Ensembl, Experimental Factor Ontology (EFO), and ChEMBL. Continuously operational, it has processed over 39 million abstracts and 4.5 million full-text articles and preprints to date, identifying more than 48.5 million unique associations that significantly help accelerate the drug discovery process and scientific research (>29.9m distinct target-disease, 11.8m distinct target-drug and 8.3m distinct disease-drug relationships). The results are made accessible through the Open Targets Platform (https://platform.opentargets.org/) as well as Europe PMC website (SciLite web app) and annotations API (https://europepmc.org/annotationsapi).