Lit-OTAR framework for extracting biological evidences from literature.

Santosh Tirunagari; Shyamasree Saha; Aravind Venkatesan; Daniel Suveges; Miguel Carmona; Annalisa Buniello; David Ochoa; Johanna McEntyre; Ellen McDonagh; Melissa Harrison

doi:10.1093/bioinformatics/btaf113

PubMed · 40097274

Lit-OTAR framework for extracting biological evidences from literature.

Santosh Tirunagari·Shyamasree Saha·Aravind Venkatesan·Daniel Suveges·Miguel Carmona·Annalisa Buniello·David Ochoa·Johanna McEntyre·Ellen McDonagh·Melissa Harrison

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Abstract

SUMMARY: The lit-OTAR framework, developed through a collaboration between Europe PMC and Open Targets, leverages deep learning to revolutionize drug discovery by extracting evidence from scientific literature for drug target identification and validation. This novel framework combines named entity recognition for identifying gene/protein (target), disease, organism, and chemical/drug within scientific texts, and entity normalization to map these entities to databases like Ensembl, Experimental Factor Ontology, 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 >29.9 m distinct target-disease, 11.8 m distinct target-drug, and 8.3 m distinct disease-drug relationships. AVAILABILITY AND IMPLEMENTATION: The results are accessible through Europe PMC's SciLite web app (https://europepmc.org/) and its annotations API (https://europepmc.org/annotationsapi), as well as via the Open Targets Platform (https://platform.opentargets.org/). The daily pipeline is available at https://github.com/ML4LitS/otar-maintenance, and the Open Targets ETL processes are available at https://github.com/opentargets.

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Santosh Tirunagari, Shyamasree Saha, Aravind Venkatesan, Daniel Suveges, Miguel Carmona, Annalisa Buniello, David Ochoa, Johanna McEntyre, Ellen McDonagh, Melissa Harrison. 2025-03-29. Lit-OTAR framework for extracting biological evidences from literature.. https://doi.org/10.1093/bioinformatics%2Fbtaf113

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