Johanna McEntyre

Lit-OTAR Framework for Extracting Biological Evidences from Literature

The paper introduces a framework for extracting biological evidence from literature to aid drug discovery, identifying millions of associations between targets, diseases, and drugs.

Enabling preprint discovery, evaluation, and analysis with Europe PMC

This paper describes how Europe PMC indexes and makes available preprint metadata and full texts to improve their discoverability and reuse in life science research.

Europe PMC Annotated Full-text Corpus for Gene/Proteins, Diseases and Organisms

The paper introduces a human-annotated full-text corpus for biomedical entities, including genes, proteins, diseases, and organisms, to support deep learning approaches in NLP.

Expansion of novel biosynthetic gene clusters from diverse environments using SanntiS

This paper introduces SanntiS, a machine learning tool for identifying biosynthetic gene clusters in genomic and metagenomic data, and demonstrates its ability to predict a large number of novel BGCs with experimental validation.

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

The paper assesses the value and sustainability of ELIXIR Core Data Resources, showing their critical role in preserving biological data and highlighting funding challenges.

Identifiers for the 21st century:How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

The paper outlines ten lessons for designing, provisioning, and reusing persistent identifiers to improve data integration in life sciences.

Literature Evidence in Open Targets - a target validation platform

The paper describes a literature mining component of the Open Targets platform that identifies and ranks target-disease associations from PubMed and Open Access articles.