PEDL1: protein-centered relation extraction from PubMed at your fingertip

Abstract

Summary: Relation extraction (RE) from large text collections is an important tool for database curation, pathway reconstruction, or functional omics data analysis. In practice, RE often is part of a complex data analysis pipeline requiring specific adaptations like restricting the types of relations or the set of proteins to be considered. However, current systems are either non-programmable web sites or research code with fixed functionality. We present PEDLþ, a user-friendly tool for extracting protein–protein and protein–chemical associations from PubMed articles. PEDLþ combines state-of-the-art NLP technology with adaptable ranking and filtering options and can easily be integrated into analysis pipelines. We evaluated PEDLþ in two pathway curation projects and found that 59% to 80% of its extractions were helpful.