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Updated: Jul 11, 2025

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications
Published on: February 23, 2019
PEDL+: protein-centered relation extraction from PubMed at your fingertip
Leon Weber1, Fabio Barth2, Leonie Lorenz3
1Center for Information and Language Processing, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, München 80539, Germany.
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 PEDL+, a user-friendly tool for extracting protein-protein and protein-chemical associations from PubMed articles. PEDL+ combines state-of-the-art NLP technology with adaptable ranking and filtering options and can easily be integrated into analysis pipelines. We evaluated PEDL+ in two pathway curation projects and found that 59% to 80% of its extractions were helpful.
Availability And Implementation:
PEDL+ is freely available at https://github.com/leonweber/pedl.
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