PEDL+: protein-centered relation extraction from PubMed at your fingertip.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 37950510.
- Also identified by DOI 10.1093/bioinformatics/btad603 and PMC identifier 10660277.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. PEDL+ is freely available at https://github.com/leonweber/pedl.
Medical subject headings
- Software