PEDL+: Protein-centered relation extraction from PubMed at your fingertip
Autor/innen
- L. Weber
- F. Barth
- L. Lorenz
- F. Konrath
- K. Huska
- J. Wolf
- U. Leser
Journal
- Bioinformatics
Quellenangabe
- Bioinformatics 39 (11): btad603
Zusammenfassung
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.