PEDL+: protein-centered relation extraction from PubMed at your fingertip

Weber, Leon ; Barth, Fabio; Lorenz, Leonie; Konrath, Fabian; Huska, Kirsten; Wolf, Jana; Leser, Ulf und Lu, Zhiyong (2023): PEDL+: protein-centered relation extraction from PubMed at your fingertip. In: Bioinformatics, Bd. 39, Nr. 11, btad603

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 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.

• Dokumententyp: Zeitschriftenartikel
• Fakultät: Mathematik, Informatik und Statistik > Informatik
• Fakultätsübergreifende Einrichtungen: Centrum für Informations- und Sprachverarbeitung (CIS)
• Themengebiete: 000 Informatik, Informationswissenschaft, allgemeine Werke > 004 Informatik
• ISSN: 1367-4803
• Sprache: Englisch
• DFG: Gefördert durch die Deutsche Forschungsgemeinschaft (DFG) - 414984028