PEDL+: protein-centered relation extraction from PubMed at your fingertip.
Bioinformatics
; 39(11)2023 11 01.
Article
em En
| MEDLINE
| ID: mdl-37950510
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.
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En
Ano de publicação:
2023
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Article