RelEx - Relation extraction using dependency parse trees. Motivation: The discovery of regulatory pathways, signal cascades, metabolic processes or disease models requires knowledge on individual relations like e.g. physical or regulatory interactions between genes and proteins. Most interactions mentioned in the free text of biomedical publications are not yet contained in structured databases. Results: We developed RelEx, an approach for relation extraction from free text. It is based on natural language preprocessing producing dependency parse trees and applying a small number of simple rules to these trees. We applied RelEx on a comprehensive set of one million MEDLINE abstracts dealing with gene and protein relations and extracted  150 000 relations with an estimated perfomance of both 80% precision and 80% recall.

References in zbMATH (referenced in 7 articles )

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  1. Bui, Quoc-Chinh; Nualláin, Breanndán Ó; Boucher, Charles A.; Sloot, Peter M. A.: Extracting causal relations on HIV drug resistance from literature (2010) ioport
  2. Kim, Seonho; Yoon, Juntae; Yang, Jihoon; Park, Seog: Walk-weighted subsequence kernels for protein-protein interaction extraction (2010) ioport
  3. Li, Yanpeng; Hu, Xiaohua; Lin, Hongfei; Yang, Zhihao: Learning an enriched representation from unlabeled data for protein-protein interaction extraction (2010) ioport
  4. Birzele, Fabian; Csaba, Gergely; Erhard, Florian; Friedel, Caroline; Küffner, Robert; Petri, Tobias; Windhager, Lukas; Zimmer, Ralf: Algorithmische Systembiologie mit Petrinetzen - von qualitativen zu quantitativen Systemmodellen (2009) ioport
  5. Fayruzov, Timur; De Cock, Martine; Cornelis, Chris; Hoste, Véronique: Linguistic feature analysis for protein interaction extraction (2009) ioport
  6. Kabiljo, Renata; Clegg, Andrew B.; Shepherd, Adrian J.: A realistic assessment of methods for extracting gene/protein interactions from free text (2009) ioport
  7. Fundel, Katrin; Küffner, Robert; Zimmer, Ralf: Relex---relation extraction using dependency parse trees (2007) ioport