{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T17:12:20Z","timestamp":1780765940069,"version":"3.54.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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.<\/jats:p><jats:p>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\u2009000 relations with an estimated perfomance of both 80% precision and 80% recall.<\/jats:p><jats:p>Availability: The used natural language preprocessing tools are free for use for academic research. Test sets and relation term lists are available from our website ().<\/jats:p><jats:p>Contact: \u00a0katrin.fundel@bio.ifi.lmu.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl616","type":"journal-article","created":{"date-parts":[[2006,12,3]],"date-time":"2006-12-03T01:12:55Z","timestamp":1165108375000},"page":"365-371","source":"Crossref","is-referenced-by-count":368,"title":["RelEx\u2014Relation extraction using dependency parse trees"],"prefix":"10.1093","volume":"23","author":[{"given":"Katrin","family":"Fundel","sequence":"first","affiliation":[{"name":"Institut f\u00fcr Informatik, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen \u00a0 Amalienstrasse 17, 80333 M\u00fcnchen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"K\u00fcffner","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Informatik, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen \u00a0 Amalienstrasse 17, 80333 M\u00fcnchen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ralf","family":"Zimmer","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Informatik, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen \u00a0 Amalienstrasse 17, 80333 M\u00fcnchen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2006,12,1]]},"reference":[{"key":"2023041109380424200_","first-page":"123","article-title":"The potential use of suiseki as a protein interaction discovery tool","volume":"12","author":"Blaschke","year":"2001","journal-title":"Genome Inform. 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