title: Text-mining assisted regulatory annotation.
abstract: BACKGROUND
  Decoding transcriptional regulatory networks and the genomic cis-regulatory logic implemented in their control nodes is a fundamental challenge in genome biology. High-throughput computational and experimental analyses of regulatory networks and sequences rely heavily on positive control data from prior small-scale experiments, but the vast majority of previously discovered regulatory data remains locked in the biomedical literature.
  
  
  RESULTS
  We develop text-mining strategies to identify relevant publications and extract sequence information to assist the regulatory annotation process. Using a vector space model to identify Medline abstracts from papers likely to have high cis-regulatory content, we demonstrate that document relevance ranking can assist the curation of transcriptional regulatory networks and estimate that, minimally, 30,000 papers harbor unannotated cis-regulatory data. In addition, we show that DNA sequences can be extracted from primary text with high cis-regulatory content and mapped to genome sequences as a means of identifying the location, organism and target gene information that is critical to the cis-regulatory annotation process.
  
  
  CONCLUSIONS
  Our results demonstrate that text-mining technologies can be successfully integrated with genome annotation systems, thereby increasing the availability of annotated cis-regulatory data needed to catalyze advances in the field of gene regulation.
authors.affiliation: Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B-3000, Belgium. stein.aerts@med.kuleuven.be
authors.forename: Stein
authors.initials: S
authors.lastname: Aerts
authors.forename: Maximilian
authors.initials: M
authors.lastname: Haeussler
authors.forename: Steven
authors.initials: S
authors.lastname: van Vooren
authors.forename: Obi L
authors.initials: OL
authors.lastname: Griffith
authors.forename: Paco
authors.initials: P
authors.lastname: Hulpiau
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Montgomery
authors.forename: Casey M
authors.initials: CM
authors.lastname: Bergman
mesh_terms: D000818:Animals; D053263:Gene Regulatory Networks; D016678:Genome; D006801:Humans; D016239:MEDLINE; D050436:Regulatory Elements, Transcriptional