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GeneReg


The GeneReg corpus consists of 314 Medline abstracts dealing with the regulation of gene expression in the model organism E. coli. The regulation of gene expression can be described as the process that modulates the frequency, rate or extent of gene expression. During gene expression, the coding sequence of a gene is converted into a mature gene product or products, namely proteins or RNA (taken from the definition of the Gene Ontology class Regulation of Gene Expression, GO:0010468). GeneReg provides three types of semantic annotations: named entities involved in gene regulatory processes, such as transcription factors and genes, pairwise relations between regulators and regulated genes, and event triggers (clue verbs) essential for the description of, e.g., gene expression and gene regulation events. For all three annotation levels, the annotation vocabulary was taken from the Gene Regulation Ontology (GRO).

Download the GeneReg corpus(.tar.gz, 290K)

Publications:

  • Ekaterina Buyko, Elena Beisswanger and Udo Hahn. The GeneReg Corpus for Gene Expression Regulation Events - An Overview of the Corpus and its In-Domain and Out-of-Domain Interoperability. In Proceedings of the 7thInternational Conference on Language Resources and Evaluation (LREC 2010), May 2010.
  • Ekaterina Buyko, Elena Beisswanger and Udo Hahn. Testing Different ACE-Style Feature Sets for the Extraction of Gene Regulation Relations from Medline Abstracts. Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), September 2008