title: SETH detects and normalizes genetic variants in text.
abstract: : Descriptions of genetic variations and their effect are widely spread across the biomedical literature. However, finding all mentions of a specific variation, or all mentions of variations in a specific gene, is difficult to achieve due to the many ways such variations are described. Here, we describe SETH, a tool for the recognition of variations from text and their subsequent normalization to dbSNP or UniProt. SETH achieves high precision and recall on several evaluation corpora of PubMed abstracts. It is freely available and encompasses stand-alone scripts for isolated application and evaluation as well as a thorough documentation for integration into other applications.
  
  
  
  SETH is released under the Apache 2.0 license and can be downloaded from http://rockt.github.io/SETH/ CONTACT: thomas@informatik.hu-berlin.de or leser@informatik.hu-berlin.de.
authors.affiliation: Language Technology Lab, DFKI Berlin, Germany Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität Zu Berlin, Unter Den Linden 6, Berlin 10099, Germany.
authors.forename: Philippe
authors.initials: P
authors.lastname: Thomas
authors.affiliation: University College London, Gower Street, LondonWC1E 6BT, UK.
authors.forename: Tim
authors.initials: T
authors.lastname: Rocktäschel
authors.affiliation: Illumina, Inc, 451 El Camino Real, Santa Clara, CA 95050, USA.
authors.forename: Jörg
authors.initials: J
authors.lastname: Hakenberg
authors.affiliation: Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität Zu Berlin, Unter Den Linden 6, Berlin 10099, Germany.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Lichtblau
authors.affiliation: Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität Zu Berlin, Unter Den Linden 6, Berlin 10099, Germany.
authors.forename: Ulf
authors.initials: U
authors.lastname: Leser
mesh_terms: D019295:Computational Biology / Q000379:methods; D066289:Data Curation; D057225:Data Mining; D005796:Genes; D014644:Genetic Variation; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D009323:Natural Language Processing; D039781:PubMed; D011642:Publications; D009626:Terminology as Topic