title: Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing.
abstract: BACKGROUND
  This article describes capture of biological information using a hybrid approach that combines natural language processing to extract biological entities and crowdsourcing with annotators recruited via Amazon Mechanical Turk to judge correctness of candidate biological relations. These techniques were applied to extract gene- mutation relations from biomedical abstracts with the goal of supporting production scale capture of gene-mutation-disease findings as an open source resource for personalized medicine.
  
  
  RESULTS
  The hybrid system could be configured to provide good performance for gene-mutation extraction (precision ∼82%; recall ∼70% against an expert-generated gold standard) at a cost of $0.76 per abstract. This demonstrates that crowd labor platforms such as Amazon Mechanical Turk can be used to recruit quality annotators, even in an application requiring subject matter expertise; aggregated Turker judgments for gene-mutation relations exceeded 90% accuracy. Over half of the precision errors were due to mismatches against the gold standard hidden from annotator view (e.g., incorrect EntrezGene identifier or incorrect mutation position extracted), or incomplete task instructions (e.g., the need to exclude nonhuman mutations).
  
  
  CONCLUSIONS
  The hybrid curation model provides a readily scalable cost-effective approach to curation, particularly if coupled with expert human review to filter precision errors. We plan to generalize the framework and make it available as open source software.
  http://www.mitre.org/publications/technical-papers/hybrid-curation-of-gene-mutation-relations-combining-automated.
authors.affiliation: The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA john@mitre.org.
authors.forename: John D
authors.initials: JD
authors.lastname: Burger
authors.affiliation: The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA.
authors.forename: Emily
authors.initials: E
authors.lastname: Doughty
authors.affiliation: The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA.
authors.forename: Ritu
authors.initials: R
authors.lastname: Khare
authors.affiliation: The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA.
authors.forename: Chih-Hsuan
authors.initials: CH
authors.lastname: Wei
authors.affiliation: The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA.
authors.forename: Rajashree
authors.initials: R
authors.lastname: Mishra
authors.affiliation: The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA.
authors.forename: John
authors.initials: J
authors.lastname: Aberdeen
authors.affiliation: The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA.
authors.forename: David
authors.initials: D
authors.lastname: Tresner-Kirsch
authors.affiliation: The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA.
authors.forename: Ben
authors.initials: B
authors.lastname: Wellner
authors.affiliation: The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA.
authors.forename: Maricel G
authors.initials: MG
authors.lastname: Kann
authors.affiliation: The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Lu
authors.affiliation: The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA lynette@mitre.org.
authors.forename: Lynette
authors.initials: L
authors.lastname: Hirschman
mesh_terms: D019295:Computational Biology / Q000379:methods; D063045:Crowdsourcing / Q000191:economics / Q000379:methods*; D066289:Data Curation / Q000191:economics / Q000379:methods*; D030541:Databases, Genetic; D020022:Genetic Predisposition to Disease; D023281:Genomics; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D009154:Mutation / Q000235:genetics*; D009323:Natural Language Processing