title: An evidence-based approach to identify aging-related genes in Caenorhabditis elegans.
abstract: BACKGROUND
  Extensive studies have been carried out on Caenorhabditis elegans as a model organism to elucidate mechanisms of aging and the effects of perturbing known aging-related genes on lifespan and behavior. This research has generated large amounts of experimental data that is increasingly difficult to integrate and analyze with existing databases and domain knowledge. To address this challenge, we demonstrate a scalable and effective approach for automatic evidence gathering and evaluation that leverages existing experimental data and literature-curated facts to identify genes involved in aging and lifespan regulation in C. elegans.
  
  
  RESULTS
  We developed a semantic knowledge base for aging by integrating data about C. elegans genes from WormBase with data about 2005 human and model organism genes from GenAge and 149 genes from GenDR, and with the Bio2RDF network of linked data for the life sciences. Using HyQue (a Semantic Web tool for hypothesis-based querying and evaluation) to interrogate this knowledge base, we examined 48,231 C. elegans genes for their role in modulating lifespan and aging. HyQue identified 24 novel but well-supported candidate aging-related genes for further experimental validation.
  
  
  CONCLUSIONS
  We use semantic technologies to discover candidate aging genes whose effects on lifespan are not yet well understood. Our customized HyQue system, the aging research knowledge base it operates over, and HyQue evaluations of all C. elegans genes are freely available at http://hyque.semanticscience.org .
authors.affiliation: Stanford Center for Biomedical Informatics Research, School of Medicine, Stanford University, Stanford California, AC, USA. acallaha@stanford.edu.
authors.forename: Alison
authors.initials: A
authors.lastname: Callahan
authors.affiliation: Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, 49 Santiago, CP, 8330025, Portugal. jjcifuentes@uc.cl.|Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile. jjcifuentes@uc.cl.
authors.forename: Juan José
authors.initials: JJ
authors.lastname: Cifuentes
authors.affiliation: Stanford Center for Biomedical Informatics Research, School of Medicine, Stanford University, Stanford California, AC, USA. michel.dumontier@stanford.edu.
authors.forename: Michel
authors.initials: M
authors.lastname: Dumontier
mesh_terms: D000375:Aging / Q000235:genetics*; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D020869:Gene Expression Profiling; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016247:Information Storage and Retrieval; D012984:Software
chemical_list: D029742:Caenorhabditis elegans Proteins