title: GenoMetric Query Language: a novel approach to large-scale genomic data management.
abstract: BACKGROUND
  Improvement of sequencing technologies and data processing pipelines is rapidly providing sequencing data, with associated high-level features, of many individual genomes in multiple biological and clinical conditions. They allow for data-driven genomic, transcriptomic and epigenomic characterizations, but require state-of-the-art 'big data' computing strategies, with abstraction levels beyond available tool capabilities.
  
  
  RESULTS
  We propose a high-level, declarative GenoMetric Query Language (GMQL) and a toolkit for its use. GMQL operates downstream of raw data preprocessing pipelines and supports queries over thousands of heterogeneous datasets and samples; as such it is key to genomic 'big data' analysis. GMQL leverages a simple data model that provides both abstractions of genomic region data and associated experimental, biological and clinical metadata and interoperability between many data formats. Based on Hadoop framework and Apache Pig platform, GMQL ensures high scalability, expressivity, flexibility and simplicity of use, as demonstrated by several biological query examples on ENCODE and TCGA datasets.
  
  
  METHODS
  The GMQL toolkit is freely available for non-commercial use at http://www.bioinformatics.deib.polimi.it/GMQL/.
authors: Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan and Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy.
authors: Marco
authors: M
authors: Masseroli
authors: Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan and Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy.
authors: Pietro
authors: P
authors: Pinoli
authors: Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan and Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy.
authors: Francesco
authors: F
authors: Venco
authors: Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan and Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy.
authors: Abdulrahman
authors: A
authors: Kaitoua
authors: Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan and Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy.
authors: Vahid
authors: V
authors: Jalili
authors: Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan and Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy.
authors: Fernando
authors: F
authors: Palluzzi
authors: Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan and Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy.
authors: Heiko
authors: H
authors: Muller
authors: Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan and Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy.
authors: Stefano
authors: S
authors: Ceri
mesh_terms: D000043:Abstracting and Indexing; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D057890:Epigenomics; D023281:Genomics / Q000379:methods*; D057166:High-Throughput Screening Assays / Q000379:methods*; D006657:Histones / Q000378:metabolism; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D006657:Histones; D014157:Transcription Factors