PMID- 30101316
OWN - NLM
STAT- MEDLINE
DCOM- 20191231
LR  - 20191231
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Linking)
VI  - 35
IP  - 5
DP  - 2019 Mar 1
TI  - Processing of big heterogeneous genomic datasets for tertiary analysis of Next 
      Generation Sequencing data.
PG  - 729-736
LID - 10.1093/bioinformatics/bty688 [doi]
AB  - MOTIVATION: We previously proposed a paradigm shift in genomic data management, 
      based on the Genomic Data Model (GDM) for mediating existing data formats and on 
      the GenoMetric Query Language (GMQL) for supporting, at a high level of 
      abstraction, data extraction and the most common data-driven computations 
      required by tertiary data analysis of Next Generation Sequencing datasets. Here, 
      we present a new GMQL-based system with enhanced accessibility, portability, 
      scalability and performance. RESULTS: The new system has a well-designed modular 
      architecture featuring: (i) an intermediate representation supporting many 
      different implementations (including Spark, Flink and SciDB); (ii) a high-level 
      technology-independent repository abstraction, supporting different repository 
      technologies (e.g., local file system, Hadoop File System, database or others); 
      (iii) several system interfaces, including a user-friendly Web-based interface, a 
      Web Service interface, and a programmatic interface for Python language. 
      Biological use case examples, using public ENCODE, Roadmap Epigenomics and TCGA 
      datasets, demonstrate the relevance of our work. AVAILABILITY AND IMPLEMENTATION: 
      The GMQL system is freely available for non-commercial use as open source project 
      at: http://www.bioinformatics.deib.polimi.it/GMQLsystem/. SUPPLEMENTARY 
      INFORMATION: Supplementary data are available at Bioinformatics online.
CI  - (c) The Author(s) 2018. Published by Oxford University Press. All rights reserved. 
      For permissions, please e-mail: journals.permissions@oup.com.
FAU - Masseroli, Marco
AU  - Masseroli M
AD  - Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 
      Milan, Italy.
FAU - Canakoglu, Arif
AU  - Canakoglu A
AD  - Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 
      Milan, Italy.
FAU - Pinoli, Pietro
AU  - Pinoli P
AD  - Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 
      Milan, Italy.
FAU - Kaitoua, Abdulrahman
AU  - Kaitoua A
AD  - The German Research Center for Artificial Intelligence (DFKI), Berlin, Germany.
FAU - Gulino, Andrea
AU  - Gulino A
AD  - Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 
      Milan, Italy.
FAU - Horlova, Olha
AU  - Horlova O
AD  - Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 
      Milan, Italy.
FAU - Nanni, Luca
AU  - Nanni L
AD  - Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 
      Milan, Italy.
FAU - Bernasconi, Anna
AU  - Bernasconi A
AD  - Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 
      Milan, Italy.
FAU - Perna, Stefano
AU  - Perna S
AD  - Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 
      Milan, Italy.
FAU - Stamoulakatou, Eirini
AU  - Stamoulakatou E
AD  - Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 
      Milan, Italy.
FAU - Ceri, Stefano
AU  - Ceri S
AD  - Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 
      Milan, Italy.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
SB  - IM
MH  - Epigenomics
MH  - Genome
MH  - Genomics
MH  - *High-Throughput Nucleotide Sequencing
MH  - *Software
EDAT- 2018/08/14 06:00
MHDA- 2020/01/01 06:00
CRDT- 2018/08/14 06:00
PHST- 2018/03/31 00:00 [received]
PHST- 2018/08/01 00:00 [revised]
PHST- 2018/08/06 00:00 [accepted]
PHST- 2018/08/14 06:00 [pubmed]
PHST- 2020/01/01 06:00 [medline]
PHST- 2018/08/14 06:00 [entrez]
AID - 5067860 [pii]
AID - 10.1093/bioinformatics/bty688 [doi]
PST - ppublish
SO  - Bioinformatics. 2019 Mar 1;35(5):729-736. doi: 10.1093/bioinformatics/bty688.