title: modMine: flexible access to modENCODE data.
abstract: In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium has generated an enormous library of genomic data along with detailed, structured information on all aspects of the experiments. The modMine database (http://intermine.modencode.org) described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data sets of interest among the thousands generated by modENCODE; (ii) access the data in an integrated form together with non-modENCODE data sets; and (iii) facilitate fine-grained analysis of the above data. The sophisticated search features are possible because of the collection of extensive experimental metadata by the consortium. Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine.
authors.affiliation: Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
authors.forename: Sergio
authors.initials: S
authors.lastname: Contrino
authors.forename: Richard N
authors.initials: RN
authors.lastname: Smith
authors.forename: Daniela
authors.initials: D
authors.lastname: Butano
authors.forename: Adrian
authors.initials: A
authors.lastname: Carr
authors.forename: Fengyuan
authors.initials: F
authors.lastname: Hu
authors.forename: Rachel
authors.initials: R
authors.lastname: Lyne
authors.forename: Kim
authors.initials: K
authors.lastname: Rutherford
authors.forename: Alex
authors.initials: A
authors.lastname: Kalderimis
authors.forename: Julie
authors.initials: J
authors.lastname: Sullivan
authors.forename: Seth
authors.initials: S
authors.lastname: Carbon
authors.forename: Ellen T
authors.initials: ET
authors.lastname: Kephart
authors.forename: Paul
authors.initials: P
authors.lastname: Lloyd
authors.forename: E O
authors.initials: EO
authors.lastname: Stinson
authors.forename: Nicole L
authors.initials: NL
authors.lastname: Washington
authors.forename: Marc D
authors.initials: MD
authors.lastname: Perry
authors.forename: Peter
authors.initials: P
authors.lastname: Ruzanov
authors.forename: Zheng
authors.initials: Z
authors.lastname: Zha
authors.forename: Suzanna E
authors.initials: SE
authors.lastname: Lewis
authors.forename: Lincoln D
authors.initials: LD
authors.lastname: Stein
authors.forename: Gos
authors.initials: G
authors.lastname: Micklem
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics*; D015870:Gene Expression; D049751:Genome, Helminth; D049750:Genome, Insect; D023281:Genomics; D020407:Internet; D014584:User-Computer Interface
references.citation: Genome Biol. 2007;8(7):R129
references.pmid: 17615057
references.citation: Bioinformatics. 2010 Sep 15;26(18):2347-8
references.pmid: 20656902
references.citation: BMC Biol. 2007 Oct 09;5:44
references.pmid: 17925023
references.citation: Genome Biol. 2005;6(5):R44
references.pmid: 15892872
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5
references.pmid: 18940856
references.citation: Science. 2010 Dec 24;330(6012):1787-97
references.pmid: 21177974
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D463-7
references.pmid: 19910365
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D525-31
references.pmid: 19850723
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81
references.pmid: 17982175
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D735-40
references.pmid: 18056084
references.citation: Nat Genet. 2001 Dec;29(4):365-71
references.pmid: 11726920
references.citation: Nat Biotechnol. 2008 Aug;26(8):889-96
references.pmid: 18688244
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D822-9
references.pmid: 21036866
references.citation: Bioinformatics. 2006 Apr 1;22(7):866-73
references.pmid: 16428806
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D658-62
references.pmid: 17151068
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D842-8
references.pmid: 21051359
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7
references.pmid: 21067998
references.citation: Database (Oxford). 2011 Aug 19;2011:bar023
references.pmid: 21856757
references.citation: Nature. 2009 Jun 18;459(7249):927-30
references.pmid: 19536255
references.citation: Bioinformatics. 2006 Jun 15;22(12):1532-3
references.pmid: 16613907
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1005-10
references.pmid: 21097893
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9
references.pmid: 18948289
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D142-8
references.pmid: 19843607
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D322-6
references.pmid: 16381878
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D698-704
references.pmid: 21071413
references.citation: Science. 2010 Dec 24;330(6012):1775-87
references.pmid: 21177976
references.citation: PLoS One. 2011 Mar 08;6(3):e17844
references.pmid: 21408081
references.citation: Bioinformatics. 2007 Jul 1;23(13):i337-46
references.pmid: 17646315
references.citation: Genome Res. 2002 Oct;12(10):1599-610
references.pmid: 12368253
references.citation: Mol Cell Proteomics. 2009 Jun;8(6):1324-37
references.pmid: 19208617
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D489-94
references.pmid: 16381918