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modMine: flexible access to modENCODE data

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. © The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. « Previous | Next Article » Table of Contents This Article Nucl. Acids Res. (2012) 40 (D1): D1082-D1088. doi: 10.1093/nar/gkr921 First published online: November 12, 2011 This article appears in: Database issue This article is Open Access OA » Abstract Free Full Text (HTML) Free Full Text (PDF) Free Screen PDF Supplementary Data All Versions of this Article: gkr921v1 40/D1/D1082 most recent Classifications Article Services Alert me when cited Alert me if corrected Alert me if commented Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Responses Submit a response No responses published Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Google Scholar Articles by Contrino, S. Articles by Micklem, G. PubMed PubMed citation Articles by Contrino, S. Articles by Micklem, G. Related Content Load related web page information Share Email this article CiteULike Connotea Delicious Facebook Google+ Mendeley Twitter What's this? People also read (Beta) What's this? Search this journal: Advanced » Current Issue January 2012 40 (1) Alert me to new issues The Journal About this journal NAR Methods online 2012 Database Issue 2011 Web Server Issue NAR Special Collections Referee Information Rights & Permissions Dispatch date of the next issue This journal is a member of the Committee on Publication Ethics (COPE) view Recent Comments on articles We are mobile – find out more Impact factor: 7.836 5-Yr impact factor: 7.314 Senior Executive Editors Keith Fox, Southampton, UK Barry Stoddard, Seattle, WA, USA View full editorial board For Authors Instructions to authors Scope and Criteria for Consideration Online submission instructions Submit a manuscript now Self-archiving policy Open access options for authors This journal enables compliance with the NIH Public Access Policy Alerting Services Email table of contents Email Advance Access CiteTrack XML RSS feed Corporate Services Advertising sales Reprints Supplements Most Most Read A new mathematical model for relative quantification in real-time RT-PCR Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting Real-time quantification of microRNAs by stem-loop RT-PCR miRBase: microRNA sequences, targets and gene nomenclature miRBase: integrating microRNA annotation and deep-sequencing data » View all Most Read articles Most Cited Gapped BLAST and PSI-BLAST: a new generation of protein database search programs CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice The CLUSTAL_X Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei The Protein Data Bank » View all Most Cited articles Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department. Online ISSN 1362-4962 - Print ISSN 0305-1048 Copyright © 2011 Oxford University Press Oxford Journals Oxford University Press Site Map Privacy Policy Frequently Asked Questions Other Oxford University Press sites: Oxford University Press Oxford Journals China Oxford Journals Japan Academic & Professional books Children's & Schools Books Dictionaries & Reference Dictionary of National Biography Digital Reference English Language Teaching Higher Education Textbooks International Education Unit Law Medicine Music Online Products & Publishing Oxford Bibliographies Online Oxford Dictionaries Online Oxford English Dictionary Oxford Language Dictionaries Online Oxford Scholarship Online Reference Rights and Permissions Resources for Retailers & Wholesalers Resources for the Healthcare Industry Very Short Introductions World's Classics http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Nucleic Acids Research Oxford University Press

modMine: flexible access to modENCODE data

Abstract

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. © The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. « Previous | Next Article » Table of Contents This Article Nucl. Acids Res. (2012) 40 (D1): D1082-D1088. doi: 10.1093/nar/gkr921 First published online: November 12, 2011 This article appears in: Database issue This article is Open Access OA » Abstract Free Full Text (HTML) Free Full Text (PDF) Free Screen PDF Supplementary Data All Versions of this Article: gkr921v1 40/D1/D1082 most recent Classifications Article Services Alert me when cited Alert me if corrected Alert me if commented Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Responses Submit a response No responses published Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Google Scholar Articles by Contrino, S. Articles by Micklem, G. PubMed PubMed citation Articles by Contrino, S. Articles by Micklem, G. Related Content Load related web page information Share Email this article CiteULike Connotea Delicious Facebook Google+ Mendeley Twitter What's this? People also read (Beta) What's this? Search this journal: Advanced » Current Issue January 2012 40 (1) Alert me to new issues The Journal About this journal NAR Methods online 2012 Database Issue 2011 Web Server Issue NAR Special Collections Referee Information Rights & Permissions Dispatch date of the next issue This journal is a member of the Committee on Publication Ethics (COPE) view Recent Comments on articles We are mobile – find out more Impact factor: 7.836 5-Yr impact factor: 7.314 Senior Executive Editors Keith Fox, Southampton, UK Barry Stoddard, Seattle, WA, USA View full editorial board For Authors Instructions to authors Scope and Criteria for Consideration Online submission instructions Submit a manuscript now Self-archiving policy Open access options for authors This journal enables compliance with the NIH Public Access Policy Alerting Services Email table of contents Email Advance Access CiteTrack XML RSS feed Corporate Services Advertising sales Reprints Supplements Most Most Read A new mathematical model for relative quantification in real-time RT-PCR Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting Real-time quantification of microRNAs by stem-loop RT-PCR miRBase: microRNA sequences, targets and gene nomenclature miRBase: integrating microRNA annotation and deep-sequencing data » View all Most Read articles Most Cited Gapped BLAST and PSI-BLAST: a new generation of protein database search programs CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice The CLUSTAL_X Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei The Protein Data Bank » View all Most Cited articles Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department. Online ISSN 1362-4962 - Print ISSN 0305-1048 Copyright © 2011 Oxford University Press Oxford Journals Oxford University Press Site Map Privacy Policy Frequently Asked Questions Other Oxford University Press sites: Oxford University Press Oxford Journals China Oxford Journals Japan Academic & Professional books Children's & Schools Books Dictionaries & Reference Dictionary of National Biography Digital Reference English Language Teaching Higher Education Textbooks International Education Unit Law Medicine Music Online Products & Publishing Oxford Bibliographies Online Oxford Dictionaries Online Oxford English Dictionary Oxford Language Dictionaries Online Oxford Scholarship Online Reference Rights and Permissions Resources for Retailers & Wholesalers Resources for the Healthcare Industry Very Short Introductions World's Classics
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