biodbcore-000070

modMine: flexible access to modENCODE data
Mining of modENCODE data




Basics
Country

USA
Taxonomic range

Database scope and data types

  • genome sequence Domain
  • gene models, ChIP-seq, ChIP-Chip, predicted binding sites Domain
  • Gene Ontology annotations Domain
  • protein domains (via InterPro) Domain
  • orthologs (via inParanoid, TreeFam) Domain
  • proteins (via UniProt) Domain
  • citations Domain
  • phenotypes Domain
Standards
Guidelines

No guidelines defined
Semantic

Syntax

Access
Condition of Use

  • Free


Data Access

  • homepage
  • file download(txt,XML,CSV)
  • SQL database dump
  • web service
  • programatic interface (Java,Perl,Python)
Curation Process

  • required metadata for experiment results
Release Process

  • quarterly release
Versioning Process

  • access to historical files available
Support
Support

rss
blog





Tools
Credits
Maintaining Organisations

  • Department of Genome Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
  • Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.
  • Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
Funding Organisations

  • NIGMS NIH HHS
  • Wellcome Trust
  • NHGRI NIH HHS
Publications

Unlocking the secrets of the genome. Nature 2009
 Pubmed:19536255
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010
 Pubmed:21177976
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010
 Pubmed:21177974

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