biodbcore-000034

ENCODE Whole-Genome Data in the UCSC Genome Browser: Update 2012
Encyclopedia of DNA Elements, all functional elements in the human genome




Basics
Country

USA
Taxonomic range

Database scope and data types

  • Whole genome annotations from ENCODE Consortium Domain
  • Open chromatin (DNaseI hypersensitivity, FAIRE), RNA profiling (RNA-seq, CAGE, RNA-PET), Transcription factor binding sites (ChIP-seq), Histone modification maps (ChIP-seq), DNA methylation, RNA-binding protein sites, Chromatin interaction (5C, ChIA-PET), Gencode Genes Domain
Standards
Guidelines

No guidelines defined
Semantic

No semantic standards defined
Syntax

Access
Condition of Use

  • Free
    • Data has usage restrictions for 9 months after public availability, as described in ENCODE Data Policy (http://encodeproject.org/ENCODE/terms.html)


Data Access

  • web interface, PNG/PDF/PS visualizations of sequences and annotations by genomic position
  • text, tabular and file downloads in a variety of formats
  • direct MySQL access through public MySQL server with anonymous login
Curation Process

  • manual curation
  • automated curation
Release Process

  • continuous release (live database)
Versioning Process

  • versioning by genome assembly
  • versioning by individual annotation
  • access to historical files possible
Support
Support

rss
blog





Tools
Credits
Maintaining Organisations

  • Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA.
Funding Organisations

  • NHGRI NIH HHS
Publications

The human genome browser at UCSC. Genome Res. 2002
 Pubmed:12045153, 20959295, 21037257, 11932250, 14681465, 15608236, 11237011, 11544197, 18842134, 21159622, 17785536, 19906737, 18996895, 18086701, 17702936, 20639541, 20185453, 21270892, 18774902, 20613842, 17984227, 21385048, 19570805, 17989246, 18218656, 17994088, 18443589, 18003932, 17983264, 17636042, 18086703, 18085818, 18514479

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