Tip of the Week: Genomic Data Resources

scitable paper thumgToday’s tip isn’t on just one resource or a part of one, it’s a whirlwind tour of many! In fact, in less than 5 minutes I’ll put you through ALL of the resources online on genomics. Ok, well, not all. Not even 1% I don’t think, but we’ll go through some categories and discuss very briefly some “Challenges and Promises.” Actually, it’s my way of introducing you to a paper we just wrote for Nature Education’s site, Scitable entitled, you guessed it, “Genomic Data Resources, Challenges and Promises.” Hopefully, after watching this short movie as I whisk you through some of the sites and topics we raise in the paper, you’ll be interested in going and reading it and checking out Scitable. Also, below the fold, you’ll find a nice table of links to all the resources we discuss in the paper, which by necessity are only a small portion of the thousands of resources available.

NCBI (GenBank)    http://www.ncbi.nlm.nih.gov/
EMBL-EBI    http://www.ebi.ac.uk/
DDBJ   http://www.ddbj.nig.ac.jp/
INSDC    http://www.insdc.org/
RefSeq    http://www.ncbi.nlm.nih.gov/RefSeq/
VEGA    http://vega.sanger.ac.uk/
CCDS   http://www.ncbi.nlm.nih.gov/CCDS/
Genome Browsers
Ensembl   http://www.ensembl.org/
UCSC Genome Browser    http://genome.ucsc.edu/
NCBI MapViewer   http://www.ncbi.nlm.nih.gov/mapview/

Projects (in Genome Browsers section)

ENCODE (project)    http://www.genome.gov/10005107
1000 Genomes   http://www.1000genomes.org/
Species & Taxa specific databases
Rat Genome Database   http://rgd.mcw.edu/
Mouse Genome Informatics    http://www.informatics.jax.org/
ZFIN, Zebrafish Model Organism Database    http://zfin.org
FlyBase, Drosophila and other species   http://flybase.org/
VectorBase, invertebrate vectors of human disease    http://www.vectorbase.org/
WormBase, C. elegans and related nematodes    http://www.wormbase.org
Gramene, crop grasses and other plants    http://www.gramene.org
TAIR, Arabidopsis    http://www.arabidopsis.org/
SGD, Saccharomyces Genome Database    http://www.yeastgenome.org/
IMG, Integrated Microbial Genomes   http://img.jgi.doe.gov/
EcoliHub, community and database for E. coli    http://www.ecolicommunity.org/
VBRC, Viral Bioinformatics Resource Center    http://athena.bioc.uvic.ca/

GMOD, Genome Database Tools (and databases using GMOD)
GMOD    http://gmod.org/
HGSDD, Human Genome Segmental Duplication Database    http://projects.tcag.ca/humandup/
HapMap    http://www.hapmap.org
James Watson Genome    http://jimwatsonsequence.cshl.edu/
List of Additional GMOD uses   http://gmod.org/wiki/GMOD_Users
Subject-Specific Databases
PDB, Protein 3D structure Database   http://www.rcsb.org/
Pfam, protein families   http://pfam.sanger.ac.uk/
GEO, Gene Expression Omnibus    http://www.ncbi.nlm.nih.gov/geo/
ArrayExpress, repository for transcriptomics data    http://www.ebi.ac.uk/microarray-as/ae/
dbGaP    http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap
HuGE Navigator    http://www.hugenavigator.net/
Additional Databases Directory
Nucleic Acids Research Database Directory    http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1
Discussion: Learning the Genome Browsers
Ensembl Online Workshops    http://www.ensembl.org/common/Workshops_Online
UCSC Genome Browser Tutorial    http://www.openhelix.com/ucsc
NCBI MapViewer Introduction    http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.chapter.ch20

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