Tag Archives: BitterDB

NAR database issue (always a treasure trove)

The advance access release of most of the  NAR database issue articles is out. As usual, this this database issue includes a wealth of new and updated data repositories and analysis tools. We’ll be writing up additional more extensive blog posts on it and doing some tips of the week over the next couple months, but I thought I’d highlight the issue and some of the reports:

There are a lot of updates to many of the databases we know and love (links to go full text article): UCSC Genome Browser, Ensembl, UniProt, MINT, SMART, WormBase, Gene Ontology,  ENCODE, KEGG, UCSC Archaeal Browser, IMG/M, DBTSS, InterPro and others (we have tutorials on all those listed here).

And, as an indication of the explosion of data available (itself a subject of a database issue article, SRA), there are a lot of new(ish) databases on specific datatypes such as MINAS, a database of metal ions in nucleic acids (nice name :D); doRiNA, a database of RNA interactions in post-transcriptional regulation; BitterDB, a database of bitter compounds and well over 100 more.

And I’ll give a special shout out to my former PI at EMBL because I can, Peer Bork’s group has 4 databases listed in the issue: eggNOG, SMART, STITCH and OGEE. (and he and a couple members are on the InterPro paper also).

This is going to be a wealth of information to wade through!

UCSC Genome Browser: http://genome.ucsc.edu
Ensembl: http://www.ensembl.org/
UniProt: http://www.uniprot.org/
MINT: http://mint.bio.uniroma2.it/mint/
SMART: http://smart.embl.de/
WormBase: http://www.wormbase.org/
Gene Ontology: http://www.geneontology.org/
ENCODE: http://genome.ucsc.edu/ENCODE/
KEGG: http://www.kegg.jp
UCSC Archaeal Brower: http://archaea.ucsc.edu/
IMG: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
DBTSS: http://dbtss.hgc.jp/
InterPro: http://www.ebi.ac.uk/interpro