Sources and Issues Next Release

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Revision as of 14:14, 11 February 2010 by PaulBoddie (talk | contribs) (→‎Sequence related resources: Updated versions and dates.)
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Last edited: xxx

Applies to iRefIndex release: xxx

Release date: xxx

Authors: Ian Donaldson,Sabry Razick and Paul Boddie

Database: iRefIndex (http://irefindex.uio.no)

Organization: Biotechnology Centre of Oslo, University of Oslo (http://www.biotek.uio.no/)

Description: This file lists interaction and protein sequence related resources used for the current build of the iRefIndex. Statistics for the iRefIndex are available and include a breakdown of interactors and interactions from each data source.

Interaction related resources

Source Format Location Version (date)
BIND, Tab-delimited text file. ftp://ftp.bind.ca/pub/BIND/data/bindflatfiles/bindindex/

20050525.complex2refs.txt

20050525.ints.txt

20050525.refs.txt

20050525.complexes.txt

20050525.labels.txt

20050525.complex2subunits.txt

These file are no longer available via ftp but are available from the authors. BIND archival content is now managed by Thomson Scientific. See http://bond.unleashedinformatics.com/ and http://bond.unleashedinformatics.com/downloads/data/BIND/

For historical purposes, a snapshot of the the Blueprint web-site may be viewed at...

http://web.archive.org/web/20050204013426/www.blueprint.org/index.html

...via the internet archive at...

http://web.archive.org/web/*/http://www.blueprint.org

05/25/05
BioGRID PSI-MI 2.5 http://www.thebiogrid.org/downloads.php /Current Release/BIOGRID-ALL-2.0.61.psi.zip Version 2.0.61 January 31st, 2010
CORUM PSI-MI 2.5 http://mips.gsf.de/genre/proj/corum/index.html (http://mips.gsf.de/genre/export/sites/default/corum/allComplexes.psimi.zip) Not available (time stamp of file 2009 ?)
DIP PSI-MI 2.5 http://dip.doe-mbi.ucla.edu/dip/Download.cgi (dip20091230.mif25) December 30, 2009
HPRD, PSI-MI 2.5 http://www.hprd.org/download/ (HPRD_SINGLE_PSIMI_070609.xml.tar.gz) Release 8. July 06, 2009
IntAct, PSI-MI 2.5 ftp://ftp.ebi.ac.uk/pub/databases/intact/2010-01-22/psi25/pmidMIF25.zip January 22, 2010
MINT PSI-MI 2.5 ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmid/ November 11th, 2009
MPACT PSI-MI 2.5 ftp://ftpmips.gsf.de/yeast/PPI/ (mpact-complete.psi25.xml.gz) January 10, 2008
MPPI PSI-MI 1.0 http://mips.gsf.de/proj/ppi/data/mppi.gz Not available
I2D PSI-MI 2.5 http://ophid.utoronto.ca/ophidv2.201/downloads.jsp ?

Sequence related resources

Source Format Location Version (date)
SEGUID Tab-delimited text ftp://bioinformatics.anl.gov/seguid/
seguidannotation
August 7th, 2007 (server gives "08/07/107")
UniProt Text http://www.uniprot.org/downloads
UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)
UniProt Knowledgebase Release 15.14:
UniProtKB/Swiss-Prot Release 57.14 (09-Feb-2010)
UniProtKB/TrEMBL Release 40.14 (09-Feb-2010)
UniProt Text http://www.uniprot.org/downloads
UniProtKB/TrEMBL (uniprot_trembl.dat.gz)
UniProt, IsoForms FASTA http://www.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz
UniProt, SGD Tab-delimited text file. http://www.expasy.org/cgi-bin/lists?yeast.txt
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
UniProt, FLY Tab-delimited text file. http://www.expasy.org/cgi-bin/lists?fly.txt
Drosophila: entries, gene names and cross-references to FlyBase.
NCBI, RefSeq GenPept ftp://ftp.ncbi.nih.gov/refseq/release/complete
see *.protein.gpff.gz files
Release 39 (January 30th, 2010)
NCBI, MMDB/PDB Tab-delimited text ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table (Downloaded on February 8th, 2010)
NCBI, PDB sequences FASTA ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz (Downloaded on February 8th, 2010)
NCBI Gene2Refseq Tab-delimited text ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
gene2refseq.gz
(Downloaded on February 8th, 2010)