Difference between revisions of "Sources iRefIndex 8.0"

From irefindex
(→‎Sequence related resources: Updated UniProt details.)
(→‎Sequence related resources: Changed SEGUID details, although the actual contents of seguidannotation is unchanged from the previous release.)
Line 95: Line 95:
| align="center" style="background:#f0f0f0;"|'''Version (date)'''
| align="center" style="background:#f0f0f0;"|'''Version (date)'''
| SEGUID||Tab-delimited text ||ftp://bioinformatics.anl.gov/seguid/<br>seguidannotation||August 7th, 2007 (server gives "08/07/107")
| SEGUID||Tab-delimited text ||ftp://bioinformatics.anl.gov/seguid/<br>seguidannotation||July 24th, 2007 (timestamp)
| UniProt||Text||http://www.uniprot.org/downloads<br>UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)
| UniProt||Text||http://www.uniprot.org/downloads<br>UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)

Revision as of 12:56, 21 September 2010

This is a planning template for the next release 8.0.  It does not correspond to a released product.
See http://irefindex.uio.no/ for the most recent release and related documentation.
This page will be updated as release 8.0 id built.  
Check for xxx before  release. 

Last edited: 2010-09-21

Applies to iRefIndex release: 8.0

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/







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...


...via the internet archive at...


25th May, 2005
BIND Translation PSI-MI 2.5 http://download.baderlab.org/BIND/PSIMI25_AllInclusive_AllSpecies.zip March 26th, 2010 (timestamp)
BioGRID PSI-MI 2.5 http://www.thebiogrid.org/downloads.php
/Current Release/BIOGRID-ALL-3.0.68.psi.zip
Version 3.0.68 (August 25th, 2010)
CORUM PSI-MI 2.5 http://mips.gsf.de/genre/proj/corum/index.html
December 2nd, 2009
DIP PSI-MI 2.5 http://dip.doe-mbi.ucla.edu/dip/Download.cgi
June 14th, 2010
HPRD PSI-MI 2.5 http://www.hprd.org/download
Release 8. April 13th, 2010
I2D PSI-MI 2.5 http://ophid.utoronto.ca/ophidv2.201/downloads.jsp Downloaded on September 14th, 2010
InnateDB ? http://www.innatedb.com/download.jsp ?
IntAct PSI-MI 2.5 ftp://ftp.ebi.ac.uk/pub/databases/intact/2010-01-22/psi25/pmidMIF25.zip January 22nd, 2010
MatrixDB PSI-MI 2.5 http://matrixdb.ibcp.fr/
August 26th, 2010 (timestamp)
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/
January 10th, 2008
MPIDB MITAB format file http://www.jcvi.org/mpidb
Downloaded on September 15th, 2010
MPPI PSI-MI 1.0 http://mips.gsf.de/proj/ppi/data/mppi.gz June 1st, 2004 (from archive)

Sequence related resources

Source Format Location Version (date)
SEGUID Tab-delimited text ftp://bioinformatics.anl.gov/seguid/
July 24th, 2007 (timestamp)
UniProt Text http://www.uniprot.org/downloads
UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)
UniProt Knowledgebase Release 2010_09:
UniProtKB/Swiss-Prot Release 2010_09 (10-Aug-2010)
UniProtKB/TrEMBL Release 2010_09 (10-Aug-2010)
(from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt)
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/
(Downloaded on February 8th, 2010)

All iRefIndex Pages

Follow this link for a listing of all iRefIndex related pages (archived and current).