Difference between revisions of "Sources iRefIndex 8.0"

From irefindex
(→‎Interaction related resources: Updated I2D details.)
(→‎Interaction related resources: Updated DIP, added MatrixDB, MPIDB, InnateDB details.)
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| CORUM||PSI-MI 2.5||http://mips.gsf.de/genre/proj/corum/index.html<br>http://mips.gsf.de/genre/export/sites/default/corum/allComplexes.psimi.zip ||December 2nd, 2009
 
| CORUM||PSI-MI 2.5||http://mips.gsf.de/genre/proj/corum/index.html<br>http://mips.gsf.de/genre/export/sites/default/corum/allComplexes.psimi.zip ||December 2nd, 2009
 
|-
 
|-
| DIP||PSI-MI 2.5||http://dip.doe-mbi.ucla.edu/dip/Download.cgi<br>dip20091230.mif25 ||December 30th, 2009
+
| DIP||PSI-MI 2.5||http://dip.doe-mbi.ucla.edu/dip/Download.cgi<br>dip20091230.mif25 ||June 14th, 2010
 
|-
 
|-
 
| HPRD||PSI-MI 2.5||http://www.hprd.org/download<br>HPRD_SINGLE_PSIMI_041310.xml.tar.gz||Release 8. April 13th, 2010
 
| HPRD||PSI-MI 2.5||http://www.hprd.org/download<br>HPRD_SINGLE_PSIMI_041310.xml.tar.gz||Release 8. April 13th, 2010
 
|-
 
|-
 
| I2D||PSI-MI 2.5||http://ophid.utoronto.ca/ophidv2.201/downloads.jsp ||Downloaded on September 14th, 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
 
| 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/<br>MatrixDB_20100826.xml.zip ||August 26th, 2010 (timestamp)
 
|-
 
|-
 
| MINT||PSI-MI 2.5|| ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmid/|| November 11th, 2009
 
| 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/<br>mpact-complete.psi25.xml.gz ||January 10th, 2008
 
| MPACT||PSI-MI 2.5||ftp://ftpmips.gsf.de/yeast/PPI/<br>mpact-complete.psi25.xml.gz ||January 10th, 2008
 +
|-
 +
| MPIDB||MITAB format file|| http://www.jcvi.org/mpidb<br>http://www.jcvi.org/mpidb/download.php || Downloaded on September 15th, 2010
 
|-
 
|-
 
| MPPI||PSI-MI 1.0||http://mips.gsf.de/proj/ppi/data/mppi.gz||June 1st, 2004 (from archive)
 
| MPPI||PSI-MI 1.0||http://mips.gsf.de/proj/ppi/data/mppi.gz||June 1st, 2004 (from archive)
 
|-
 
|-
 
| OPHID||PSI-MI || ||  
 
| OPHID||PSI-MI || ||  
|-
 
| MatrixDB||?|| http://matrixdb.ibcp.fr/ ? ||?
 
|-
 
| MPIDB||?|| http://www.jcvi.org/mpidb ? ||?
 
|-
 
| InnateDB ||?|| www.innatedb.com ? ||?
 
 
|-
 
|-
 
|}
 
|}

Revision as of 11:39, 15 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: 2010-09-15

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/

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

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
http://mips.gsf.de/genre/export/sites/default/corum/allComplexes.psimi.zip
December 2nd, 2009
DIP PSI-MI 2.5 http://dip.doe-mbi.ucla.edu/dip/Download.cgi
dip20091230.mif25
June 14th, 2010
HPRD PSI-MI 2.5 http://www.hprd.org/download
HPRD_SINGLE_PSIMI_041310.xml.tar.gz
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/
MatrixDB_20100826.xml.zip
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/
mpact-complete.psi25.xml.gz
January 10th, 2008
MPIDB MITAB format file http://www.jcvi.org/mpidb
http://www.jcvi.org/mpidb/download.php
Downloaded on September 15th, 2010
MPPI PSI-MI 1.0 http://mips.gsf.de/proj/ppi/data/mppi.gz June 1st, 2004 (from archive)
OPHID PSI-MI

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)

All iRefIndex Pages

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