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Difference between revisions of "Sources iRefIndex 8.0"

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(Updated MINT, Intact (probably unchanged, timestamp adjusted), NCBI resources.)
(Added InnateDB details, removed OPHID.)
Line 69: Line 69:
 
| 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 ||?
+
| InnateDB ||PSI-MI 2.5|| http://www.innatedb.com/download.jsp<br>Curated InnateDB Data ||July 16th, 2010
 
|-
 
|-
 
| IntAct||PSI-MI 2.5||ftp://ftp.ebi.ac.uk/pub/databases/intact/2010-01-22/psi25/pmidMIF25.zip|| January 25th, 2010 (timestamp)
 
| IntAct||PSI-MI 2.5||ftp://ftp.ebi.ac.uk/pub/databases/intact/2010-01-22/psi25/pmidMIF25.zip|| January 25th, 2010 (timestamp)
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|-
 
|-
 
| 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 || ||
 
|-
 
 
|}
 
|}
  

Revision as of 08:54, 23 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: 2010-09-23

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 PSI-MI 2.5 http://www.innatedb.com/download.jsp
Curated InnateDB Data
July 16th, 2010
IntAct PSI-MI 2.5 ftp://ftp.ebi.ac.uk/pub/databases/intact/2010-01-22/psi25/pmidMIF25.zip January 25th, 2010 (timestamp)
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/ July 28th, 2010 (timestamp)
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)

Sequence related resources

Source Format Location Version (date)
SEGUID Tab-delimited text ftp://bioinformatics.anl.gov/seguid/
seguidannotation
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 43 (September 16th, 2010)
(from http://www.ncbi.nlm.nih.gov/refseq/)
NCBI, MMDB/PDB Tab-delimited text ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table (Downloaded on September 23rd, 2010)
NCBI, PDB sequences FASTA ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz (Downloaded on September 23rd, 2010)
NCBI Gene2Refseq Tab-delimited text ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
gene2refseq.gz
(Downloaded on September 23rd, 2010)

All iRefIndex Pages

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