Difference between revisions of "Sources iRefIndex 8.0"

From irefindex
(→‎Sequence related resources: Changed SEGUID details, although the actual contents of seguidannotation is unchanged from the previous release.)
(Updated MINT, Intact (probably unchanged, timestamp adjusted), NCBI resources.)
Line 71: Line 71:
 
| InnateDB ||?|| http://www.innatedb.com/download.jsp ||?
 
| 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 25th, 2010 (timestamp)
 
|-
 
|-
 
| MatrixDB||PSI-MI 2.5|| http://matrixdb.ibcp.fr/<br>MatrixDB_20100826.xml.zip ||August 26th, 2010 (timestamp)
 
| 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/|| July 28th, 2010 (timestamp)
 
|-
 
|-
 
| 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
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| UniProt, FLY||Tab-delimited text file.||http://www.expasy.org/cgi-bin/lists?fly.txt<br> Drosophila: entries, gene names and cross-references to FlyBase.
 
| UniProt, FLY||Tab-delimited text file.||http://www.expasy.org/cgi-bin/lists?fly.txt<br> Drosophila: entries, gene names and cross-references to FlyBase.
 
|-
 
|-
| NCBI, RefSeq||GenPept||ftp://ftp.ncbi.nih.gov/refseq/release/complete<br>see *.protein.gpff.gz files||Release 39 (January 30th, 2010)
+
| NCBI, RefSeq||GenPept||ftp://ftp.ncbi.nih.gov/refseq/release/complete<br>see *.protein.gpff.gz files||Release 43 (September 16th, 2010)<br>(from http://www.ncbi.nlm.nih.gov/refseq/)
 
|-
 
|-
| NCBI, MMDB/PDB||Tab-delimited text ||ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table|| (Downloaded on February 8th, 2010)
+
| 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 February 8th, 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/<br>gene2refseq.gz||(Downloaded on February 8th, 2010)
+
| NCBI Gene2Refseq||Tab-delimited text||ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/<br>gene2refseq.gz||(Downloaded on September 23rd, 2010)
 
|-
 
|-
 
|  
 
|  

Revision as of 15:32, 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 ? 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 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)
OPHID PSI-MI

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).