Sources iRefIndex 8.0
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: 2010-09-14
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.
- For statistics on full public dataset please refer to: http://irefindex.uio.no/wiki/Statistics_iRefIndex_xxx
- For statistics on the public dataset (distributed on the FTP site contains) please refer to:http://irefindex.uio.no/wiki/Statistics_iRefIndex_free_xxx
| 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... |
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 |
December 30th, 2009 | |
| HPRD | PSI-MI 2.5 | http://www.hprd.org/download/ HPRD_SINGLE_PSIMI_070609.xml.tar.gz |
Release 8. July 6th, 2009 | |
| IntAct | PSI-MI 2.5 | ftp://ftp.ebi.ac.uk/pub/databases/intact/2010-01-22/psi25/pmidMIF25.zip | January 22nd, 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 10th, 2008 | |
| MPPI | PSI-MI 1.0 | http://mips.gsf.de/proj/ppi/data/mppi.gz | June 1st, 2004 (from archive) | |
| OPHID | PSI-MI | |||
| I2D | PSI-MI 2.5 | http://ophid.utoronto.ca/ophidv2.201/downloads.jsp | Downloaded on February 8th, 2010 | |
| MatrixDB | ? | http://matrixdb.ibcp.fr/ ? | ? | |
| MPIDB | ? | http://www.jcvi.org/mpidb ? | ? | |
| InnateDB | ? | www.innatedb.com ? | ? |
| 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).
