Sources iRefIndex 9.0
Last edited: 2012-04-20
Applies to iRefIndex release: 9.0
Release date: 2011-11-07
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 the full dataset please refer to: http://irefindex.uio.no/wiki/Statistics_iRefIndex_9.0
| Source | Format | Location | Version (date) |
| BIND | Tab-delimited text file. | ftp://ftp.bind.ca/pub/BIND/data/bindflatfiles/bindindex/ (no longer available - see below).
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... |
2005-05-25 |
| BIND Translation | PSI-MI 2.5 | http://download.baderlab.org/BINDTranslation/release1_0/BINDTranslation_v1_xml_AllSpecies.tar.gz | Version 1.0 (2010-12-15) |
| BioGRID | PSI-MI 2.5 | http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.1.81/BIOGRID-ALL-3.1.81.psi25.zip | Version 3.1.81 (2011-10-01) |
| 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 |
2009-12-02 |
| DIP | PSI-MI 2.5 | http://dip.doe-mbi.ucla.edu/dip/Download.cgi
|
2010-10-10 |
| HPRD | PSI-MI 2.5 | http://www.hprd.org/download HPRD_PSIMI_041310.tar.gz |
Release 9 (2010-04-13) |
| IntAct | PSI-MI 2.5 | ftp://ftp.ebi.ac.uk/pub/databases/intact/2011-09-29/psi25/pmidMIF25.zip | 2011-09-29 |
| MINT | PSI-MI 2.5 | ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmid/ | 2010-12-21 |
| MPACT | PSI-MI 2.5 | ftp://ftpmips.gsf.de/yeast/PPI/mpact-complete.psi25.xml.gz | 2008-01-10 |
| MPPI | PSI-MI 1.0 | http://mips.gsf.de/proj/ppi/data/mppi.gz | 2004-06-01 (from archive) |
| OPHID | PSI-MI 1.0 | http://ophid.utoronto.ca/ophid/downloads.html (This service no longer available, please refer to http://ophid.utoronto.ca/ophidv2.201/) | 2006-07-07 |
| New for this release | |||
| InnateDB | PSI-MI 2.5 | http://www.innatedb.org/download.jsp Curated InnateDB Data |
2011-03-06 |
| MPIDB | MITAB format file | http://www.jcvi.org/mpidb (information) http://www.jcvi.org/mpidb/download.php (general downloads) |
Downloaded on 2011-10-03 |
| MatrixDB | PSI-MI 2.5 | http://matrixdb.ibcp.fr/ MatrixDB_20100826.xml.zip |
2010-08-26 (timestamp) |
| Source | Format | Location | Version (date) |
| SEGUID | Tab-delimited text | ftp://bioinformatics.anl.gov/seguid/ seguidannotation |
2007-07-24 (timestamp) |
| UniProt | Text | http://www.uniprot.org/downloads UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) |
UniProt Knowledgebase Release 2011_09 (2011-09-21) (Downloaded on 2011-10-04): UniProtKB/Swiss-Prot UniProtKB/TrEMBL (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 49 (2011-09-09) (Downloaded on 2011-10-04) (from http://www.ncbi.nlm.nih.gov/refseq/) |
| NCBI, MMDB/PDB | Tab-delimited text | ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table | (Downloaded on 2011-10-04) |
| NCBI, PDB sequences | FASTA | ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz | (Downloaded on 2011-10-03) |
| NCBI Gene2Refseq | Tab-delimited text | ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz |
(Downloaded on 2011-10-04) |
All iRefIndex Pages
Follow this link for a listing of all iRefIndex related pages (archived and current).
