Difference between revisions of "Sources iRefIndex 8.0"
From irefindex
PaulBoddie (talk | contribs) (→Sequence related resources: Changed SEGUID details, although the actual contents of seguidannotation is unchanged from the previous release.) |
PaulBoddie (talk | contribs) (Updated MINT, Intact (probably unchanged, timestamp adjusted), NCBI resources.) |
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| 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 | + | | 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/|| | + | | 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 | ||
| Line 108: | Line 108: | ||
| 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 | + | | 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, | + | | NCBI, MMDB/PDB||Tab-delimited text ||ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table|| (Downloaded on September 23rd, 2010) |
|- | |- | ||
| − | | NCBI, | + | | 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 | + | | 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.
- 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 |
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 |
| 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).
