Difference between revisions of "Sources"
From irefindex
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| align="center" style="background:#f0f0f0;"|'''Version (date)''' | | align="center" style="background:#f0f0f0;"|'''Version (date)''' | ||
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| − | | SEGUID||Tab-delimited text ||ftp://bioinformatics.anl.gov/seguid/ seguidannotation|| | + | | SEGUID||Tab-delimited text ||ftp://bioinformatics.anl.gov/seguid/ seguidannotation||September 23rd, 2008 |
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| − | | UniProt||Text||http://beta.uniprot.org/downloads Download : 1.UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) 2.UniProtKB/TrEMBL (uniprot_trembl.dat.gz)||UniProt | + | | UniProt||Text||http://beta.uniprot.org/downloads Download : 1.UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) 2.UniProtKB/TrEMBL (uniprot_trembl.dat.gz)||UniProt release 14.0 (September 02, 2008) |
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| − | | UniProt, IsoForms||FASTA||http://beta.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz|| | + | | UniProt, IsoForms||FASTA||http://beta.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz||September 25th, 2008 |
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| − | | 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||Release: | + | | 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||Release: 56.2 (September 23rd, 2008) |
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| − | | UniProt, FLY||Tab-delimited text file.||http://www.expasy.org/cgi-bin/lists?fly.txt Drosophila: entries, gene names and cross-references to FlyBase.||Release: | + | | UniProt, FLY||Tab-delimited text file.||http://www.expasy.org/cgi-bin/lists?fly.txt Drosophila: entries, gene names and cross-references to FlyBase.||Release: 56.2 (September 25th, 2008) |
|- | |- | ||
| − | | NCBI, RefSeq||GenPept||ftp://ftp.ncbi.nih.gov/refseq/release/complete see *.protein.gpff.gz files||Release | + | | NCBI, RefSeq||GenPept||ftp://ftp.ncbi.nih.gov/refseq/release/complete see *.protein.gpff.gz files||Release 31 (August 30, 2008) |
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| − | | NCBI, MMDB/PDB||Tab-delimited text ||ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table|| | + | | NCBI, MMDB/PDB||Tab-delimited text ||ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table|| (Downloaded on October 08th,2008) |
|- | |- | ||
| − | | NCBI, PDB sequences||FASTA||ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz|| | + | | NCBI, PDB sequences||FASTA||ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz||(Downloaded on October 08th,2008) |
|- | |- | ||
| − | | NCBI Gene2Refseq||Tab-delimited text||ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz|| | + | | NCBI Gene2Refseq||Tab-delimited text||ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz||(Downloaded on October 08th,2008) |
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|} | |} | ||
Revision as of 10:45, 6 November 2008
Last edited: November 11th, 2008 Applies to iRefIndex release: beta 2.0 Release date: November 11th, 2008 Authors: Ian Donaldson and Sabry Razick 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.
| 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/ | 05/25/05 |
| BioGRID | PSI-MI 2.5 | http://www.thebiogrid.org/BIOGRID-ORGANISM-2.0.45.psi25.zip | Version 2.0.45 |
| DIP | PSI-MI 2.5 | http://dip.doe-mbi.ucla.edu/dip/Download.cgi dip20080708.mif25 | 07/08/08 |
| HPRD, | PSI-MI 2.5 | http://www.hprd.org/download/HPRD_SINGLE_PSIMI_090107.xml.tar.gz | Release 7. September 01, 2007 |
| IntAct, | PSI-MI 2.5 | ftp://ftp.ebi.ac.uk/pub/databases/intact/2008-08-22/psi25/ pmidMIF25.zip | August 22, 2008 |
| MINT | PSI-MI 2.5 | ftp://ftp://mint.bio.uniroma2.it/pub/release/psi/2008-04-07/full.psi25.zip | April 07, 2008 |
| MPact | PSI-MI 2.5 | ftp://ftpmips.gsf.de/yeast/PPI/ mpact-complete.psi25.xml | April 19, 2007 |
| MPPI | PSI-MI 1.0 | http://mips.gsf.de/proj/ppi/data/mppi.gz | Not available |
| 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/) | 07/18/06 |
| Source | Format | Location | Version (date) |
| SEGUID | Tab-delimited text | ftp://bioinformatics.anl.gov/seguid/ seguidannotation | September 23rd, 2008 |
| UniProt | Text | http://beta.uniprot.org/downloads Download : 1.UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) 2.UniProtKB/TrEMBL (uniprot_trembl.dat.gz) | UniProt release 14.0 (September 02, 2008) |
| UniProt, IsoForms | FASTA | http://beta.uniprot.org/downloads uniprot_sprot_varsplic.fasta.gz | September 25th, 2008 |
| 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 | Release: 56.2 (September 23rd, 2008) |
| UniProt, FLY | Tab-delimited text file. | http://www.expasy.org/cgi-bin/lists?fly.txt Drosophila: entries, gene names and cross-references to FlyBase. | Release: 56.2 (September 25th, 2008) |
| NCBI, RefSeq | GenPept | ftp://ftp.ncbi.nih.gov/refseq/release/complete see *.protein.gpff.gz files | Release 31 (August 30, 2008) |
| NCBI, MMDB/PDB | Tab-delimited text | ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table | (Downloaded on October 08th,2008) |
| NCBI, PDB sequences | FASTA | ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz | (Downloaded on October 08th,2008) |
| NCBI Gene2Refseq | Tab-delimited text | ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz | (Downloaded on October 08th,2008) |
