Difference between revisions of "Sources iRefIndex 8.0"

From irefindex
(→‎Sequence related resources: Updated UniProt details.)
 
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<pre>
 
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This is a planning template for the next release 8.0.  It does not correspond to a released product.
 
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See http://irefindex.uio.no/ for the most recent release and related documentation.
 
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This page will be updated as release 8.0 id built. 
 
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Check for xxx before  release.
 
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</pre>
 
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Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}
 
Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}
  
 
Applies to iRefIndex release: 8.0
 
Applies to iRefIndex release: 8.0
  
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Release date:  xxx
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Release date:  2011-01-19
  
 
Authors: Ian Donaldson, Sabry Razick and Paul Boddie
 
Authors: Ian Donaldson, Sabry Razick and Paul Boddie
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Description: This file lists interaction and protein sequence related resources used for the current build of the iRefIndex.
 
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.
 
Statistics for the iRefIndex are available and include a breakdown of interactors and interactions from each data source.
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*For statistics on full public dataset please refer to: http://irefindex.uio.no/wiki/Statistics_iRefIndex_xxx
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*For statistics on full public dataset please refer to: http://irefindex.uio.no/wiki/Statistics_iRefIndex_8.0
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*For statistics on the public dataset (distributed on the FTP site contains) please refer to:http://irefindex.uio.no/wiki/Statistics_iRefIndex_free_xxx
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== Interaction related resources ==
 
== Interaction related resources ==
  
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{| {{table}}
+
{| {{table}} cellpadding="10" cellspacing="0" border="1"
 
| align="center" style="background:#f0f0f0;"|'''Source'''
 
| align="center" style="background:#f0f0f0;"|'''Source'''
 
| align="center" style="background:#f0f0f0;"|'''Format'''
 
| align="center" style="background:#f0f0f0;"|'''Format'''
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||25th May, 2005
 
||25th May, 2005
 
|-
 
|-
−
| BIND Translation ||PSI-MI 2.5|| http://download.baderlab.org/BIND/PSIMI25_AllInclusive_AllSpecies.zip || March 26th, 2010 (timestamp)
+
| BIND Translation ||PSI-MI 2.5|| http://download.baderlab.org/BINDTranslation/release1_0/BINDTranslation_v1_xml_AllSpecies.tar.gz || release1_0, December 16th, 2010 (timestamp)
 
|-
 
|-
−
| BioGRID||PSI-MI 2.5||http://www.thebiogrid.org/downloads.php<br>/Current Release/BIOGRID-ALL-3.0.68.psi.zip ||Version 3.0.68 (August 25th, 2010)
+
| BioGRID||PSI-MI 2.5||http://http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.1.71/BIOGRID-ALL-3.1.71.psi25.zip ||Version 3.1.71 (November 25th 2010)
 
|-
 
|-
 
| CORUM||PSI-MI 2.5||http://mips.gsf.de/genre/proj/corum/index.html<br>http://mips.gsf.de/genre/export/sites/default/corum/allComplexes.psimi.zip ||December 2nd, 2009
 
| CORUM||PSI-MI 2.5||http://mips.gsf.de/genre/proj/corum/index.html<br>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<br>dip20091230.mif25 ||June 14th, 2010
+
| DIP||PSI-MI 2.5||http://dip.doe-mbi.ucla.edu/dip/Download.cgi<br>dip20101010.mif25.gz ||October 10th, 2010
 +
|-
 +
| HPRD||PSI-MI 2.5||http://www.hprd.org/download<br>HPRD_SINGLE_PSIMI_041310.xml.tar.gz||Release 9. April 13th, 2010
 
|-
 
|-
−
| HPRD||PSI-MI 2.5||http://www.hprd.org/download<br>HPRD_SINGLE_PSIMI_041310.xml.tar.gz||Release 8. April 13th, 2010
+
| IntAct||PSI-MI 2.5||ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/pmidMIF25.zip|| December 16th, 2010 (timestamp)
 
|-
 
|-
−
| I2D||PSI-MI 2.5||http://ophid.utoronto.ca/ophidv2.201/downloads.jsp ||Downloaded on September 14th, 2010
+
| MINT||PSI-MI 2.5|| /biotek/cnkeeper/storage/databases/donmysql/Sabry/data/MINT/2010-12-21/ || December 21st, 2010  
 
|-
 
|-
−
| InnateDB ||?|| http://www.innatedb.com/download.jsp ||?
+
| MPACT||PSI-MI 2.5||ftp://ftpmips.gsf.de/yeast/PPI/<br>mpact-complete.psi25.xml.gz ||January 10th, 2008
 
|-
 
|-
−
| IntAct||PSI-MI 2.5||ftp://ftp.ebi.ac.uk/pub/databases/intact/2010-01-22/psi25/pmidMIF25.zip|| January 22nd, 2010
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| MPPI||PSI-MI 1.0||http://mips.gsf.de/proj/ppi/data/mppi.gz||June 1st, 2004 (from archive)
 
|-
 
|-
−
| MatrixDB||PSI-MI 2.5|| http://matrixdb.ibcp.fr/<br>MatrixDB_20100826.xml.zip ||August 26th, 2010 (timestamp)
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| 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/)||July 07th, 2006
 +
<!--
 +
|Evaluated but not included in this release, will be available in the beta 9.0.|
 
|-
 
|-
−
| MINT||PSI-MI 2.5|| ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmid/|| November 11th, 2009
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| I2D||PSI-MI 2.5||http://ophid.utoronto.ca/ophidv2.201/downloads.jsp ||Downloaded on September 14th, 2010
 
|-
 
|-
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| MPACT||PSI-MI 2.5||ftp://ftpmips.gsf.de/yeast/PPI/<br>mpact-complete.psi25.xml.gz ||January 10th, 2008
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| InnateDB ||PSI-MI 2.5|| http://www.innatedb.com/download.jsp<br>Curated InnateDB Data ||July 16th, 2010
 
|-
 
|-
 
| MPIDB||MITAB format file|| http://www.jcvi.org/mpidb<br>http://www.jcvi.org/mpidb/download.php || Downloaded on September 15th, 2010
 
| MPIDB||MITAB format file|| http://www.jcvi.org/mpidb<br>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)
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| MatrixDB||PSI-MI 2.5|| http://matrixdb.ibcp.fr/<br>MatrixDB_20100826.xml.zip ||August 26th, 2010 (timestamp)
−
|-
+
-->
−
| OPHID||PSI-MI || ||
+
 
−
|-
 
 
|}
 
|}
  
 
== Sequence related resources ==
 
== Sequence related resources ==
  
−
{| {{table}}
+
{| {{table}} cellpadding="10" cellspacing="0" border="1"
 
| align="center" style="background:#f0f0f0;"|'''Source'''
 
| align="center" style="background:#f0f0f0;"|'''Source'''
 
| align="center" style="background:#f0f0f0;"|'''Format'''
 
| align="center" style="background:#f0f0f0;"|'''Format'''
Line 95: Line 91:
 
| align="center" style="background:#f0f0f0;"|'''Version (date)'''
 
| align="center" style="background:#f0f0f0;"|'''Version (date)'''
 
|-
 
|-
−
| SEGUID||Tab-delimited text ||ftp://bioinformatics.anl.gov/seguid/<br>seguidannotation||August 7th, 2007 (server gives "08/07/107")
+
| SEGUID||Tab-delimited text ||ftp://bioinformatics.anl.gov/seguid/<br>seguidannotation||July 24th, 2007 (timestamp)
 
|-
 
|-
 
| UniProt||Text||http://www.uniprot.org/downloads<br>UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)
 
| UniProt||Text||http://www.uniprot.org/downloads<br>UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)
−
| rowspan="5" | UniProt Knowledgebase Release 2010_09:<br>UniProtKB/Swiss-Prot Release 2010_09 (10-Aug-2010)<br>UniProtKB/TrEMBL Release 2010_09 (10-Aug-2010)<br>(from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt)
+
| rowspan="5" | UniProt Knowledgebase Release 2010_12(Downloaded 21-December-2010):<br>UniProtKB/Swiss-Prot <br>UniProtKB/TrEMBL <br>(from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt)
 
|-
 
|-
 
| UniProt||Text|| http://www.uniprot.org/downloads<br>UniProtKB/TrEMBL (uniprot_trembl.dat.gz)
 
| UniProt||Text|| http://www.uniprot.org/downloads<br>UniProtKB/TrEMBL (uniprot_trembl.dat.gz)
Line 108: Line 104:
 
| 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 44 (Downloaded on December 21st, 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, PDB sequences||FASTA||ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz||(Downloaded on February 8th, 2010)
+
| NCBI, MMDB/PDB||Tab-delimited text ||ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table|| (Downloaded on December 21st, 2010)
 
|-
 
|-
−
| NCBI Gene2Refseq||Tab-delimited text||ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/<br>gene2refseq.gz||(Downloaded on February 8th, 2010)
+
| NCBI, PDB sequences||FASTA||ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz||(Downloaded on December 21st, 2010)
 
|-
 
|-
−
|  
+
| NCBI Gene2Refseq||Tab-delimited text||ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/<br>gene2refseq.gz||(Downloaded on December 21st, 2010)
 
|}
 
|}
  

Latest revision as of 08:45, 20 January 2011

Last edited: 2011-01-20

Applies to iRefIndex release: 8.0

Release date: 2011-01-19

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/BINDTranslation/release1_0/BINDTranslation_v1_xml_AllSpecies.tar.gz release1_0, December 16th, 2010 (timestamp)
BioGRID PSI-MI 2.5 http://http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.1.71/BIOGRID-ALL-3.1.71.psi25.zip Version 3.1.71 (November 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
dip20101010.mif25.gz		 October 10th, 2010
HPRD PSI-MI 2.5 http://www.hprd.org/download
HPRD_SINGLE_PSIMI_041310.xml.tar.gz		 Release 9. April 13th, 2010
IntAct PSI-MI 2.5 ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/pmidMIF25.zip December 16th, 2010 (timestamp)
MINT PSI-MI 2.5 /biotek/cnkeeper/storage/databases/donmysql/Sabry/data/MINT/2010-12-21/ December 21st, 2010
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 1.0 http://ophid.utoronto.ca/ophid/downloads.html (This service no longer available, please refer to http://ophid.utoronto.ca/ophidv2.201/) July 07th, 2006

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_12(Downloaded 21-December-2010):
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 44 (Downloaded on December 21st, 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 December 21st, 2010)
NCBI, PDB sequences FASTA ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz (Downloaded on December 21st, 2010)
NCBI Gene2Refseq Tab-delimited text ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
gene2refseq.gz		 (Downloaded on December 21st, 2010)

All iRefIndex Pages

Follow this link for a listing of all iRefIndex related pages (archived and current).

Retrieved from "http://irefindex.vib.be/wiki/index.php?title=Sources_iRefIndex_8.0&oldid=3209"