Sources and Issues Next Release

Note

This is a planning template for the next release. It does not correspond to a released product. See http://irefindex.uio.no/ for the most recent release and related documentation. This page can be used to create the sources page. Check for xxx before copying and pasting to the appropriate sources page for the new release. Do not edit xxx in this page. Leave this page as a template. After making a new release page, update the general Sources for iRefIndex redirect page.

Last edited: 2012-02-13

Applies to iRefIndex release: xxx

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

Issues

DIP interaction types

Not all interaction types are properly extracted from DIP XML records because some are stored in an unexpected field.

See Bugzilla:251.

Review interaction detection type mappings

Some InnateDB detection types have been reported to be mapped to a parent term.

See Bugzilla:252.

Check that BIND small-molecules are not mis-mapped to proteins

See Bugzilla:253.

Estimate accurate time to build iRefIndex

See Bugzilla:254.

BioGRID interaction record ids (pre-build issue)

Capture BioGRID interaction record ids so iRefWeb can link out to BioGRID.

The only interaction id available from the BioGRID files are already being used and also there in the iRefWeb, such as...

<primaryRef db="grid" id="103" refType="identity" refTypeAc="MI:0356" dbAc="MI:0463" />

See Bugzilla:250.

MITAB/iRefScape canonicalization

Change this to choose canonical sequence rather than longest sequence (mapping score L). Examples GeneID 84148 and 512564 unnecessarily separates Grid interaction data from interaction data from other databases.

See Bugzilla:255.

Interaction related resources

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... http://web.archive.org/web/*/http://www.blueprint.org	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 dip20101010.mif25 Note: date on last IMEx release file is from 2008	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.com/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) http://www.jcvi.org/mpidb/interaction.php?dbsource=MPI-LIT (specific download for MPI-LIT) http://www.jcvi.org/mpidb/interaction.php?dbsource=MPI-IMEX (specific download for MPI-IMEX)	Downloaded on 2011-10-03
MatrixDB	PSI-MI 2.5	http://matrixdb.ibcp.fr/ MatrixDB_20100826.xml.zip	2010-08-26 (timestamp)

Sequence related resources (not updated yet)

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).