Sources and Issues Next Release

Note

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Last edited: 2011-08-18

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

Yeast taxon id changes

See http://www.uniprot.org/news/2011/05/03/release

Paul	There appears to be correction of taxids in the build.

See Bugzilla:247.

New databases

InnateDB, MatrixDB, MPIDB are added.

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" />

RIGID recalculation (pre-build issue)

See bug #242. Modify existing RIGID table or lose continuity of iRIGIDs with last release.

Paul	A program has been added to the iRefIndex sources which produces a mapping from correct to "legacy" RIGIDs. The decision was made to assign new iRIGIDs to the new RIGIDs.

Taxon specific MITAB files (post-processing issue)

Taxon specific files should contain interactions ONLY if one or both taxa, taxb have the appropriate taxon (regardless of what the source database said the interaction taxon was. Change README. For example, see PMID...

http://wodaklab.org/iRefWeb/pubReport/detail?pubmed=12565857+

A "mouse" interaction from HPRD lists only human interactors (the paper is about mouse and they have made a transfer to human without noting what they have done.) As a result, this human interaction ends up in the mouse MITAB (because HPRD says it was mouse). BioGRID correctly curates the paper as about mouse.

See Bugzilla:248.

CORUM methods (code change implemented)

Ensure that all CORUM methods (with MI terms) are parsed.

Sabry

This is now fixed - please get the latest mapper from CVS.

See Bugzilla:249.

Repeated lines (post-processing issue)

There are multiple lines that are repeated many times. These appear to arise from BIND 3DBP division (see for example lines 5,13,117,125 in Ecoli MITAB and others arising from BIND ID 92720 - 44 pieces of experimental evidence and 5 PMIDs) because the accessions for the different experimental forms are not present in MITAB. See Antonio and bug #245. Could be handled as a post-processing step on MITAB to take the unique set of all MITAB lines.

Paul	This will probably be handled by using sort -u with the files.

MITAB/iRefScape canonicalization (post-processing issue)

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.

Decided not to change L method...instead:

Resolve by distributing non-canonicalized data as before AND a canonicalized MITAB file with complete provenance info (this will become the main MITAB file we release and it will support PSICQUIC services and we will drop non-canonicalised version in future releases). Also, canonicalize iRefScape data and include provenance data for interactors in edge attribute viewer.

Requires review of current MITAB file format by Ian.

Build issues

Two BIND Translation files use non-ASCII byte values that are not part of valid UTF-8 byte sequences, but do not declare an encoding explicitly:

• taxid10090_PSIMI25.xml
• taxid9606_PSIMI25.xml

MPIDB

The MPIDB data files are non-standard in various respects and require some special measures to structure the data for iRefIndex use. See iRefIndex MITAB Mapping for details of the way iRefIndex should retain MITAB-originating data.

innatedb.

Innatedb has data from other sources as well. I see in the download page that these is a link for curated innateDB data and we should find out whether this is a collection of all data or are these curated by innatedb. Paul has made a parser for the PSI XML and this data will be from 2011-03-06. They say however that they update the MI TAB version every week.

MatrixDB

They have non-proteins and protein fragments not only proteins as interactors. This database must be tested before homogenizing.

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-3.1.77/BIOGRID-ALL-3.1.77.psi25.zip	Version 3.1.77 (2011-06-01)
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/2011-05-23/psi25/pmidMIF25.zip	2011-05-25
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 2011-06-14
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	xxxx (timestamp)
UniProt	Text	http://www.uniprot.org/downloads UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)	UniProt Knowledgebase Release 2011_06 (2011-05-31) (Downloaded on 2011-06-11): 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 47 (2011-05-12) (Downloaded on 2011-06-11) (from http://www.ncbi.nlm.nih.gov/refseq/)
NCBI, MMDB/PDB	Tab-delimited text	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/table	(Downloaded on 2011-06-11)
NCBI, PDB sequences	FASTA	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/pdbaa.gz	(Downloaded on 2011-06-11)
NCBI Gene2Refseq	Tab-delimited text	ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz	(Downloaded on 2011-06-14)

All iRefIndex Pages

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