Sources and Issues Next Release

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Last edited: 2014-02-26

Applies to iRefIndex release: xxx

Release date: xxx

Authors: Ian Donaldson

Database: iRefIndex (http://irefindex.org)

Organization: http://irefindex.org

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

Deprecated taxids appear in export for iRefWeb

See list from Yuri. Examples are 273, 510, 515, 591, 592, 601, 602, 677, 887, 1139, 1156, 1312...133899, 137208, 144556, 150147, 160268, 163106, 163653, 196590, 216593.

These appear in the 'interactor' and 'interaction_interactor_assignment' , but are not in new taxonomy 'taxonomy_scientific' and 'names" tables. A random selection of these do not appear in the mitab files so the fault likely lies in the export script for irfweb.

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.

PDB identifiers

In previous releases we have replaced the pipe character (|) of the PDB identifiers with an underscore character (_) . In this release, this is only done when there are multiple database:accession entries in a field otherwise the |) character is maintained as part of the PDB identifier. This is a regression and will be corrected in a future release.

IMEX identifiers

IMEx identifiers should be present in column 52 but appear to be missing. This is a regression and will be corrected in a future release. There are 6004 lines in release 10 with imex:... This number needs to be cross-checked before the next release. This is still an issue as of release 13.

Compatibility with Java PSI parser needs to be improved

Java parser from psimi https://code.google.com/p/psimi/downloads/detail?name=psimitab-1.8.3-distribution.zip. But there are at least a few examples where the files don't follow the specs:

-reserved characters are not quoted.

       Like for instance in file for human:

       taxid:11706(HIV-1 M:B_HXB2R)
       taxid:10299(Herpes simplex virus (type 1 / strain 17))
       go:GO:0005783|rigid:d//bz+DaMrbuxGA3i1Xe4hqlrXI|edgetype:X

       In case of controlled terms to be standard conform it should look like this:

       psi-mi:"MI:0496"(bait)

-empty columns need to be consistently filled with '-' . For example, column 15 in the human file.

-dates should be represented as yyyy/mm/dd but look like yyyy-mm-dd Thanks to Thomas Schmitt for pointing out these problems

Various issues reported by Andrei Turinsky

There are a few remaining issues, as follows:

6630 interactors have obsolete Entrez Gene IDs shown (of which 3449 in Human). 

2696 RefSeq IDs (of which 935 are Human) have no Entrez ID shown in the MITAB, but such ID is actually known from NCBI maps - not sure whether your canonicalization process may recover these IDs. Only one such case remains for UniProt IDs (uniprotkb:P0CE96 a.k.a. YL156_YEAST actually has known genes 850851, 850856, 850858 but none of these are shown) - so the rest of UniProts have been resolved, which is great.

A minor thing: 6 interactors are shown with either two different taxons due to different strains of either E.coli or yeast.

A minor thing: 5 interactors are sometimes shown with no taxon at all (4 human and 1 from A. fulgidus). 

A noticeable percentage of PubMeds have been lost for some of the source DBs, with InnateDB and DIP having lost hundreds of Pubs. Human annotations especially affected: e.g. Human DIP lost 266 pubmeds, or 16%; Human InnateDB lost 347 pubs, or 13%).

There are 17 obsolete PSI-MI IDs that appear in the MITAB files, of which 15 are detection methods and 2 interaction types (MI:0191 "aggregation" and MI:0218 "physical interaction"). Their listing is attached. Of these, MI:0229 is actually still valid (it's an alt_id) but should be replaced with MI:0809 -- see the last line in the attached list. 

Also, the detection method id "MI:0044" is not valid -- could be a typo? (it's not listed in the attached file). 

In column 13, for mpi-imex and mpi-lit, should the code "MI:0000" be changed to MI:0903?

In column 14, CORUM records are referenced by their publication ID, not by their complex ID.

Outdated Entrez Gene identifier

Some users have reported that retired Entrez Gene identifiers have appeared in release 10 that were correctly updated in release 9.

Examples

release 9:

uniprotkb:P21675|refseq:NP_620278|entrezgene/locuslink:6872|rogid:P0LoULOvon+Wp2G17lBlqn3Fo4E9606|irogid:3476704

release 10:

entrezgene/locuslink:100287968|entrezgene/locuslink:100291704|entrezgene/locuslink:1863|rogid:P0LoULOvon+Wp2G17lBlqn3Fo4E9606|irogid:3476704

Release 9 used the correct id for TAF1, 6872. In release 10, 3 outdated entrez gene ids are used instead, which all say in their record: This record was replaced with Gene ID: 6872

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).