Sources and Issues Next Release
 Note |
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Last edited: 2011-08-17
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
Contents
- 1 Issues
- 1.1 Yeast taxon id changes
- 1.2 New databases
- 1.3 BioGrid interaction record ids (pre-build issue)
- 1.4 RIGID recalculation (pre-build issue)
- 1.5 Taxon specific MITAB files (post-processing issue)
- 1.6 CORUM methods (code change implemented)
- 1.7 Repeated lines (post-processing issue)
- 1.8 MITAB/iRefScape canonicalization (post-processing issue)
- 2 Build issues
- 3 Interaction related resources
- 4 Sequence related resources (not updated yet)
- 5 All iRefIndex Pages
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 loose continuity of iRIGIDs with last release.
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.
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. |
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.
| 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... |
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
|
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) |
Downloaded on 2011-06-14 |
| MatrixDB | PSI-MI 2.5 | http://matrixdb.ibcp.fr/ MatrixDB_20100826.xml.zip |
2010-08-26 (timestamp) |
| 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).
