Sources and Issues Next Release
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 cut and paste to the appropriate sources page for the new release. Do not edit xxx in this page. Leave this page as a template.
Last edited: 2011-05-26
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
Issues
Taxon specific MITAB files
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. 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
Ensure that all CORUM methods (with MI terms) are parsed.
Repeated lines
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.
RIGID recalculation
See bug 242.
Resolution of ambiguous gene ids
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 chnage 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 provenace data for interactors in edge attribute viewer.
Requires review of current MITAB file format by Ian.
BioGrid interaction record ids
Capture Biogrid interaction record ids so iRefWeb can link out to BioGrid.
Yeast taxon id changes See http://www.uniprot.org/news/2011/05/03/release
| 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... |
25th May, 2005 | |
| BioGRID | PSI-MI 2.5 | http://www.thebiogrid.org/downloads.php /Current Release/BIOGRID-ALL-2.0.61.psi.zip |
Version 2.0.61 (January 31st, 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 dip20091230.mif25 |
December 30th, 2009 | |
| HPRD, | PSI-MI 2.5 | http://www.hprd.org/download/ HPRD_SINGLE_PSIMI_070609.xml.tar.gz |
Release 8. July 6th, 2009 | |
| IntAct, | PSI-MI 2.5 | ftp://ftp.ebi.ac.uk/pub/databases/intact/2010-01-22/psi25/pmidMIF25.zip | January 22nd, 2010 | |
| MINT | PSI-MI 2.5 | ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmid/ | November 11th, 2009 | |
| 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) | |
| I2D | PSI-MI 2.5 | http://ophid.utoronto.ca/ophidv2.201/downloads.jsp | Downloaded on February 8th, 2010 |
| Source | Format | Location | Version (date) |
| SEGUID | Tab-delimited text | ftp://bioinformatics.anl.gov/seguid/ seguidannotation |
August 7th, 2007 (server gives "08/07/107") |
| UniProt | Text | http://www.uniprot.org/downloads UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz) |
UniProt Knowledgebase Release 15.14: UniProtKB/Swiss-Prot Release 57.14 (09-Feb-2010) UniProtKB/TrEMBL Release 40.14 (09-Feb-2010) |
| 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 39 (January 30th, 2010) |
| 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 Gene2Refseq | Tab-delimited text | ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2refseq.gz |
(Downloaded on February 8th, 2010) |
All iRefIndex Pages
Follow this link for a listing of all iRefIndex related pages (archived and current).
