Sources and Issues Next Release
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Last edited: 2012-02-08
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 DIP interaction types
- 1.2 Review interaction detection type mappings
- 1.3 Check that BIND small-molecules are not mis-ampped to proteins
- 1.4 Estimate accurate time to build irefindex
- 1.5 change
- 1.6 BioGrid interaction record ids (pre-build issue)
- 1.7 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
DIP interaction types
Not all interaction types are properly extracted from DIP XML records because some are stored in an unexpected filed.
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-ampped to proteins
See Bugzilla:253.
Estimate accurate time to build irefindex
See Bugzilla:254.
change
See Bugzilla:xxx.
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 (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.
See Bugzilla:255.
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-3.1.81/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
|
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) |
Downloaded on 2011-10-03 |
| 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 |
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).
