Sources and Issues Next Release

From irefindex

This is a planning template for the next release. It does not correspond to a released product. See for the most recent release and related documentation. This page can be used to create the sources page. Check for xxx before copying and pasting to the appropriate sources page for the new release. Do not edit xxx in this page. Leave this page as a template. After making a new release page, update the general Sources for iRefIndex redirect page.

Last edited: 2012-02-08

Applies to iRefIndex release: xxx

Release date: xxx

Authors: Ian Donaldson, Sabry Razick and Paul Boddie

Database: iRefIndex (

Organization: Biotechnology Centre of Oslo, University of Oslo (

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.


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.


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


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 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.


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. (no longer available - see below).







These file are no longer available via ftp but are available from the authors. BIND archival content is now managed by Thomson Scientific. See and

For historical purposes, a snapshot of the the Blueprint web-site may be viewed at...

...via the internet archive at...*/

BIND Translation PSI-MI 2.5 Version 1.0 (2010-12-15)
BioGRID PSI-MI 2.5 Version 3.1.81 (2011-10-01)

Note: date on last IMEx release file is from 2008

Release 9 (2010-04-13)
IntAct PSI-MI 2.5 2011-09-29
MINT PSI-MI 2.5 2010-12-21
MPACT PSI-MI 2.5 2008-01-10
MPPI PSI-MI 1.0 2004-06-01 (from archive)
OPHID PSI-MI 1.0 (This service no longer available, please refer to 2006-07-07
New for this release
InnateDB PSI-MI 2.5
Curated InnateDB Data
MPIDB MITAB format file (information) (general downloads) (specific download for MPI-LIT) (specific download for MPI-IMEX)

Downloaded on 2011-10-03
MatrixDB PSI-MI 2.5
2010-08-26 (timestamp)

Sequence related resources (not updated yet)

Source Format Location Version (date)
SEGUID Tab-delimited text
2007-07-24 (timestamp)
UniProt Text
UniProtKB/Swiss-Prot (uniprot_sprot.dat.gz)
UniProt Knowledgebase Release 2011_09 (2011-09-21) (Downloaded on 2011-10-04):
UniProt Text
UniProtKB/TrEMBL (uniprot_trembl.dat.gz)
UniProt, IsoForms FASTA uniprot_sprot_varsplic.fasta.gz
UniProt, SGD Tab-delimited text file.
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
UniProt, FLY Tab-delimited text file.
Drosophila: entries, gene names and cross-references to FlyBase.
NCBI, RefSeq GenPept
see *.protein.gpff.gz files
Release 49 (2011-09-09) (Downloaded on 2011-10-04)
NCBI, MMDB/PDB Tab-delimited text (Downloaded on 2011-10-04)
NCBI, PDB sequences FASTA (Downloaded on 2011-10-03)
NCBI Gene2Refseq Tab-delimited text
(Downloaded on 2011-10-04)

All iRefIndex Pages

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