Release Notes - iRefWeb - Wodak Lab

Version 2.3: 2010 September 08

• Bug fix for download of search results in MITAB format (results incorrectly filtered/matched).

Version 2.2: 2010 August 26

• Some filters changed from discrete steps (1,2,3, etc.) to ranges (1 or more, 2 or more, etc.). Filters affected: Number of Supporting PubMeds, Number of Database Records, Number of Annotating Databases.
• Small warning added to the Detection Methods and Interaction Type filters (click on the help icon beside the title).

Version 2.1: 2010 July 23

• Clarifcation notes added to stats page/tab.
• New search filters:
  • whether or not the interaction was predicted or experimental
  • the count of distinct source databases annotating the interaction
  • the total number of source database records supporting the interaction

Version 2.0: 2010 July 13

• Using iRefIndex version 7.
• Improved search results: now in a table format with sortable columns.
• New search filters, now with slider controls for custom filter settings.
• Interactome downloads are no longer limited to 50,000 records or less.
• Search results can also be exported as a list of interaction ids for use in OrthoNets.
• You can now upload a list of Entrez Gene IDs to search on instead of searching for just one ID at a time.
• This release includes data from BINDTranslation. This data is being treated as if it was a non-public database because it is from an early version. Future versions of iRefIndex/iRefWeb will include BINDTranslation as public data.

Version 1.0: 2009 March

• iRefWeb 1.0 contains the first release of the iRefIndex dataset (iRefIndex 6) in which an additional isoform-consolidation step was introduced into the iRefIndex procedure. Starting from this release, every interacting protein is mapped to the canonical splice isoform of the corresponding gene whenever possible. This enables further consolidation and more reliable comparison of the interaction data across the source databases (see irefindex.uio.no/wiki/Canonicalization).
• iRefWeb 1.0 and iRefIndex 6 were used in the preparation of two upcoming publications:
  • Turner et al. "iRefWeb: Interactive analysis of consolidated protein interaction data and their supporting evidence", Database Journal, 2010 (in press) -- a detailed description of the iRefWeb resource, its many interactive features and several usage scenarios.
  • Turinsky et al. "Literature curation of protein interactions: measuring agreement across major public databases" (manuscript under review) -- a comparative study of current literature-curation practices that pertain to protein-interaction data.
• The original source-database releases used in iRefWeb 1.0 / iRefIndex 6 are listed at irefindex.uio.no/wiki/Sources_iRefIndex_6.0.