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GIDMP: Good protein-protein interaction data metamining practice

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Abstract

Studying the interactome is one of the exciting frontiers of proteomics, as shown lately at the recent bioinformatics conferences (for example ISMB 2010, or ECCB 2010). Distribution of data is facilitated by a large number of databases. Metamining databases have been created in order to allow researchers access to several databases in one search, but there are serious difficulties for end users to evaluate the metamining effort. Therefore we suggest a new standard, “Good Interaction Data Metamining Practice” (GIDMP), which could be easily automated and requires only very minor inclusion of statistical data on each database homepage. Widespread adoption of the GIDMP standard would provide users with:

  • a standardized way to evaluate the statistics provided by each metamining database, thus enhancing the end-user experience

  • a stable contact point for each database, allowing the smooth transition of statistics

  • a fully automated system, enhancing time- and cost-effectiveness.

The proposed information can be presented as a few hidden lines of text on the source database www page, and a constantly updated table for a metamining database included in the source/credits web page.

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Correspondence to Dariusz Plewczynski.

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Key words

  • Proteins
  • Interactome
  • Pathways
  • Signaling
  • Metamining
  • Literature curation
  • Protein-protein interaction
  • Bioinformatics
  • Systems biology