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The Biomolecular Interaction Network Database in PSI-MI 2.5.

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Summary

The Biomolecular Interaction Network Database (BIND) was converted to a standard format to preserve vital biomolecular interaction data. This effort updates outdated identifiers, ensuring broader species and interactor coverage for future research.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • The Biomolecular Interaction Network Database (BIND) is a critical resource for curated biomolecular interactions.
  • BIND has been unmaintained, risking the loss of unique interaction data due to outdated identifiers.

Purpose of the Study:

  • To convert the last curated release of BIND (2005) into the Proteomics Standard Initiative-Molecular Interaction (PSI-MI) 2.5 format.
  • To make the core components of BIND, including interactions and complexes, available for download.
  • To address data modeling, controlled vocabulary, and data cleaning issues for interaction databases.

Main Methods:

  • Extracted data from BIND's custom XML format.
  • Mapped and converted data to the PSI-MI 2.5 standard.
  • Updated outdated molecule identifiers to enhance data comprehensiveness.

Main Results:

  • Successfully converted BIND's core components (interactions, complexes) and curated information to PSI-MI 2.5.
  • Achieved broader coverage of species and interactor types compared to existing BIND data.
  • Created a downloadable dataset available at http://download.baderlab.org/BINDTranslation/.

Conclusions:

  • The conversion preserves essential biomolecular interaction data from BIND.
  • The updated dataset offers a more comprehensive resource for researchers.
  • This work serves as a case study for maintaining and ensuring the compatibility of biological databases.