MINT, the molecular interaction database: 2012 update

The Molecular INTeraction Database (MINT, http://mint.bio.uniroma2.it/mint/) is a public repository for protein–protein interactions (PPI) reported in peer-reviewed journals. The database grows steadily over the years and at September 2011 contains approximately 235 000 binary interactions captured from over 4750 publications. The web interface allows the users to search, visualize and download interactions data. MINT is one of the members of the International Molecular Exchange consortium (IMEx) and adopts the Molecular Interaction Ontology of the Proteomics Standard Initiative (PSI-MI) standards for curation and data exchange. MINT data are freely accessible and downloadable at http://mint.bio.uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction.

[1]  Sylvie Ricard-Blum,et al.  MatrixDB, the extracellular matrix interaction database , 2010, Nucleic Acids Res..

[2]  Luana Licata,et al.  Linking entries in protein interaction database to structured text: The FEBS Letters experiment , 2008, FEBS letters.

[3]  Y. Zhang,et al.  IntAct—open source resource for molecular interaction data , 2006, Nucleic Acids Res..

[4]  Evelyn Camon,et al.  The EMBL Nucleotide Sequence Database , 2000, Nucleic Acids Res..

[5]  Andrew Chatr-aryamontri,et al.  DOMINO: a database of domain–peptide interactions , 2006, Nucleic Acids Res..

[6]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[7]  Gary D Bader,et al.  PSICQUIC and PSISCORE: accessing and scoring molecular interactions , 2011, Nature Methods.

[8]  Luana Licata,et al.  Protein interactions: integration leads to belief. , 2008, Trends in biochemical sciences.

[9]  Dan Wu,et al.  EMBL Nucleotide Sequence Database in 2006 , 2006, Nucleic Acids Res..

[10]  Henning Hermjakob,et al.  Submit Your Interaction Data the IMEx Way , 2007, Proteomics.

[11]  Michele Tinti,et al.  VirusMINT: a viral protein interaction database , 2008, Nucleic Acids Res..

[12]  Gary D Bader,et al.  BMC Biology BioMed Central , 2007 .

[13]  M. Vidal,et al.  Literature-curated protein interaction , 2009 .

[14]  Matthew R. Laird,et al.  Protein Protein Interaction Network Evaluation for Identifying Potential Drug Targets , 2009 .

[15]  Ioannis Xenarios,et al.  DIP: The Database of Interacting Proteins: 2001 update , 2001, Nucleic Acids Res..

[16]  Sylvie Ricard-Blum,et al.  MatrixDB, a database focused on extracellular protein–protein and protein–carbohydrate interactions , 2009, Bioinform..

[17]  Gary D. Bader,et al.  cPath: open source software for collecting, storing, and querying biological pathways , 2006, BMC Bioinformatics.

[18]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[19]  Hideaki Sugawara,et al.  DDBJ with new system and face , 2007, Nucleic Acids Res..

[20]  Bin Liu,et al.  Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together , 2006, Nucleic Acids Res..

[21]  Baldomero Oliva,et al.  PIANA: protein interactions and network analysis , 2006, Bioinform..

[22]  Livia Perfetto,et al.  MINT, the molecular interaction database: 2009 update , 2009, Nucleic Acids Res..

[23]  Peter Woollard,et al.  The minimum information required for reporting a molecular interaction experiment (MIMIx) , 2007, Nature Biotechnology.

[24]  Lincoln Stein,et al.  Reactome knowledgebase of human biological pathways and processes , 2008, Nucleic Acids Res..

[25]  Peter Uetz,et al.  MPIDB: the microbial protein interaction database , 2008, Bioinform..

[26]  Gabriele Ausiello,et al.  MINT: the Molecular INTeraction database , 2006, Nucleic Acids Res..

[27]  John Boyle,et al.  Cytoscape: a community-based framework for network modeling. , 2009, Methods in molecular biology.

[28]  Alfonso Valencia,et al.  Overview of BioCreAtIvE: critical assessment of information extraction for biology , 2005, BMC Bioinformatics.

[29]  Andrew M. Jenkinson,et al.  Ensembl 2009 , 2008, Nucleic Acids Res..

[30]  M. Vidal,et al.  Literature-curated protein interaction datasets , 2009, Nature Methods.

[31]  Lynette Hirschman,et al.  The FEBS Letters/BioCreative II.5 experiment: making biological information accessible , 2010, Nature Biotechnology.

[32]  Robert Hoffmann,et al.  HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms , 2005, BMC Bioinformatics.

[33]  Ian M. Donaldson,et al.  iRefIndex: A consolidated protein interaction database with provenance , 2008, BMC Bioinformatics.