Current status of proteomic standards development

The generation of proteomic data is becoming ever more high throughput. Both the technologies and experimental designs used to generate and analyze data are becoming increasingly complex. The need for methods by which such data can be accurately described, stored and exchanged between experimenters and data repositories has been recognized. Work by the Proteome Standards Initiative of the Human Proteome Organization has laid the foundation for the development of standards by which experimental design can be described and data exchange facilitated. The Minimum Information About a Proteomic Experiment data model describes both the scope and purpose of a proteomics experiment and encompasses the development of more specific interchange formats such as the mzData model of mass spectrometry. The eXtensible Mark-up Language-MI data interchange format, which allows exchange of molecular interaction data, has already been published and major databases within this field are supplying data downloads in this format.

[1]  Dipanwita Roy Chowdhury,et al.  Human protein reference database as a discovery resource for proteomics , 2004, Nucleic Acids Res..

[2]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[3]  Rolf Apweiler,et al.  Common interchange standards for proteomics data: Public availability of tools and schema. Report on the Proteomic Standards Initiative Workshop, 2nd Annual HUPO Congress, Montreal, Canada, 8–11th October 2003 , 2004, Proteomics.

[4]  Dmitrij Frishman,et al.  MIPS: analysis and annotation of proteins from whole genomes in 2005 , 2005, Nucleic Acids Res..

[5]  Jocelyn Kaiser,et al.  Public-Private Group Maps Out Initiatives , 2002, Science.

[6]  Ioannis Xenarios,et al.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..

[7]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[8]  Ian M. Donaldson,et al.  BIND: the Biomolecular Interaction Network Database , 2001, Nucleic Acids Res..

[9]  Martin Vingron,et al.  IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..

[10]  C. Sander,et al.  The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.

[11]  Jason E. Stewart,et al.  Design and implementation of microarray gene expression markup language (MAGE-ML) , 2002, Genome Biology.