XML format for proteomics database

We. propose the XML (eXtensible Markup Language) format for proteomics databases to exchange proteome analysis data. The XML-based data is highly machine-readable and easily represent information hierarchy and relationships. There have been several XML formats of proteome data which mainly represent the sequence information stored in the PIR (Protein Identification Resource) and the PDB (Protein Data Base). Our XML-based data model is a proteome-analysis-oriented structure and describes information of sample preparation, 2D gel electrophoresis images, spot identification information in the gels and the sequence information of the spots. The model is used to exchange both preparation parameters and the results of 2D gel electrophoresis analysis. It would accelerate collaboration among proteomics researchers if a platform exchanging these data is developed on the Internet. By using our XML-based model for proteomics, we have developed a Web-based prototype system which consists of an XML database, agent, security and GUI (Graphical User Interface).