An XML Format for Proteomics Database to Accelerate Collaboration among Bioresearchers

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  • MIZUGUCHI Hironori
    Internet Systems Research Laboratories, NEC Corporation
  • KAMIJO Ken'ichi
    Proteomics Research Center, Fundamental Research Laboratories, NEC Corporation
  • TSUGITA Akira
    Proteomics Research Center, Fundamental Research Laboratories, NEC Corporation

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  • バイオ研究者間の情報共有のためのプロテオームXML記述方式
  • バイオ ケンキュウシャ カン ノ ジョウホウ キョウユウ ノ タメ ノ プロテオーム XML キジュツ ホウシキ

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Abstract

We propose an XML (eXtensible Markup Language) format for proteomics database to exchange proteome analysis data. The XML-based data is highly machine-readable and easy to represent information hierarchy and relationships. There have been several XML formats of proteome data which mainly represent the sequence information stored in the Protein Identification Resource (PIR) and the Protein Data Base (PDB). Our XML-based data format has 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 of 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 the XML-based data format for proteomics, we have developed an XML editor and a web-based prototype system which consists of XML database, agent, security and graphical user interface (GUI).

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