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Apr 1, 2008 (Vol. 28, No. 7)

Metabolomics Studies Rise in Quality

HPLC, Mass Spec, and Nuclear Magnetic Resonance Are Among Elucidating Technologies

  • As with the other omics, metabolomics can only be of value if dedicated and effective data-management systems are in place. At “metabomeeting,” Dr. Spasic will present MeMo, a data model she developed to support effective and efficient computational analysis of large volumes of experimental data generated through the use of high-throughput metabolomics technologies.

    The development of MeMo arose from the need for storage and analysis of the GC-MS data generated for the metabolic footprints of the genome-wide collection of yeast mutants. MeMo was implemented as a relational database to support the storage, management, and dissemination of large amounts of curated metabolomic data and related metadata.

    In order to make room for incoming methods, instruments, and data resources and to support ongoing standardization efforts, MeMo was designed to be modular and easily extensible. These properties, in addition to the MeMo metadata description module, make the systems portable between the omics domains, according to Dr. Spasic.

    MeMo has continued to evolve to reflect the information needs at MCISB, which include storing and analyzing various types of omics data in an integrated fashion. The metadata module of MeMo is used to store the core metadata common to various experiments performed. The experimental data produced is mainly stored in a MeMo database.

    Since the introduction of MeMo, Dr. Spasic’s team has used Pierre, a model-driven, user-interface development tool, to provide a user interface to MeMo, including a web interface, a stand-alone application, a command-line service, and a web service. Apart from providing access to domain experts, the MeMo interface provides programmatic access to the data through the use of web services. “This is particularly important in the context of systems biology, whose integrative nature poses a typical problem of dealing with data from disparate sources,” she says.

    “We are now well placed to start putting together an experimentally verified functioning model of the human metabolic network. This is the grand challenge of metabolic systems biology.”

    Finally, Alexander Amberg Ph.D., head of metabonomics, drug safety evaluation at sanofi-aventis, will talk about the application of metabolomics in preclinical drug-safety evaluation within the PredTox consortium. This is a major initiative between the European Commission, industry, and academia with the goal of improving drug safety, where metabolomics can make a contribution to ADME studies.



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