RSBI Detail

Rationale for the formation of RSBI

Since microarrays have been incorporated into complex biological investigations such as environmental genomics, nutrigenomics and toxicogenomics minimal descriptors minimal descriptors have been developed by different disciplines (extending MIAME). These include the MIAME/Env, MIAME/Tox [MS-WORD - 118kb] [PDF - 47kb ] and MIAME/Nutr [MS-WORD - 106kb ] checklists by the environmental genomics, toxicogenomics and nutrigenomics and groups.

Discipline-specific initiatives are important, however, these checklists should not be developed in isolation, as it could results in an unnecessary duplication of descriptors across these checklists or problems when third parties try to use these. For example, when reporting an eco-toxicogenomics investigation, should one comply with the MIAME/Env or MIAME/Tox requirements, or combine the two?

It has also become evident that when other omics-technologies, such as proteomics and metabolomics, are used in combination with microarrays, these MIAME-based checklists will soon be insufficient. Although reporting structures, using similar principles to MIAME, are being developed for metabolomics (by MSI) and proteomics (by PSI), if taken individually, these reporting structures will not be sufficient to serve the experimenters who are using ‘multi-omic’ approaches to their biological research.

It is necessary therefore that technology-centred reporting structures and their specific extensions into biological domains of interest are developed not only to stand alone but also to function together as interchangeable modules. To achieve this aim, from a technical perspective it will be necessary to remove redundancies and fill the gaps between the domains covered by these checklists. This is true also for ontologies and exchange formats, the other two pillars of data communication standards.

Environmental genomics, nutrigenomics and toxicogenomics groups employing multiple OMICS technologies have stumbled over these same problems. Their shared interest in overcoming such obstacles has been a good catalyst for producing synergy and forming the RSBI WGs in 2004.

Activities and Supported Projects

  1. Building a reporting structure for biological investigations - The MIcheck Project

    As a way to avoid redundancies and fill the gaps between the domains covered by existing checklists, RSBI WGs propose to reorganize the checklist by including three common high-level abstractions (Investigation, Study, Assay), where to place the information relevant to the biology as well as that relevant to the different technologies employed.
    • See here the RSBI ‘top-level concepts’ and their relationships - Mar 06.
      An Investigation is as a self-contained contained unit of scientific enquiry, with a holistic hypothesis or objective and a Design, defined by the relationships between Study(s) and Assay(s). While the first is a ‘container’ for the description of and steps performed on the subject(s), the latter contains the test(s) - and its produced data -performed on the subject(s). (see Sansone et al, 2006, ref 1)

    The current reporting structures are designed around one technology (or type of Assay) for example microarray for MIAME. According to the proposed reorganization an Assay would be a microarray or a mass-spectrometry experiment (shared by proteomics and metabolomics domains), a histopathology examination or a set of biometrics (shared for example by toxicology and nutrition domains).

    The proposed reorganization currently forms the basis of the toxicogenomics data dictionary containing terms, definitions and relationships (Fostel et al., 2005, ref 7) and the Env checklist (Morrison et al, 2006. ref 6 ).

    RSBI WGs will work on this proposed reorganization further under the umbrella of the Minimum Information for Biological and Biomedical Investigations (MIBBI) initiative (Taylor et al, submitted, ref 3).
  2. Adding semantics and syntax to the reporting structure - FuGO and FuGE Projects

    RSBI WGs have made a decision to focus on the identification and description of the ‘high level concepts’ of a reporting structure that encompasses any biological or technical domain of application. More difficult issues are how to capture descriptions of biological investigations employing multiple OMICS technologies at a high level of granularity and how to model and exchange the information. These have been deferred to two collaborative informatics projects, developing an ontology and an object model for functional genomics.
    • The RSBI WGs contribute to the Ontology for Biomedical Investigations (OBI) in two ways: firstly, by contributing common ‘top-level concepts’; secondly, by the terms specific to environment, nutrition and toxicology domains.
    • The RSBI WGs have contributed modeling requirements to the development of the Functional Genomics Experiment Object Model (FuGE) . The RSBI use cases have provided FuGE developers with real examples and terminology that bench researchers believe should be reported in a data model.
      • The use cases and the common ‘top-level concepts’ have also highlighted several components that required changes in FuGE to report annotation in a format that could be queried. A textual description of how the RSBI ‘top-level concepts’ can be encoded using FuGE classes is here.
  3. Weaving the threads - Omics and Beyond

    Many threads have been woven through extensive liaisons with several standards efforts (Sansone et al, 2004, ref 2). The RSBI WGs have established a strong alliance with the initiative in the proteomics, metabolomics and genomics domains:
    • HUPO Proteomics Standards Initiative (PSI).
      • Currently PSI tracks the work of the RSBI WGs, both to guide HUPO’s internal development and also to assist in promoting the development of a modular reporting structure for biological investigation.
    • Metabolomics Standards Initiative (MSI).
      • The RSBI WGs’ coordinators also serve as moderators of the Biological Metadata and Ontology groups within the nascent MSI in the metabolomics domain.
    • Genomic Standards Consortium (GSC).
      • The RSBI Environmental Genomics WG (EGWG) is also working in collaboration with the GSC to formalise the description of genomic sequence metadata under the Minimum Information about a Genome Sequence (MIGS) project.

    Data standardization is now considered beyond the research application of omics technologies and several initiatives have been set up also to address management (minimal requirements and format for the exchange of information) and validation issues. The RSBI WGs coordinators are actively participating in these discussions, bringing awareness of relevant ongoing efforts.

    Regulatory-driven efforts, aiming for a broader understanding and use of ‘omics data, are also working to define standards for data submission to regulators. Global organization such as the OECD have also initiated a dialogue between technological experts, regulators, and the principal validation bodies to draw road maps for validation and regulatory use of omics-based investigations, particularly in chemical assessment (Corvi et al, 2006. ref 10).

Related Publications

[* Part of A special issue on data standards] by Field D and Sansone SA.OMICS 2006, 2(10): 84-93

  1. * A strategy capitalizing on synergies – The Reporting Structure for Biological Investigation (RSBI) working group.
    Sansone SA, Rocca-Serra P, Tong W, Fostel J, Morrison N, Jones A. OMICS 2006, 2(10):164-171.
  2. Standardization initiatives in the (eco)toxicogenomics domain: a review.
    Sansone SA, Morrison M, Rocca-Serra P, Fostel J. Comp Funct Genom 2004; 5: 633-641.
  3. MICheck: A Minimum Information Checklist Resource.
    Taylor CF, Field D, Sansone SA, Apweiler R, Ashburner M, Ball CA et al. Nat Biotech (Submitted).
  4. * Development of FuGO: An Ontology for Functional Genomics Investigations.
    Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J et al.; Fugo Working Group. OMICS. 2006 Summer;10(2):199-204.
  5. * FuGE: Functional Genomics Experiment Object Model.
    Jones AR, Pizarro A, Spellman P, Miller M; Fuge Working Group. OMICS. 2006 Summer;10(2):179-84.
  6. * Annotation of Environmental OMICS Data: Application to the Transcriptomics Domain.
    Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T et al. OMICS. 2006 Summer;10(2):172-8.
  7. Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data.
    Fostel J, Choi D, Zwickl C, Morrison N, Rashid A, Hasan A et al. Toxicol Sci. 2005 Dec;88(2):585-601. Epub 2005 Sep 8.
  8. * Establishing reporting standards for metabolomic and metabonomic studies: a call for participation.
    Fiehn O, Kristal B, Ommen BV, Sumner LW, Sansone SA, Taylor C et al. OMICS. 2006 Summer;10(2):158-63.
  9. * The Work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).
    Taylor CF, Hermjakob H, Julian RK, Garavelli JS, Aebersold R, Apweiler R. OMICS. 2006 Summer;10(2):145-51.
  10. Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use.
    Corvi R, Ahr HJ, Albertini S, Blakey DH, Clerici L, Coecke S et al. Environ Health Perspect. 2006 Mar;114(3):420-9.

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