The MIBBI Foundry and its Modules


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  • Non-MICheckout-based demo: show individual modules, show linking mechanism, show some compilations.
  • The MIBBI Foundry and its Modules

    1. 1. The MIBBI Foundry and its modules Chris Taylor, Susanna Sansone, Dawn Field, The MIBBI Project Project website:
    2. 2. Mechanisms of scientific advance
    3. 3. ProteoRED’s MIAPE satisfaction survey • Spanish multi-site collaboration: provision of proteomics services • MIAPE customer satisfaction survey (compiled November 2008) — — Responses from 31 proteomics experts representing 17 labs Yes: 95% No: 5%
    4. 4. Technologically-delineated views of the world A: transcriptomics B: proteomics C: metabolomics …and… Biologically-delineated views of the world A: plant biology B: epidemiology C: microbiology …and… Generic features (‘common core’) — Description of source biomaterial — Experimental design components Arrays Scanning Arrays & Scanning Columns Gels MS MS FTIR NMR Columns Modelling the biosciences
    5. 5. Modelling the biosciences (slightly differently) Assay: Omics and miscellaneous techniques Investigation: Medical syndrome, environmental effect, etc. Study: Toxicology, environmental science, etc.
    6. 6. Investigation / Study / Assay (ISA) Infrastructure Ontology of Biomedical Investigations (OBI) Functional Genomics Experiment (FuGE) Rise of the Metaprojects
    7. 7. Reporting guidelines — a case in point • MIAME, MIAPE, MIAPA, MIACA, MIARE, MIFACE, MISFISHIE, MIGS, MIMIx, MIQAS, MIRIAM, (MIAFGE, MIAO), My Goodness… • ‘MI’ checklists usually developed independently, by groups working within particular biological or technological domains — Difficult to obtain an overview of the full range of checklists — Tracking the evolution of single checklists is non-trivial — Checklists are inevitably partially redundant one against another — Where they overlap arbitrary decisions on wording and sub structuring make integration difficult • Significant difficulties for those who routinely combine information from multiple biological domains and technology platforms — Example: An investigation looking at the impact of toxins on a sentinel species using proteomics (‘eco-toxico-proteomics’) — What reporting standard(s) should they be using?
    8. 8. Nature Biotechnol 26(8), 889–896 (2008)
    9. 9. The MIBBI Project ( [†] Denotes that a specification is provided as a suite of related documents CONCEPT SPECIALISATION ●CIMR[†] ●MIACA ●MIAME ●MIAME/Env ●MIAME/Nutr ●MIAME/Plant ●MIAME/Tox ●MIAPA ●MIAPE[†] ●MIARE ●MIFlowCyt ●MIGen ●MIGS/MIMS ●MIMIx ●MIMPP ●MINI study inputs study design ● generic organism ● cells / microbes plant animal mouse human population environmental sample environment / habitat in silico model study procedures organism maintenance animal husbandry cell / microbe culture plant cultivation acclimation preconditioning / pretreatment ● organism manipulation assay inputs generic study input organism part ● organism state organism trait biomolecule synthetic analyte ● silencing RNA reagent Version 0.7 (2008-04-10) Comparison of MIBBI-registered projects [21] ● Release Granularity Coarse Medium Fine Maturity ● Planned ● Drafting
    10. 10. The MIBBI Project (
    11. 11. The MIBBI Project ( Interaction graph for projects (line thickness & colour saturation show similarity)
    12. 12. The MIBBI Project (
    13. 13. Drafting MIBBI Foundry modules Analytical approach proved challenging • Cross analyses were either too coarse or too depressing • Conclusion: no ‘perfect’ solution… If in doubt, hack (a.k.a. ‘iterative development’) • Start with one set of guidelines, breaking it into ‘paragraphs’ • Add another set, breaking it up similarly (‘shared subject’) • Where there are overlaps, seek to resolve — If similar, aim for an ‘average’ module — If distinct, use core and extension modules — Record dependencies in a matrix (for reference) • ‘Normalise’ (look for efficiencies, to a point) Validation • Asking for something like MIxxx should get something like MIxxx • Weigh the conflicts/compromises; reexamine extensions etc.
    14. 14. Current coverage: Portal versus Foundry Checklists covered to date (x) • MIGS/MIMS, MIAPE, MIFlowCyt, MIARE, ‘Env’ extensions Modules developed to date • 35 (set to rise rapidly)…
    15. 15. ‘Pedro’ tool → XML → (via XSLT) Wiki code (etc.)
    16. 16. Creating and Using MIBBI Foundry modules Stage one • Pedro tool (Garwood et al., 2004) using the MIBBI module schema • Highly-configurable (mostly XML Schema, partly a configuration file) • Validates data and exports XML (also saves in a ‘native’ zipped XML) Stage two • Mini shell scripts for XSL transformation using Saxon — Initially just to get the (media)wiki code for Foundry pages — Now have MediaWiki and HTML (both as table & list), tab- delimited text, XML Schema (for MDA) and ISA config (XML) • Java (command line) tool (using DOM) built to combine and transform modules using the above XSLTs (=MyMICheckout) Stage three • ‘MICheckout the movie’ built using Flash (catalyst/builder) • Same functionality (same XSLTs), rather nicer UI (i.e., it has one)
    17. 17. MICheckout: Supporting Users
    18. 18. MIBBI and other standardisation efforts Ontology support: • MIBBI module schema allows for specified ontology references • Any number of terms (leaf or node) can be ‘attached’ to an element — We expect software to offer the specified choices to users Format support: • MIBBI has no specific implementation for data exchange formats • BUT: we can achieve the same end by supporting tools — Currently implementing ISAcreator configuration file generation — Will allow capture of MIBBI Foundry-specified content in ISA-Tab — Also an example of software implementing our ontology links
    19. 19. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone 20 Example of guiding the experimentalist to search and select a term from the EnvO ontology, to describe the habitat of a sample Ontologies, accessed in real time via the Ontology Lookup Service and BioPortal