1. The MIBBI Foundry
and its modules
Chris Taylor, Susanna Sansone,
Dawn Field, The MIBBI Project
Project website: http://mibbi.org/

2. Mechanisms of scientific advance

3. ProteoRED’s MIAPE satisfaction survey
• Spanish multi-site collaboration: provision of proteomics services
• MIAPE customer satisfaction survey (compiled November 2008)
— http://www.proteored.org/MIAPE_Survey_Results_Nov08.html
— Responses from 31 proteomics experts representing 17 labs
Yes: 95%
No: 5%

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. Modelling the biosciences (slightly differently)
Assay: Omics and miscellaneous techniques
Investigation: Medical syndrome, environmental effect, etc.
Study: Toxicology, environmental science, etc.

6. Investigation / Study / Assay (ISA) Infrastructure
http://isa-tools.org/
Ontology of Biomedical Investigations (OBI)
http://obi.sourceforge.net/
Functional Genomics Experiment (FuGE)
http://fuge.sourceforge.net/
Rise of the Metaprojects

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. Nature Biotechnol 26(8), 889–896 (2008)
http://dx.doi.org/10.1038/nbt.1411

9. The MIBBI Project (mibbi.org)
[†] 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. The MIBBI Project (mibbi.org)

11. The MIBBI Project (mibbi.org)
Interaction graph for projects (line thickness & colour saturation show similarity)

12. The MIBBI Project (mibbi.org)

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. 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. ‘Pedro’ tool → XML → (via XSLT) Wiki code (etc.)

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. MICheckout: Supporting Users

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

20. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-project
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