The document discusses the MIBBI Foundry and its modules, which aim to standardize reporting guidelines for various omics technologies and study types. It provides an overview of existing reporting standards, compares different standards, and outlines MIBBI's process for developing standardized modules by breaking down and integrating related reporting guidelines. The goal is to make it easier for studies combining multiple omics technologies or domains to determine which standard(s) to use for reporting.

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