The MIBBI Foundry and its Modules

The MIBBI Foundryand its modules

Chris Taylor, Susanna Sansone, Dawn Field, The MIBBI Project

Project website: http://mibbi.org/

Mechanisms of scientific advance

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%

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

GelsMS MS

FTIR

NMR

Columns

Modelling the biosciences

Modelling the biosciences (slightly differently)

Assay: Omics and miscellaneous techniques

Investigation:

Medical syndrome, environmental effect, etc.Study: Toxicology, environmental science, etc.

Investigation / Study / Assay (ISA) Infrastructurehttp://isa-tools.org/

Ontology of Biomedical Investigations (OBI)http://obi.sourceforge.net/

Functional Genomics Experiment (FuGE)http://fuge.sourceforge.net/

Rise of the Metaprojects

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?

Nature Biotechnol 26(8), 889–896 (2008)

http://dx.doi.org/10.1038/nbt.1411

The MIBBI Project (mibbi.org)

[†] Denotes that a specification is provided as a suite of related documents

CONCEPT SPECIALISATION ● C

IMR [†]

● M

IACA

● M

IAM

E

● M

IAM

E/E

nv

● M

IAM

E/N

utr

● M

IAM

E/P

lant

● M

IAM

E/T

ox

● M

IAPA

● M

IAPE [†]

● M

IARE

● M

IFlo

wCyt

● M

IGen

● M

IGS/M

IMS

● M

IMIx

● M

IMPP

● M

INI

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

The MIBBI Project (mibbi.org)

The MIBBI Project (mibbi.org)

Interaction graph for projects (line thickness & colour saturation show similarity)

The MIBBI Project (mibbi.org)

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.

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)…

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

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)

MICheckout: Supporting Users

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

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