libAnnotationSBML

Neil SwainstonManchester Centre for Integrative Systems Biology

29 March 2009

Introduction

• Library (not a tool) for linking annotated SBML models to MIRIAM and related web services• Writing and reading of annotations

• Java – could be extended

Purpose of annotations

• Provide definitive, unique identifier for “stuff”• One motivation: mapping experimental data to

models• Need annotated models AND annotated data

AnnotationWizard

• Shameless copy of Falko’s semanticSBML– See also SAINT (Allyson)

• Principle:– Iterate through model– Submit each species to an appropriate web service

search facility (ChEBI or UniProt)– Prompt user for confirmation– Update model with annotation

– Has also been wrapped as a web service itself

Annotating models: yeast

• Genome-scale SBML model of yeast metabolism– All 2153 molecules have MIRIAM annotations

Project overview

Enzyme kineticsQuantitativemetabolomics

Quantitativeproteomics

SBML Model

Parameters(KM, Kcat)

Variables(metabolite, proteinconcentrations)

PRIDE MeMo SABIO-RK

Web serviceWeb serviceWeb service

MeMo-RK

KineticsWizard

Project overview

Enzyme kineticsQuantitativemetabolomics

Quantitativeproteomics

SBML Model

Parameters(KM, Kcat)

Variables(metabolite, proteinconcentrations)

PRIDE MeMo SABIO-RK

Web serviceWeb serviceWeb service

MeMo-RK

CellDesigner plugin

Purpose of annotations

• Provide definitive, unique identifier for “stuff”• One motivation: mapping experimental data to

models• Need annotated models AND annotated data• “Tagging”

• More interesting purpose…• Use the annotations to reason over the model

Purpose of annotations

• Easy question• Is my model annotated?• Simple answer: yes• Can be answered solely by libSBML

• More interesting question• Is my model annotated well?• Do my reactions elementally balance?• Simple answer may be yes or no, but harder to

determine• Can’t be determined solely by libSBML

Isn’t ChEBI grrrreat…

<species id=”glc" name="D-Glucose">

<annotation>

<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI:17634"/>

</annotation>

</species>

libAnnotationSBML: what it does

• Provides unified interface to following web services:– ChEBI– KEGG– UniProt– SBO– others…

– Wraps these calls so that it appears that you are accessing these locally

MIRIAM UniProtChEBIKEGG

libAnnotationSBML

SBase annotation OntologyTerm(s)

Determineontology

Map toweb service

OntologyTerm

• Model components can be parsed to return OntologyTerms

• OntologyTerms have the following interface:

• Development of tools to exploit annotations becomes greatly simplified:OntologyTerm[] ots = sbmlUtils.getOntologyTerms( sbase );

OntologyTerm ot = ots[0];

ot.getName(); ot.getSynonyms(); ot.getFormula();

Purpose of annotations: to allow automation of tedious jobs

D-Glyceraldehyde + NAD+ <=> D-Glycerate + NADH + H+

Purpose of annotations: to allow automation of tedious jobs

• Suggest corrections to existing models• Incorrect annotations• Missing reactants / products• Stoichiometry

• Better still: intelligent generation of models?• AutoComplete?

Wish list

• Support more web services• Write it in C++

• WSDLs in MIRIAM??

Wish list

• BUT dynamic linking of models to databases is still a little way off• Web services are inconsistent

getName()? getDescription()? getTitle()?Semantic web services needed

Finally…

• Hopefully makes doing things with annotations easier

• Have a look if you’re interested:• http://mcisb.sourceforge.net

libAnnotationSBML

Neil SwainstonManchester Centre for Integrative Systems Biology

29 March 2009