The Subliminal Toolbox: automating steps in the reconstruction of metabolic networks

The Subliminal Toolbox: automating steps in the reconstruction of metabolic networks Neil Swainston Manchester Centre for Integrative Systems Biology 1st Conference on Constraint-based Reconstruction and Analysis Reykjavik, Iceland 24 June2011

Automation
Many of these steps can be automated
Subliminal Toolbox
How much of the reconstruction process can be aided by publicly available resources?
Manual curation still necessary
BUT reduce what needs to be done
Relies on semantic model annotations
e.g. ChEBI , KEGG terms for metabolites
UniProt terms for enzymes

Model annotations
Model annotations provide unambiguous, unique identifiers for model components
Not very interesting
But – also provide link to chem/bioinformatics resources via web services
Automatically extract data through web services
Potentially more interesting / useful

Publicly available resources Formula, Charge, Structure GPR relationships Compartment data Sequence, Metadata Web services

Subliminal Toolbox

Protonate
ChEBI provides web service access to structural data
InChI , SMILES strings
Cheminformatics software (ChemAxon) can be used to predict charge state at given pH
Updates FORMULA , CHARGE , metabolite name and annotation
Consistency – facilitates merging
✓ ✗

Balance
Reaction elemental and charge balancing
Prevents mass violation and stoichiometric inconsistencies
Reactions in resources don ’ t always balance
Incorrect stoichiometry
Missing protons, water, etc.
Solution: extract formulae and charges and apply linear programming

Balance carbon dioxide + 2-Acetolacetate  Pyruvate Ab = 0 A = b represents a vector of stoichiometries CO 2 + C 5 H 7 O 4 -  C 3 H 3 O 3 - Reactants Products Optional reactants Optional products CO2 C5H7O4 C3H3O3 H+ H20 H+ H20 CO2 C 1 5 -3 0 0 0 0 -1 O 2 4 -3 0 1 0 -1 -2 H 0 7 -3 1 2 -1 -2 0 charge 0 -1 1 1 0 -1 0 0 b min T 1 1 1 0 0 0 0 0

Balance
Linear programming solver solves Ab = 0
carbon dioxide + 2-Acetolacetate  2 Pyruvate + H + CO 2 + C 5 H 7 O 4 -  2 C 3 H 3 O 3 - + H + Reactants Products Optional reactants Optional products CO2 C5H7O4 C3H3O3 H+ H20 H+ H20 CO2 C 1 5 -3 0 0 0 0 -1 O 2 4 -3 0 1 0 -1 -2 H 0 7 -3 1 2 -1 -2 0 charge 0 -1 1 1 0 -1 0 0 b min T 1 1 1 0 0 0 0 0 b T 1 1 2 0 0 1 0 0

Merge
Works on simple premises
Metabolites / enzymes are the same if the share the same annotation and compartment
Reactions are the same if the have the same stoichiometry
Hence balancing
Isoenzymes collated ( “ OR ” relationship in GPR definition)

“ Fuzzy ” Merge
Sources can be inconsistent in their definition of stereochemical precision
Considered different: apparently minor but can cause gaps in the network
beta-D-glucose D-glucose

“ Fuzzy ” Merge
ChEBI is an ontology and contains relationships between metabolites
Edges not just nodes

Compartment
Determination of intracellular compartment in which enzymes operate
Two approaches:
Extract curated information from UniProt annotation
Extract protein sequence from UniProt and pipe to WoLF PSORT localisation prediction algorithm
Infer reaction localisation from enzyme localisation
Hypothetical transport reactions added to be validated / deleted in manual curation phase

Transporters and biomass
Extracellular and intracellular transporters are required
TransportDB and Transporter Classification DB are sources of transporter proteins
BUT not comprehensive enough to automatically assign these to individual reactions
Biomass reaction should be added manually
Automation breaks down…

Shorthand Converted to SBML, protonated, balanced and merged as before

Usage and availability
Java programming API
Simple command line interface
SBML file in / SBML file out
Has some dependencies on third-party software
Free to academic users
http://www.mcisb.org/subliminal/

Thanks…

The Subliminal Toolbox: automating steps in the reconstruction of metabolic networks Neil Swainston Manchester Centre for Integrative Systems Biology 1st Conference on Constraint-based Reconstruction and Analysis Reykjavik, Iceland 24 June 2011

UniProt compartmentalisation

UniProt compartmentalisation UniProt curated information

PSORT compartmentalisation

PSORT compartmentalisation WoLF PSORT prediction

The Subliminal Toolbox: automating steps in the reconstruction of metabolic networks

by Neil Swainston

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The Subliminal Toolbox: automating steps in the reconstruction of metabolic networks Presentation Transcript