test_sbo

Tests for SBO terms performed on an instance of cobra.Model.

Module Contents

test_sbo.test_metabolite_sbo_presence(model)[source]

Expect all metabolites to have a some form of SBO-Term annotation.

The Systems Biology Ontology (SBO) allows researchers to annotate a model with terms which indicate the intended function of its individual components. The available terms are controlled and relational and can be viewed here http://www.ebi.ac.uk/sbo/main/tree.

Implementation: Check if each cobra.Metabolite has a non-zero “annotation” attribute that contains the key “sbo”.

test_sbo.test_reaction_sbo_presence(model)[source]

Expect all reactions to have a some form of SBO-Term annotation.

The Systems Biology Ontology (SBO) allows researchers to annotate a model with terms which indicate the intended function of its individual components. The available terms are controlled and relational and can be viewed here http://www.ebi.ac.uk/sbo/main/tree.

Implementation: Check if each cobra.Reaction has a non-zero “annotation” attribute that contains the key “sbo”.

test_sbo.test_gene_sbo_presence(model)[source]

Expect all genes to have a some form of SBO-Term annotation.

The Systems Biology Ontology (SBO) allows researchers to annotate a model with terms which indicate the intended function of its individual components. The available terms are controlled and relational and can be viewed here http://www.ebi.ac.uk/sbo/main/tree.

Check if each cobra.Gene has a non-zero “annotation” attribute that contains the key “sbo”.

test_sbo.test_metabolic_reaction_specific_sbo_presence(model)[source]

Expect all metabolic reactions to be annotated with SBO:0000176.

SBO:0000176 represents the term ‘biochemical reaction’. Every metabolic reaction that is not a transport or boundary reaction should be annotated with this. The results shown are relative to the total amount of pure metabolic reactions.

Implementation: Check if each pure metabolic reaction has a non-zero “annotation” attribute that contains the key “sbo” with the associated value being the SBO term above.

test_sbo.test_transport_reaction_specific_sbo_presence(model)[source]

Expect all transport reactions to be annotated properly.

‘SBO:0000185’, ‘SBO:0000588’, ‘SBO:0000587’, ‘SBO:0000655’, ‘SBO:0000654’, ‘SBO:0000660’, ‘SBO:0000659’, ‘SBO:0000657’, and ‘SBO:0000658’ represent the terms ‘transport reaction’ and ‘translocation reaction’, in addition to their children (more specific transport reaction labels). Every transport reaction that is not a pure metabolic or boundary reaction should be annotated with one of these terms. The results shown are relative to the total of all transport reactions.

Implementation: Check if each transport reaction has a non-zero “annotation” attribute that contains the key “sbo” with the associated value being one of the SBO terms above.

test_sbo.test_metabolite_specific_sbo_presence(model)[source]

Expect all metabolites to be annotated with SBO:0000247.

SBO:0000247 represents the term ‘simple chemical’. Every metabolite should be annotated with this.

Implementation: Check if each cobra.Metabolite has a non-zero “annotation” attribute that contains the key “sbo” with the associated value being one of the SBO terms above.

test_sbo.test_gene_specific_sbo_presence(model)[source]

Expect all genes to be annotated with SBO:0000243.

SBO:0000243 represents the term ‘gene’. Every gene should be annotated with this.

Implementation: Check if each cobra.Gene has a non-zero “annotation” attribute that contains the key “sbo” with the associated value being one of the SBO terms above.

test_sbo.test_exchange_specific_sbo_presence(model)[source]

Expect all exchange reactions to be annotated with SBO:0000627.

SBO:0000627 represents the term ‘exchange reaction’. The Systems Biology Ontology defines an exchange reaction as follows: ‘A modeling process to provide matter influx or efflux to a model, for example to replenish a metabolic network with raw materials (eg carbon / energy sources). Such reactions are conceptual, created solely for modeling purposes, and do not have a physical correspondence. Exchange reactions, often represented as ‘R_EX_’, can operate in the negative (uptake) direction or positive (secretion) direction. By convention, a negative flux through an exchange reaction represents uptake of the corresponding metabolite, and a positive flux represent discharge.’ Every exchange reaction should be annotated with this. Exchange reactions differ from demand reactions in that the metabolites are removed from or added to the extracellular environment only.

Implementation: Check if each exchange reaction has a non-zero “annotation” attribute that contains the key “sbo” with the associated value being one of the SBO terms above.

test_sbo.test_demand_specific_sbo_presence(model)[source]

Expect all demand reactions to be annotated with SBO:0000627.

SBO:0000628 represents the term ‘demand reaction’. The Systems Biology Ontology defines a demand reaction as follows: ‘A modeling process analogous to exchange reaction, but which operates upon “internal” metabolites. Metabolites that are consumed by these reactions are assumed to be used in intra-cellular processes that are not part of the model. Demand reactions, often represented ‘R_DM_’, can also deliver metabolites (from intra-cellular processes that are not considered in the model).’ Every demand reaction should be annotated with this. Demand reactions differ from exchange reactions in that the metabolites are not removed from the extracellular environment, but from any of the organism’s compartments. Demand reactions differ from sink reactions in that they are designated as irreversible.

Implementation: Check if each demand reaction has a non-zero “annotation” attribute that contains the key “sbo” with the associated value being one of the SBO terms above.

test_sbo.test_sink_specific_sbo_presence(model)[source]

Expect all sink reactions to be annotated with SBO:0000632.

SBO:0000632 represents the term ‘sink reaction’. The Systems Biology Ontology defines a sink reaction as follows: ‘A modeling process to provide matter influx or efflux to a model, for example to replenish a metabolic network with raw materials (eg carbon / energy sources). Such reactions are conceptual, created solely for modeling purposes, and do not have a physical correspondence. Unlike the analogous demand (SBO:….) reactions, which are usually designated as irreversible, sink reactions always represent a reversible uptake/secretion processes, and act as a metabolite source with no cost to the cell. Sink reactions, also referred to as R_SINK_, are generally used for compounds that are metabolized by the cell but are produced by non-metabolic, un-modeled cellular processes.’ Every sink reaction should be annotated with this. Sink reactions differ from exchange reactions in that the metabolites are not removed from the extracellular environment, but from any of the organism’s compartments.

Implementation: Check if each sink reaction has a non-zero “annotation” attribute that contains the key “sbo” with the associated value being one of the SBO terms above.

test_sbo.test_biomass_specific_sbo_presence(model)[source]

Expect all biomass reactions to be annotated with SBO:0000629.

SBO:0000629 represents the term ‘biomass production’. The Systems Biology Ontology defines an exchange reaction as follows: ‘Biomass production, often represented ‘R_BIOMASS_’, is usually the optimization target reaction of constraint-based models, and can consume multiple reactants to produce multiple products. It is also assumed that parts of the reactants are also consumed in unrepresented processes and hence products do not have to reflect all the atom composition of the reactants. Formulation of a biomass production process entails definition of the macromolecular content (eg. cellular protein fraction), metabolic constitution of each fraction (eg. amino acids), and subsequently the atomic composition (eg. nitrogen atoms). More complex biomass functions can additionally incorporate details of essential vitamins and cofactors required for growth.’ Every reaction representing the biomass production should be annotated with this.

Implementation: Check if each biomass reaction has a non-zero “annotation” attribute that contains the key “sbo” with the associated value being one of the SBO terms above.