memote.support.sbo

Supporting functions for sbo checks performed on the model object.

Module Contents

Functions

find_components_without_sbo_terms(model, components) Find model components that are not annotated with any SBO terms.
check_component_for_specific_sbo_term(items, term) Identify model components that lack a specific SBO term(s).
memote.support.sbo.LOGGER[source]
memote.support.sbo.find_components_without_sbo_terms(model, components)[source]

Find model components that are not annotated with any SBO terms.

Parameters:
model : cobra.Model

The metabolic model under investigation.

components : {“metabolites”, “reactions”, “genes”}

A string denoting cobra.Model components.

Returns:
list

The components without any SBO term annotation.

memote.support.sbo.check_component_for_specific_sbo_term(items, term)[source]

Identify model components that lack a specific SBO term(s).

Parameters:
items : list

A list of model components i.e. reactions to be checked for a specific SBO term.

term : str or list of str

A string denoting a valid SBO term matching the regex ‘^SBO:d{7}$’ or a list containing such string elements.

Returns:
list

The components without any or that specific SBO term annotation.