memote.support.annotation module

Supporting functions for annotation checks performed on the model object.

memote.support.annotation.find_components_without_annotation(model, components)[source]

Find model components with empty annotation attributes.

Parameters:

model : cobra.Model

A cobrapy metabolic model.

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

A string denoting cobra.Model components.

Returns:

list

The components without any annotation.

memote.support.annotation.generate_component_annotation_miriam_match(model, components)[source]

Tabulate which MIRIAM databases the component’s annotation match.

Parameters:

model : cobra.Model

A cobrapy metabolic model.

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

A string denoting cobra.Model components.

Returns:

pandas.DataFrame

The index of the table is given by the component identifiers. Each column corresponds to one MIRIAM database and a Boolean entry determines whether the annotation matches.

memote.support.annotation.generate_component_annotation_overview(model, components)[source]

Tabulate which MIRIAM databases the component’s annotation match.

Parameters:

model : cobra.Model

A cobrapy metabolic model.

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

A string denoting cobra.Model components.

Returns:

pandas.DataFrame

The index of the table is given by the component identifiers. Each column corresponds to one MIRIAM database and a Boolean entry determines whether the annotation matches.

memote.support.annotation.generate_component_id_namespace_overview(model, components)[source]

Tabulate which MIRIAM databases the component’s identifier matches.

Parameters:

model : cobra.Model

A cobrapy metabolic model.

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

A string denoting cobra.Model components.

Returns:

pandas.DataFrame

The index of the table is given by the component identifiers. Each column corresponds to one MIRIAM database and a Boolean entry determines whether the annotation matches.