`memote.support.annotation`¶

Supporting functions for annotation checks performed on the model object.

Module Contents¶

`find_components_without_annotation`(model, components)	Find model components with empty annotation attributes.
`generate_component_annotation_overview`(elements, db)	Tabulate which MIRIAM databases the component’s annotation match.
`generate_component_annotation_miriam_match`(elements, component, db)	Tabulate which MIRIAM databases the element’s annotation match.
`generate_component_id_namespace_overview`(model, components)	Tabulate which MIRIAM databases the component’s identifier matches.

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_overview(elements, db)[source]¶

Tabulate which MIRIAM databases the component’s annotation match.

Parameters:	elements : list Elements of a model, either metabolites, reactions, or genes. db : str One of the MIRIAM database identifiers.
Returns:	list The components that are not annotated with the specified MIRIAM database.

memote.support.annotation.generate_component_annotation_miriam_match(elements, component, db)[source]¶

Tabulate which MIRIAM databases the element’s annotation match.

If the relevant MIRIAM identifier is not in an element’s annotation it is ignored.

Parameters:	elements : list Elements of a model, either metabolites or reactions. component : {“metabolites”, “reactions”} A string denoting a type of `cobra.Model` component. db : str One of the MIRIAM database identifiers.
Returns:	list The components whose annotation does not match the pattern for the MIRIAM database.

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.