Enrichment

Enrich BEL graphs

In the current build it is possible to enrich BEL graphs containing metabolites with associated disease or protein information and to enrich BEL graphs containing disease or protein information with associated metabolites. This can be done with the functions further explained in BEL Serialization

2. Enriching BEL graphs

Using an BEL graph with metabolites (represented using the HMDB namespace) it can be enriched with disease and protein information from HMDB.

2.1 Metabolites-Proteins

For a graph containing metabolites:

>>> enrich_metabolites_proteins(bel_graph, manager)

The result of this will be a BEL graph which now includes relations between the metabolites and proteins.

For a graph containing proteins (named using uniprot identifiers):

>>> enrich_proteins_metabolites(bel_graph, manager)

This will result in a BEL graph where the proteins are linked to associated metabolites.

2.2 Metabolites-Diseases

For a graph containing metabolites:

>>> enrich_metabolites_diseases(bel_graph, manager)

The result of this will be a BEL graph which now includes relations between the metabolites and diseases.

For a graph containing diseases (named using HMDB identifiers):

>>> enrich_diseases_metabolites(bel_graph, manager)

This will result in a BEL graph where the diseases are linked to associated metabolites.

bio2bel_hmdb.enrich.enrich_diseases_metabolites(graph: pybel.struct.graph.BELGraph, manager: Optional[bio2bel_hmdb.manager.Manager] = None)[source]

Enrich a given BEL graph, which includes HMDB diseases with HMDB metabolites, which are associated to the diseases.

bio2bel_hmdb.enrich.enrich_metabolites_diseases(graph: pybel.struct.graph.BELGraph, manager: Optional[bio2bel_hmdb.manager.Manager] = None)[source]

Enrich a given BEL graph, which includes metabolites with diseases, to which the metabolites are associated.

bio2bel_hmdb.enrich.enrich_metabolites_proteins(graph: pybel.struct.graph.BELGraph, manager: Optional[bio2bel_hmdb.manager.Manager] = None)[source]

Enrich a given BEL graph, which includes metabolites with proteins, that are associated to the metabolites.

bio2bel_hmdb.enrich.enrich_proteins_metabolites(graph: pybel.struct.graph.BELGraph, manager: Optional[bio2bel_hmdb.manager.Manager] = None)[source]

Enrich a given BEL graph, which includes uniprot proteins with HMDB metabolites, that are associated to the proteins.