Enrichment

Manager for Bio2BEL GO.

bio2bel_go.manager.add_parents(go, identifier: str, graph: pybel.struct.graph.BELGraph, child: pybel.dsl.node_classes.BaseEntity)

Add parents to the network.

Parameters:

• go – GO Network
• identifier – GO Identifier of the child
• graph – A BEL graph
• child – A BEL node

bio2bel_go.manager.normalize_go_id(identifier: str) → str

If a GO term does not start with the GO: prefix, add it.

class bio2bel_go.manager.Manager(*args, **kwargs)

Biological process multi-hierarchy.

namespace_model

alias of bio2bel_go.models.Term

is_populated() → bool

Check if the database is already populated.

get_term_by_id(go_id: str) → Optional[bio2bel_go.models.Term]

Get a GO entry by its identifier.

get_term_by_name(name: str) → Optional[bio2bel_go.models.Term]

Get a GO entry by name.

populate(path=None, force_download=False) → None

Populate the database.

Parameters:

• path – Path to the GO OBO file
• force_download –

count_terms() → int

Count the number of entries in GO.

count_synonyms() → int

Count the number of synonyms in GO.

count_hierarchies() → int

Count the number of synonyms in GO.

list_hierarchies() → List[bio2bel_go.models.Hierarchy]

List hierarchy entries.

count_annotations() → int

Count the number of annotations.

list_annotations() → List[bio2bel_go.models.Annotation]

List annotation entries.

summarize() → Mapping[str, int]

Return a summary dictionary over the content of the database.

lookup_term(node: pybel.dsl.node_classes.BaseEntity) → Optional[bio2bel_go.models.Term]

Guess the identifier from a PyBEL node data dictionary.

iter_terms(graph: pybel.struct.graph.BELGraph, use_tqdm: bool = False) → Iterable[Tuple[pybel.dsl.node_classes.BaseEntity, bio2bel_go.models.Term]]

Iterate over nodes in the graph that can be looked up.

normalize_terms(graph: pybel.struct.graph.BELGraph, use_tqdm: bool = False) → None

Add identifiers to all GO terms.

enrich_bioprocesses(graph: pybel.struct.graph.BELGraph, use_tqdm: bool = False) → None

Enrich a BEL graph’s biological processes.

get_release_date() → str

Convert the OBO release date to a ISO 8601 version.

Example: ‘releases/2017-03-26’

to_bel() → pybel.struct.graph.BELGraph

Convert Gene Ontology to BEL, with given strategies.