Bio2BEL GO¶
Bio2BEL GO.
Enrichment¶
Manager for Bio2BEL GO.
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bio2bel_go.manager.
add_parents
(go, identifier: str, graph: pybel.struct.graph.BELGraph, child: pybel.dsl.node_classes.BaseEntity)[source]¶ Add parents to the network.
Parameters: - go – GO Network
- identifier – GO Identifier of the child
- graph – A BEL graph
- child – A BEL node
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bio2bel_go.manager.
normalize_go_id
(identifier: str) → str[source]¶ If a GO term does not start with the
GO:
prefix, add it.
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class
bio2bel_go.manager.
Manager
(*args, **kwargs)[source]¶ Biological process multi-hierarchy.
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namespace_model
¶ alias of
bio2bel_go.models.Term
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get_term_by_id
(go_id: str) → Optional[bio2bel_go.models.Term][source]¶ Get a GO entry by its identifier.
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populate
(path=None, force_download=False) → None[source]¶ Populate the database.
Parameters: - path – Path to the GO OBO file
- force_download –
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summarize
() → Mapping[str, int][source]¶ Return a summary dictionary over the content of the database.
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lookup_term
(node: pybel.dsl.node_classes.BaseEntity) → Optional[bio2bel_go.models.Term][source]¶ Guess the identifier from a PyBEL node data dictionary.
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iter_terms
(graph: pybel.struct.graph.BELGraph, use_tqdm: bool = False) → Iterable[Tuple[pybel.dsl.node_classes.BaseEntity, bio2bel_go.models.Term]][source]¶ Iterate over nodes in the graph that can be looked up.
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normalize_terms
(graph: pybel.struct.graph.BELGraph, use_tqdm: bool = False) → None[source]¶ Add identifiers to all GO terms.
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enrich_bioprocesses
(graph: pybel.struct.graph.BELGraph, use_tqdm: bool = False) → None[source]¶ Enrich a BEL graph’s biological processes.
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Constants¶
Constants for Bio2BEL GO.
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bio2bel_go.constants.
GO_OBO_URL
= 'http://purl.obolibrary.org/obo/go/go-basic.obo'¶ The web location of the GO OBO file
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bio2bel_go.constants.
GO_OBO_PATH
= '/home/docs/.bio2bel/go/go-basic.obo'¶ The local cache location where the GO OBO file is stored
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bio2bel_go.constants.
GO_OBO_PICKLE_PATH
= '/home/docs/.bio2bel/go/go-basic.obo.gpickle'¶ The local cache location where the parsed and pickled GO OBO file is stored
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bio2bel_go.constants.
GAF_COLUMNS
= ['db', 'db_id', 'db_symbol', 'qualifier', 'go_id', 'provenance', 'evidence_code', 'modifications', 'aspect', 'db_label', 'db_synonym', 'db_type', 'taxonomy_id', 'date', 'assigned_by', 'annotation_extensions', 'gene_product_id']¶ GAF columns, see: http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/