Manager¶
Bio2BEL HGNC Manager.
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class
bio2bel_hgnc.manager.
Manager
(*args, **kwargs)[source]¶ Human gene nomenclature and orthologies to mouse and rat.
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add_central_dogma
(graph: pybel.struct.graph.BELGraph, node: pybel.dsl.node_classes.BaseEntity) → Optional[pybel.dsl.node_classes.CentralDogma][source]¶ Add the central dogma of biology.
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add_namespace_to_graph
(graph: pybel.struct.graph.BELGraph)[source]¶ Add this manager’s namespace to the graph.
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build_entrez_id_to_hgnc_id_mapping
() → Mapping[str, str][source]¶ Build a mapping from Entrez gene identifier to HGNC identifier.
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build_entrez_id_to_hgnc_symbol_mapping
() → Mapping[str, str][source]¶ Build a mapping from Entrez gene identifier to HGNC gene symbols.
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build_hgnc_id_symbol_mapping
() → Mapping[str, str][source]¶ Build a mapping from HGNC identifiers to HGNC gene symbols.
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build_hgnc_symbol_entrez_id_mapping
() → Mapping[str, str][source]¶ Build a mapping from HGNC symbol to ENTREZ identifier.
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build_hgnc_symbol_id_mapping
() → Mapping[str, str][source]¶ Build a mapping from HGNC gene symbols to HGNC identifiers.
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build_uniprot_id_hgnc_id_mapping
() → Mapping[str, str][source]¶ Build a mapping from UniProt identifiers to HGNC identifiers.
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build_uniprot_id_hgnc_symbol_mapping
() → Mapping[str, str][source]¶ Build a mapping from UniProt identifiers to HGNC gene symbols.
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enrich_families_with_genes
(graph: pybel.struct.graph.BELGraph)[source]¶ Enrich gene families in the BEL graph with their member genes.
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enrich_genes_with_equivalences
(graph: pybel.struct.graph.BELGraph) → None[source]¶ Enrich genes with their corresponding UniProt.
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enrich_genes_with_families
(graph: pybel.struct.graph.BELGraph) → None[source]¶ Enrich genes in the BEL graph with their families.
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enrich_hgnc_with_entrez_equivalences
(graph: pybel.struct.graph.BELGraph)[source]¶ Add equivalent Entrez nodes for all HGNC genes.
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get_all_hgnc_symbols_family
() → Set[str][source]¶ Get all Gene symbols that appear in gene families.
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get_enzyme_by_ec_number
(ec_number: str) → Optional[pyhgnc.manager.models.HGNC][source]¶ Get a enzyme by its associated EC number.
- Parameters
ec_number – EC number
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get_family_by_id
(family_identifier: str) → Optional[pyhgnc.manager.models.GeneFamily][source]¶ Get a gene family by its hgnc.genefamily identifier, if it exists.
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get_family_by_name
(family_name: str) → Optional[pyhgnc.manager.models.GeneFamily][source]¶ Get a gene family by its name, if it exists.
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get_gene_by_ensembl_id
(ensembl_id: str) → Optional[pyhgnc.manager.models.HGNC][source]¶ Get a human gene by its ENSEMBL gene identifier.
- Parameters
ensembl_id – The ENSEMBL gene identifier
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get_gene_by_entrez_id
(entrez_id: str) → Optional[pyhgnc.manager.models.HGNC][source]¶ Get a human gene by its Entrez gene identifier.
- Parameters
entrez_id – The Entrez gene identifier
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get_gene_by_hgnc_id
(hgnc_id: str) → Optional[pyhgnc.manager.models.HGNC][source]¶ Get a human gene by HGNC identifier.
- Parameters
hgnc_id – The HGNC gene identifier
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get_gene_by_hgnc_symbol
(hgnc_symbol: str) → Optional[pyhgnc.manager.models.HGNC][source]¶ Get a human gene by HGNC symbol.
- Parameters
hgnc_symbol – The HGNC gene symbol
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get_gene_by_mgi_id
(mgi_id: str) → Optional[pyhgnc.manager.models.HGNC][source]¶ Get a human gene by an orthologous MGI identifier.
- Parameters
mgi_id – MGI identifier
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get_gene_by_rgd_id
(rgd_id: str) → Optional[pyhgnc.manager.models.HGNC][source]¶ Get a human gene by an orthologous RGD identifier.
- Parameters
rgd_id – RGD identifier
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get_gene_by_uniprot_id
(uniprot_id: str) → Optional[pyhgnc.manager.models.HGNC][source]¶ Get a human gene by its UniProt gene identifier.
- Parameters
uniprot_id – The UniProt gene identifier
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get_hgnc_from_alias_symbol
(alias_symbol: str) → Optional[pyhgnc.manager.models.HGNC][source]¶ Get HGNC from alias symbol.
- Parameters
alias_symbol – alias symbol
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get_node
(node: pybel.dsl.node_classes.BaseEntity) → Optional[pyhgnc.manager.models.HGNC][source]¶ Get a node from the database, whether it has a HGNC, RGD, MGI, or EG identifier.
- Parameters
node – The node to look for
- Raises
KeyError
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property
hgnc_symbol_entrez_id_mapping
¶ Get a mapping from Entrez gene identifiers to HGNC gene symbols.
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iter_genes
(graph: pybel.struct.graph.BELGraph, use_tqdm: bool = False) → Iterable[Tuple[pybel.dsl.node_classes.BaseEntity, pyhgnc.manager.models.HGNC]][source]¶ Iterate over pairs of BEL nodes and HGNC genes.
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namespace_model
¶ alias of
pyhgnc.manager.models.HGNC
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normalize_genes
(graph: pybel.struct.graph.BELGraph, use_tqdm: bool = False) → None[source]¶ Add identifiers to all HGNC genes.
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