Manager

Manager for Bio2BEL ExPASy.

class bio2bel_expasy.manager.Manager(*args, **kwargs)

Creates a connection to database and a persistent session using SQLAlchemy.

namespace_model

alias of bio2bel_expasy.models.Enzyme

id_enzyme = None

Maps canonicalized ExPASy enzyme identifiers to their SQLAlchemy models

is_populated() → bool

Check if the database is already populated.

count_enzymes() → int

Count the number of enzyme entries in the database.

count_enzyme_prosites() → int

Count the number of enzyme-prosite annotations.

count_prosites() → int

Count the number of ProSite entries in the database.

count_enzyme_proteins() → int

Count the number of enzyme-protein annotations.

count_proteins() → int

Count the number of protein entries in the database.

summarize() → Mapping[str, int]

Return a summary dictionary over the content of the database.

get_or_create_enzyme(expasy_id: str, description: Optional[str] = None) → bio2bel_expasy.models.Enzyme

Get an enzyme from the database or creates it.

get_or_create_prosite(prosite_id: str, **kwargs) → bio2bel_expasy.models.Prosite

Get a prosite from the database or creates it.

get_or_create_protein(accession_number: str, entry_name: str, **kwargs) → bio2bel_expasy.models.Protein

Get a protein by its UniProt accession or create it.

Parameters:

• accession_number –
• entry_name –
• kwargs –

populate(tree_path: Optional[str] = None, database_path: Optional[str] = None) → None

Populate the database..

Parameters:

• tree_path –
• database_path –

populate_tree(path: Optional[str] = None, force_download: bool = False) → None

Download and populate the ExPASy tree.

Parameters:

• path – A custom url to download
• force_download – If true, overwrites a previously cached file

populate_database(path: Optional[str] = None, force_download: bool = False) → None

Populate the ExPASy database.

Parameters:

• path – A custom url to download
• force_download – If true, overwrites a previously cached file

get_enzyme_by_id(expasy_id: str) → Optional[bio2bel_expasy.models.Enzyme]

Get an enzyme by its ExPASy identifier.

Implementation note: canonicalizes identifier to remove all spaces first.

Parameters:expasy_id – An ExPASy identifier. Example: 1.3.3.- or 1.3.3.19

get_parent_by_expasy_id(expasy_id: str) → Optional[bio2bel_expasy.models.Enzyme]

Return the parent ID of ExPASy identifier if exist otherwise returns None.

Parameters:expasy_id – An ExPASy identifier

get_children_by_expasy_id(expasy_id: str) → Optional[List[bio2bel_expasy.models.Enzyme]]

Return a list of enzymes which are children of the enzyme with the given ExPASy enzyme identifier.

Parameters:expasy_id – An ExPASy enzyme identifier

get_protein_by_uniprot_id(uniprot_id: str) → Optional[bio2bel_expasy.models.Protein]

Get a protein having the given UniProt identifier.

Parameters:uniprot_id – A UniProt identifier

>>> from bio2bel_expasy import Manager
>>> manager = Manager()
>>> protein = manager.get_protein_by_uniprot_id('Q6AZW2')
>>> protein.accession_number
'Q6AZW2'

get_prosite_by_id(prosite_id: str) → Optional[bio2bel_expasy.models.Prosite]

Get a ProSite having the given ProSite identifier.

Parameters:prosite_id – A ProSite identifier

get_prosites_by_expasy_id(expasy_id: str) → Optional[List[bio2bel_expasy.models.Prosite]]

Get a list of ProSites associated with the enzyme corresponding to the given identifier.

Parameters:expasy_id – An ExPASy identifier

get_enzymes_by_prosite_id(prosite_id: str) → Optional[List[bio2bel_expasy.models.Enzyme]]

Return a list of enzymes associated with the given ProSite ID.

Parameters:prosite_id – ProSite identifier

get_proteins_by_expasy_id(expasy_id: str) → Optional[List[bio2bel_expasy.models.Protein]]

Return a list of UniProt entries as tuples (accession_number, entry_name) of the given enzyme_id.

Parameters:expasy_id – An ExPASy identifier

get_enzymes_by_uniprot_id(uniprot_id: str) → Optional[List[bio2bel_expasy.models.Enzyme]]

Return a list of enzymes annotated to the protein with the given UniProt accession number.

Parameters:uniprot_id – A UniProt identifier

Example:

>>> from bio2bel_expasy import Manager
>>> manager = Manager()
>>> manager.get_enzymes_by_uniprot_id('Q6AZW2')
>>> ...

enrich_proteins_with_enzyme_families(graph: pybel.struct.graph.BELGraph) → None

Enrich proteins in the BEL graph with IS_A relations to their enzyme classes.

1. Gets a list of UniProt proteins
2. Annotates pybel.constants.IS_A relations for all enzyme classes it finds

look_up_enzyme(node: pybel.dsl.node_classes.BaseEntity) → Optional[bio2bel_expasy.models.Enzyme]

Try to get an enzyme model from the given node.

enrich_enzyme_with_proteins(graph: pybel.struct.graph.BELGraph, node: pybel.dsl.node_classes.BaseEntity) → None

Enrich an enzyme with all of its member proteins.

enrich_enzyme_parents(graph: pybel.struct.graph.BELGraph, node: pybel.dsl.node_classes.BaseEntity) → None

Enrich an enzyme with its parents.

enrich_enzyme_children(graph: pybel.struct.graph.BELGraph, node: pybel.dsl.node_classes.BaseEntity) → None

Enrich an enzyme with all of its children.

enrich_enzymes(graph: pybel.struct.graph.BELGraph) → None

Add all children of entries.

enrich_enzymes_with_prosites(graph: pybel.struct.graph.BELGraph) → None

Enrich enzyme classes in the graph with ProSites.