Models

SQLAlchemy models for Bio2BEL ExPASy.

class bio2bel_expasy.models.Enzyme(**kwargs)

ExPASy’s main entry.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

expasy_id

The ExPASy enzyme code.

description

The ExPASy enzyme description. May need context of parents.

level

Return what level (1, 2, 3, or 4) this enzyme is based on the number of dashes in its id.

to_json() → Mapping

Return the data from this model as a dictionary.

as_bel() → pybel.dsl.node_classes.Protein

Return a PyBEL node representing this enzyme.

class bio2bel_expasy.models.Prosite(**kwargs)

Maps ec to prosite entries.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

prosite_id

ProSite Identifier

as_bel() → pybel.dsl.node_classes.Protein

Return a PyBEL node data dictionary representing this ProSite entry.

class bio2bel_expasy.models.Protein(**kwargs)

Maps enzyme to SwissProt or UniProt.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

accession_number

UniProt accession number

entry_name

UniProt entry name.

as_bel() → pybel.dsl.node_classes.Protein

Return a PyBEL node data dictionary representing this UniProt entry.