Models

Database models.

Reactome database model.

class bio2bel_reactome.models.Species(**kwargs)

Species Table.

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.

name

NCBI taxonomy label

taxonomy_id

NCBI taxonomy identifier

class bio2bel_reactome.models.Protein(**kwargs)

Protein Table.

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.

to_pybel() → pybel.dsl.node_classes.Protein

Serialize to PyBEL node data dictionary.

class bio2bel_reactome.models.Chemical(**kwargs)

Chemical Table.

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.

to_pybel() → pybel.dsl.node_classes.Abundance

Serialize to PyBEL node data dictionary.

class bio2bel_reactome.models.Pathway(**kwargs)

A reactome pathway.

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.