Models

SQLAlchemy database models for Bio2BEL InterPro.

class bio2bel_interpro.models.Type(**kwargs)

InterPro Entry Type.

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

The InterPro entry type

class bio2bel_interpro.models.Protein(**kwargs)

Represents proteins that are annotated to InterPro families.

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.

uniprot_id

UniProt identifier

as_bel() → pybel.dsl.node_classes.Protein

Return this protein as a PyBEL node.

class bio2bel_interpro.models.GoTerm(**kwargs)

Represents a GO term.

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.

go_id

Gene Ontology identifier

name

Label

class bio2bel_interpro.models.Entry(**kwargs)

Represents families, domains, etc. in InterPro.

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.

interpro_id

The InterPro identifier

name

The InterPro entry name

as_bel() → pybel.dsl.node_classes.Protein

Return this InterPro entry as a PyBEL node.

class bio2bel_interpro.models.Annotation(**kwargs)

Mapping of InterPro to protein.

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.

start

Starting position on reference sequence of annotation

end

Ending position on reference sequence of annotation