Models

SQLAlchemy models for Bio2BEL Entrez.

class bio2bel_entrez.models.Species(**kwargs)[source]

Represents a Species.

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.

taxonomy_id

NCBI Taxonomy Identifier

class bio2bel_entrez.models.Homologene(**kwargs)[source]

Represents a HomoloGene Group.

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.

as_bel(func: Optional[str] = None) → pybel.dsl.node_classes.CentralDogma[source]

Make a PyBEL DSL object from this HomoloGene.

class bio2bel_entrez.models.Gene(**kwargs)[source]

Represents a gene.

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.

entrez_id

NCBI Entrez Gene Identifier

name

Entrez Gene Symbol

description

Gene Description

type_of_gene

Type of Gene

property bel_encoding

Return the BEL encoding.

as_bel(func=None) → pybel.dsl.node_classes.CentralDogma[source]

Make a PyBEL DSL object from this gene.

property is_transcribed

Return if this gene can be transcribed to an RNA.

property is_translated

Return if this gene can be translated to a protein.

to_json() → Mapping[str, int][source]

Return this Gene as a JSON dictionary.

class bio2bel_entrez.models.Xref(**kwargs)[source]

Represents a database cross reference.

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.

database

Database name

value

Database entry name