Models

SQLAlchemy models for Bio2BEL miRTarBase.

class bio2bel_mirtarbase.models.Species(**kwargs)

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

The NCBI taxonomy identifier

name

The scientific name for the species

to_json(include_id: bool = True) → Mapping

Serialize to JSON.

Parameters

include_id – Include the database identifier?

class bio2bel_mirtarbase.models.Mirna(**kwargs)

Create mirna table that stores information about the miRNA.

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

miRTarBase name

mirbase_id

miRBase identifier

entrez_id

Entrez Gene identifier

species_id

The host species

as_bel() → pybel.dsl.node_classes.MicroRna

Serialize to a PyBEL node data dictionary.

static filter_name_in(names: Iterable[str])

Build a name filter.

class bio2bel_mirtarbase.models.Target(**kwargs)

Represents a target RNA.

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

Target gene name

entrez_id

Entrez gene identifier

hgnc_symbol

HGNC gene symbol

hgnc_id

HGNC gene identifier

species_id

The host species

serialize_to_entrez_node() → pybel.dsl.node_classes.Rna

Serialize to PyBEL node data dictionary.

serialize_to_hgnc_node() → pybel.dsl.node_classes.Rna

Serialize to PyBEL node data dictionary.

to_json(include_id=True) → Mapping

Return this object as JSON.

class bio2bel_mirtarbase.models.Interaction(**kwargs)

Build Interaction table used to store miRNA and target relations.

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.

mirtarbase_id

miRTarBase interaction identifier which is unique for a pair of miRNA and RNA targets

mirna_id

The miRTarBase identifier of the interacting miRNA

target_id

The Entrez gene identifier of the interacting RNA

class bio2bel_mirtarbase.models.Evidence(**kwargs)

Build Evidence table used to store MTI’s and their evidence.

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.

experiment

Experiments made to find miRNA - target interaction. E.g. ‘Luciferase reporter assay//qRT-PCR//Western blot’

support

Type and strength of the miRNA - target interaction. E.g. ‘Functional MTI (Weak)’

reference

Reference PubMed Identifier

interaction_id

The interaction for which this evidence was captured

add_to_graph(graph: pybel.struct.graph.BELGraph) → str

Add this edge to the BEL graph and return the ket for that edge.