Models
This module contains the SQLAlchemy database models that support the definition cache and graph cache.
- class pybel.manager.models.Base(**kwargs)
The base class of the class hierarchy.
When called, it accepts no arguments and returns a new featureless instance that has no instance attributes and cannot be given any.
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.
- class pybel.manager.models.Namespace(**kwargs)[source]
Represents a BEL Namespace.
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.
- uploaded
The date of upload
- keyword
Keyword that is used in a BEL file to identify a specific namespace
- pattern
Contains regex pattern for value identification.
- miriam_id
MIRIAM resource identifier matching the regular expression
^MIR:001\d{5}$
- version
Version of the namespace
- url
BELNS Resource location as URL
- name
Name of the given namespace
- domain
Domain for which this namespace is valid
- species
Taxonomy identifiers for which this namespace is valid
- description
Optional short description of the namespace
- created
DateTime of the creation of the namespace definition file
- query_url
URL that can be used to query the namespace (externally from PyBEL)
- author
The author of the namespace
- license
License information
- contact
Contact information
- class pybel.manager.models.NamespaceEntry(**kwargs)[source]
Represents a name within a BEL namespace.
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
Name that is defined in the corresponding namespace definition file
- identifier
The database accession number
- encoding
The biological entity types for which this name is valid
- class pybel.manager.models.Network(**kwargs)[source]
Represents a collection of edges, specified by a BEL Script.
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
Name of the given Network (from the BEL file)
- version
Release version of the given Network (from the BEL file)
- authors
Authors of the underlying BEL file
- contact
Contact email from the underlying BEL file
- description
Descriptive text from the underlying BEL file
- copyright
Copyright information
- disclaimer
Disclaimer information
- licenses
License information
- blob
A pickled version of this network
- classmethod name_contains(name_query)[source]
Build a filter for networks whose names contain the query.
- classmethod description_contains(description_query)[source]
Build a filter for networks whose descriptions contain the query.
- class pybel.manager.models.Node(**kwargs)[source]
Represents a BEL 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.
- type
The type of the represented biological entity e.g. Protein or Gene
- bel
Canonical BEL term that represents the given node
- data
PyBEL BaseEntity as JSON
- class pybel.manager.models.Author(**kwargs)[source]
Contains all author names.
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.
- class pybel.manager.models.Citation(**kwargs)[source]
The information about the citations that are used to prove a specific relation are stored in this 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.
- db
Type of the stored publication e.g. PubMed
- db_id
Reference identifier of the publication e.g. PubMed_ID
- article_type
Type of the publication
- title
Title of the publication
- journal
Journal name
- volume
Volume of the journal
- issue
Issue within the volume
- pages
Pages of the publication
- date
Publication date
- first_id
First author
- last_id
Last author
- class pybel.manager.models.Evidence(**kwargs)[source]
This table contains the evidence text that proves a specific relationship and refers the source that is cited.
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.
- text
Supporting text from a given publication
- class pybel.manager.models.Edge(**kwargs)[source]
Relationships between BEL nodes and their properties, annotations, and provenance.
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.
- bel
Valid BEL statement that represents the given edge
- source_modifier
Modifiers for the source of the edge
- target_modifier
Modifiers for the target of the edge
- md5
The hash of the source, target, and associated metadata
- data
The stringified JSON representing this edge