Models¶
SQLAlchemy models for Bio2BEL Entrez.
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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.
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taxonomy_id
¶ NCBI Taxonomy Identifier
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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.
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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.
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entrez_id
¶ NCBI Entrez Gene Identifier
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name
¶ Entrez Gene Symbol
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description
¶ Gene Description
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type_of_gene
¶ Type of Gene
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property
bel_encoding
¶ Return the BEL encoding.
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as_bel
(func=None) → pybel.dsl.node_classes.CentralDogma[source]¶ Make a PyBEL DSL object from this gene.
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property
is_transcribed
¶ Return if this gene can be transcribed to an RNA.
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property
is_translated
¶ Return if this gene can be translated to a protein.
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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.
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database
¶ Database name
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value
¶ Database entry name
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