PhenotypeVocabulary#

class biopax-explorer.biopax.phenotypevocabulary.PhenotypeVocabulary(*args, **kwargs)[source]#

Bases: ControlledVocabulary

Class PhenotypeVocabulary

Definition: The phenotype measured in the experiment e.g. growth rate or

viability of a cell. This is only the type, not the value e.g. for a synthetic lethal interaction, the phenotype is viability, specified by ID: PATO:0000169, “viability”, not the value (specified by ID: PATO:0000718, “lethal (sensu genetics)”. A single term in a phenotype controlled vocabulary can be referenced using the xref, or the PhenoXML describing the PATO EQ model phenotype description can be stored as a string in PATO-DATA.

code generator : rdfobj (author F.Moreews 2023-2024).

Methods

`get_comment`()	Attribute _comment getter
`get_patoData`()	Attribute _patoData getter
`get_term`()	Attribute _term getter
`get_xref`()	Attribute _xref getter

attribute_type_by_name
get_uri_string
object_attributes
set_comment
set_patoData
set_term
set_uri_string
set_xref
to_json
type_attributes

Methods Summary

`attribute_type_by_name`()
`get_patoData`()	Attribute _patoData getter
`get_uri_string`()
`object_attributes`()
`set_patoData`(value)
`set_uri_string`(uristr)
`to_json`()
`type_attributes`()

Methods Documentation

attribute_type_by_name()[source]#

get_patoData()[source]#

Attribute _patoData getter
The phenotype data from PATO, formatted as PhenoXML (defined at

http://www.fruitfly.org/~cjm/obd/formats.html)

get_uri_string()[source]#

object_attributes()[source]#

set_patoData(value)[source]#

set_uri_string(uristr)[source]#

to_json()[source]#

type_attributes()[source]#