Source code for PyOpenWorm.channel
import rdflib as R
from .dataObject import DatatypeProperty, ObjectProperty, Alias
from .channelworm import ChannelModel
from .biology import BiologyType
from .channel_common import CHANNEL_RDF_TYPE
from .cell_common import CELL_RDF_TYPE
[docs]class ExpressionPattern(BiologyType):
class_context = BiologyType.class_context
wormbaseid = DatatypeProperty()
''' The ID for the expression pattern in Wormbase '''
wormbaseID = Alias(wormbaseid)
''' Alias to `wormbaseid` '''
wormbaseURL = DatatypeProperty()
''' The URL for the expression pattern in Wormbase '''
description = DatatypeProperty()
''' Natural language description of the expression pattern '''
def __init__(self, wormbaseid=None, **kwargs):
super(ExpressionPattern, self).__init__(**kwargs)
if wormbaseid:
self.wormbaseid(wormbaseid)
self.wormbaseURL(R.URIRef("http://www.wormbase.org/species/all/expr_pattern/" + wormbaseid))
[docs] def defined_augment(self):
return self.wormbaseid.has_defined_value()
[docs] def identifier_augment(self):
return self.make_identifier(self.wormbaseid.defined_values[0])
[docs]class Channel(BiologyType):
"""
A biological ion channel.
Attributes
----------
Models : Property
"""
class_context = BiologyType.class_context
rdf_type = CHANNEL_RDF_TYPE
subfamily = DatatypeProperty()
''' Ion channel's subfamily '''
name = DatatypeProperty()
''' Ion channel's name '''
description = DatatypeProperty()
''' A description of the ion channel '''
gene_name = DatatypeProperty()
''' Name of the gene that codes for this ion channel '''
gene_class = DatatypeProperty()
''' Classification of the encoding gene '''
gene_WB_ID = DatatypeProperty()
''' Wormbase ID of the encoding gene '''
expression_pattern = ObjectProperty(multiple=True,
value_type=ExpressionPattern)
''' A pattern of expression of this cell within an organism '''
neuroml_file = DatatypeProperty()
''' A NeuroML describing a model of this ion channel '''
proteins = DatatypeProperty(multiple=True)
''' Proteins associated with this channel '''
appearsIn = ObjectProperty(multiple=True, value_rdf_type=CELL_RDF_TYPE)
''' Cell types in which the ion channel has been expressed '''
model = ObjectProperty(value_type=ChannelModel)
''' Get experimental models of this ion channel '''
def __init__(self, name=None, **kwargs):
super(Channel, self).__init__(name=name, **kwargs)
[docs] def defined_augment(self):
return self.name.has_defined_value()
[docs] def identifier_augment(self):
return self.make_identifier(self.name.defined_values[0])
__yarom_mapped_classes__ = (Channel, ExpressionPattern)