Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Y
|
Z
A
add_graph() (PyOpenWorm.command.POW method)
add_reference() (PyOpenWorm.data.DataUser method)
add_statements() (PyOpenWorm.data.DataUser method)
after_mapper_module_load() (PyOpenWorm.dataObject.ContextMappedClass method)
aneuron() (PyOpenWorm.network.Network method)
author (PyOpenWorm.document.Document attribute)
author() (in module PyOpenWorm.bibtex)
B
BadConf
BaseDataObject (class in PyOpenWorm.dataObject)
BaseDataTranslator (class in PyOpenWorm.datasource)
BaseDocument (class in PyOpenWorm.document)
bibtex_to_document() (in module PyOpenWorm.bibtex)
BibTexDataSource (class in PyOpenWorm.bibtex)
BibTexDataTranslator (class in PyOpenWorm.bibtex)
BiologyType (class in PyOpenWorm.biology)
blast() (PyOpenWorm.cell.Cell method)
C
Cell (class in PyOpenWorm.cell)
Channel (class in PyOpenWorm.channel)
ChannelModel (class in PyOpenWorm.channelworm)
clear() (PyOpenWorm.simpleProperty.RealSimpleProperty method)
clear_po_cache() (PyOpenWorm.dataObject.BaseDataObject method)
clone() (PyOpenWorm.command.POW method)
closeDatabase() (PyOpenWorm.data.Data method)
commit() (PyOpenWorm.command.POW method)
config() (in module PyOpenWorm)
config_file (PyOpenWorm.command.POW attribute)
Configure (class in PyOpenWorm.configure)
Configureable (class in PyOpenWorm.configure)
ConfigValue (class in PyOpenWorm.configure)
connect() (in module PyOpenWorm)
Connection (class in PyOpenWorm.connection)
ConnectionProperty (class in PyOpenWorm.neuron)
ConnectomeCSVDataSource (class in PyOpenWorm.data_trans.connections)
Context (class in PyOpenWorm.context)
ContextContextManager (class in PyOpenWorm.context)
ContextDataObject (class in PyOpenWorm.contextDataObject)
ContextMappedClass (class in PyOpenWorm.dataObject)
ContextMappedPropertyClass (class in PyOpenWorm.simpleProperty)
ContextMeta (class in PyOpenWorm.context)
ContextStoreException
Contextualizable (class in PyOpenWorm.contextualize)
ContextualizableClass (class in PyOpenWorm.contextualize)
contextualize_helper() (in module PyOpenWorm.contextualize)
copy() (PyOpenWorm.configure.Configure method)
CSVDataSource (class in PyOpenWorm.data_trans.csv_ds)
CSVDataTranslator (class in PyOpenWorm.data_trans.csv_ds)
customizations() (in module PyOpenWorm.bibtex)
D
Data (class in PyOpenWorm.data)
data_source_type (PyOpenWorm.bibtex.BibTexDataTranslator attribute)
DataObject (class in PyOpenWorm.dataObject)
DataObjectContextDataSource (class in PyOpenWorm.datasource)
DataSource (class in PyOpenWorm.datasource)
DataSourceType (class in PyOpenWorm.datasource)
DataTransatorType (class in PyOpenWorm.datasource)
DataTranslator (class in PyOpenWorm.datasource)
DatatypeProperty (class in PyOpenWorm.simpleProperty)
DatatypeProperty() (PyOpenWorm.dataObject.BaseDataObject class method)
DataUser (class in PyOpenWorm.data)
DataWithEvidenceDataSource (class in PyOpenWorm.data_trans.data_with_evidence_ds)
date (PyOpenWorm.document.Document attribute)
decontextualize() (PyOpenWorm.dataObject.BaseDataObject method)
decontextualize_helper() (in module PyOpenWorm.contextualize)
DefaultSource (class in PyOpenWorm.data)
defined_augment() (PyOpenWorm.cell.Cell method)
(PyOpenWorm.data_trans.connections.NeuronConnectomeCSVTranslation method)
(PyOpenWorm.data_trans.wormatlas.WormAtlasCellListDataTranslation method)
(PyOpenWorm.datasource.DataSource method)
(PyOpenWorm.datasource.GenericTranslation method)
(PyOpenWorm.datasource.Translation method)
(PyOpenWorm.document.Document method)
(PyOpenWorm.evidence.Evidence method)
(PyOpenWorm.network.Network method)
(PyOpenWorm.relationship.Relationship method)
(PyOpenWorm.website.Website method)
(PyOpenWorm.worm.Worm method)
definition_context (PyOpenWorm.dataObject.ContextMappedClass attribute)
description (PyOpenWorm.cell.Cell attribute)
diff() (PyOpenWorm.command.POW method)
disconnect() (in module PyOpenWorm)
divisionVolume (PyOpenWorm.cell.Cell attribute)
Document (class in PyOpenWorm.document)
DocumentContext (class in PyOpenWorm.documentContext)
DocumentContextMeta (class in PyOpenWorm.documentContext)
doi (PyOpenWorm.document.Document attribute)
doi() (in module PyOpenWorm.bibtex)
DuplicateAlsoException
E
Evidence (class in PyOpenWorm.evidence)
EvidenceError
Experiment (class in PyOpenWorm.experiment)
ExpressionPattern (class in PyOpenWorm.channel)
F
fetch_graph() (PyOpenWorm.command.POW method)
G
generate() (PyOpenWorm.my_neuroml.NeuroML class method)
GenericTranslation (class in PyOpenWorm.datasource)
get() (PyOpenWorm.configure.Configure method)
(PyOpenWorm.configure.Configureable method)
(PyOpenWorm.neuron.ConnectionProperty method)
(PyOpenWorm.neuron.Neighbor method)
(PyOpenWorm.pProperty.Property method)
get_conditions() (PyOpenWorm.experiment.Experiment method)
get_data() (PyOpenWorm.plot.Plot method)
get_data_objects() (PyOpenWorm.datasource.BaseDataTranslator method)
get_incidents() (PyOpenWorm.neuron.Neuron method)
get_neuron_network() (PyOpenWorm.worm.Worm method)
get_owners() (PyOpenWorm.dataObject.BaseDataObject method)
get_semantic_net() (PyOpenWorm.worm.Worm method)
GJ_degree() (PyOpenWorm.neuron.Neuron method)
graph_accessor_finder (PyOpenWorm.command.POW attribute)
graph_pattern() (PyOpenWorm.dataObject.BaseDataObject method)
grouper() (in module PyOpenWorm.utils)
H
has_value() (PyOpenWorm.pProperty.Property method)
HomologyChannelModel (class in PyOpenWorm.channelworm)
I
id_is_variable() (PyOpenWorm.dataObject.BaseDataObject method)
identifier_augment() (PyOpenWorm.cell.Cell method)
(PyOpenWorm.data_trans.connections.NeuronConnectomeCSVTranslation method)
(PyOpenWorm.data_trans.wormatlas.WormAtlasCellListDataTranslation method)
(PyOpenWorm.datasource.DataSource method)
(PyOpenWorm.datasource.GenericTranslation method)
(PyOpenWorm.datasource.Translation method)
(PyOpenWorm.document.Document method)
(PyOpenWorm.evidence.Evidence method)
(PyOpenWorm.network.Network method)
(PyOpenWorm.relationship.Relationship method)
(PyOpenWorm.website.Website method)
(PyOpenWorm.worm.Worm method)
IdMixin() (in module PyOpenWorm.identifier_mixin)
ImportContextualizer (class in PyOpenWorm.import_contextualizer)
infer() (PyOpenWorm.data.DataUser method)
init() (PyOpenWorm.command.POW method)
init_database() (PyOpenWorm.data.Data method)
input_type (PyOpenWorm.data_trans.neuron_data.NeuronCSVDataTranslator attribute)
(PyOpenWorm.data_trans.wormbase.MuscleWormBaseCSVTranslator attribute)
(PyOpenWorm.data_trans.wormbase.NeuronWormBaseCSVTranslator attribute)
(PyOpenWorm.data_trans.wormbase.WormbaseIonChannelCSVTranslator attribute)
(PyOpenWorm.data_trans.wormbase.WormbaseTextMatchCSVTranslator attribute)
(PyOpenWorm.datasource.BaseDataTranslator attribute)
interneurons() (PyOpenWorm.network.Network method)
InvalidGraphException
InversePropertyException
InversePropertyMixin (class in PyOpenWorm.inverse_property)
L
lineageName (PyOpenWorm.cell.Cell attribute)
link() (PyOpenWorm.configure.Configure method)
load() (PyOpenWorm.data.Data class method)
loadConfig() (in module PyOpenWorm)
loadData() (in module PyOpenWorm)
LocalFileDataSource (class in PyOpenWorm.data_trans.local_file_ds)
M
make_translation() (PyOpenWorm.data_trans.connections.NeuronConnectomeCSVTranslator method)
(PyOpenWorm.data_trans.wormatlas.WormAtlasCellListDataTranslator method)
(PyOpenWorm.datasource.BaseDataTranslator method)
(PyOpenWorm.datasource.DataTranslator method)
merge() (PyOpenWorm.command.POW method)
motor() (PyOpenWorm.network.Network method)
Muscle (class in PyOpenWorm.muscle)
muscles() (PyOpenWorm.worm.Worm method)
MuscleWormBaseCSVTranslator (class in PyOpenWorm.data_trans.wormbase)
N
name (PyOpenWorm.cell.Cell attribute)
Neighbor (class in PyOpenWorm.neuron)
Network (class in PyOpenWorm.network)
NeuroML (class in PyOpenWorm.my_neuroml)
Neuron (class in PyOpenWorm.neuron)
neuron_names() (PyOpenWorm.network.Network method)
NeuronConnectomeCSVTranslation (class in PyOpenWorm.data_trans.connections)
NeuronConnectomeCSVTranslator (class in PyOpenWorm.data_trans.connections)
NeuronCSVDataSource (class in PyOpenWorm.data_trans.neuron_data)
NeuronCSVDataTranslator (class in PyOpenWorm.data_trans.neuron_data)
NeuronWormBaseCSVTranslator (class in PyOpenWorm.data_trans.wormbase)
O
ObjectProperty (class in PyOpenWorm.simpleProperty)
ObjectProperty() (PyOpenWorm.dataObject.BaseDataObject class method)
one() (PyOpenWorm.pProperty.Property method)
open() (PyOpenWorm.configure.Configure class method)
(PyOpenWorm.data.Data class method)
(PyOpenWorm.data.DefaultSource method)
(PyOpenWorm.data.RDFSource method)
(PyOpenWorm.data.SPARQLSource method)
(PyOpenWorm.data.SerializationSource method)
(PyOpenWorm.data.SleepyCatSource method)
(PyOpenWorm.data.ZODBSource method)
output_type (PyOpenWorm.data_trans.connections.NeuronConnectomeCSVTranslator attribute)
(PyOpenWorm.data_trans.neuron_data.NeuronCSVDataTranslator attribute)
(PyOpenWorm.data_trans.wormatlas.WormAtlasCellListDataTranslator attribute)
(PyOpenWorm.data_trans.wormbase.MuscleWormBaseCSVTranslator attribute)
(PyOpenWorm.data_trans.wormbase.NeuronWormBaseCSVTranslator attribute)
(PyOpenWorm.data_trans.wormbase.WormbaseIonChannelCSVTranslator attribute)
(PyOpenWorm.data_trans.wormbase.WormbaseTextMatchCSVTranslator attribute)
(PyOpenWorm.datasource.BaseDataTranslator attribute)
P
PatchClampChannelModel (class in PyOpenWorm.channelworm)
PatchClampExperiment (class in PyOpenWorm.channelworm)
PersonDataTranslator (class in PyOpenWorm.datasource)
Plot (class in PyOpenWorm.plot)
pmid (PyOpenWorm.document.Document attribute)
po_cache (PyOpenWorm.dataObject.BaseDataObject attribute)
POCache (class in PyOpenWorm.simpleProperty)
POW (class in PyOpenWorm.command)
properties_are_init_args (PyOpenWorm.dataObject.BaseDataObject attribute)
Property (class in PyOpenWorm.pProperty)
PropertyMeta (class in PyOpenWorm.pProperty)
PubmedRetrievalException
push() (PyOpenWorm.command.POW method)
PyOpenWorm (module)
PyOpenWorm.bibtex (module)
PyOpenWorm.biology (module)
PyOpenWorm.cell (module)
PyOpenWorm.channel (module)
PyOpenWorm.channelworm (module)
PyOpenWorm.command (module)
PyOpenWorm.configure (module)
PyOpenWorm.connection (module)
PyOpenWorm.context (module)
PyOpenWorm.context_common (module)
PyOpenWorm.context_store (module)
PyOpenWorm.contextDataObject (module)
PyOpenWorm.contextualize (module)
PyOpenWorm.data (module)
PyOpenWorm.data_trans (module)
PyOpenWorm.data_trans.common_data (module)
PyOpenWorm.data_trans.connections (module)
PyOpenWorm.data_trans.csv_ds (module)
PyOpenWorm.data_trans.data_with_evidence_ds (module)
PyOpenWorm.data_trans.local_file_ds (module)
PyOpenWorm.data_trans.neuron_data (module)
PyOpenWorm.data_trans.wormatlas (module)
PyOpenWorm.data_trans.wormbase (module)
PyOpenWorm.dataObject (module)
PyOpenWorm.dataObjectUtils (module)
PyOpenWorm.datasource (module)
PyOpenWorm.document (module)
PyOpenWorm.documentContext (module)
PyOpenWorm.evidence (module)
PyOpenWorm.experiment (module)
PyOpenWorm.identifier_mixin (module)
PyOpenWorm.import_contextualizer (module)
PyOpenWorm.import_override (module)
PyOpenWorm.inverse_property (module)
PyOpenWorm.muscle (module)
PyOpenWorm.my_neuroml (module)
PyOpenWorm.network (module)
PyOpenWorm.neuron (module)
PyOpenWorm.package_utils (module)
PyOpenWorm.plot (module)
PyOpenWorm.pProperty (module)
PyOpenWorm.relationship (module)
PyOpenWorm.relationshipProxy (module)
PyOpenWorm.simpleProperty (module)
PyOpenWorm.statement (module)
PyOpenWorm.utils (module)
PyOpenWorm.website (module)
PyOpenWorm.worm (module)
Q
QueryContext (class in PyOpenWorm.context)
R
RDFSource (class in PyOpenWorm.data)
RealSimpleProperty (class in PyOpenWorm.simpleProperty)
reconstitute() (PyOpenWorm.command.POW method)
reference (PyOpenWorm.evidence.Evidence attribute)
refutes (PyOpenWorm.evidence.Evidence attribute)
Rel (class in PyOpenWorm.relationshipProxy)
Relationship (class in PyOpenWorm.relationship)
retract() (PyOpenWorm.dataObject.BaseDataObject method)
retract_statements() (PyOpenWorm.data.DataUser method)
S
save() (PyOpenWorm.dataObject.BaseDataObject method)
sensory() (PyOpenWorm.network.Network method)
SerializationSource (class in PyOpenWorm.data)
set() (PyOpenWorm.neuron.ConnectionProperty method)
(PyOpenWorm.neuron.Neighbor method)
(PyOpenWorm.pProperty.Property method)
set_data() (PyOpenWorm.plot.Plot method)
SleepyCatSource (class in PyOpenWorm.data)
SPARQLSource (class in PyOpenWorm.data)
Statement (class in PyOpenWorm.statement)
store_name (PyOpenWorm.command.POW attribute)
supports (PyOpenWorm.evidence.Evidence attribute)
Syn_degree() (PyOpenWorm.neuron.Neuron method)
T
tag() (PyOpenWorm.command.POW method)
title (PyOpenWorm.document.Document attribute)
translate() (PyOpenWorm.bibtex.BibTexDataTranslator method)
(PyOpenWorm.command.POW method)
(PyOpenWorm.data_trans.connections.NeuronConnectomeCSVTranslator method)
(PyOpenWorm.data_trans.neuron_data.NeuronCSVDataTranslator method)
(PyOpenWorm.data_trans.wormatlas.WormAtlasCellListDataTranslator method)
(PyOpenWorm.data_trans.wormbase.MuscleWormBaseCSVTranslator method)
(PyOpenWorm.data_trans.wormbase.NeuronWormBaseCSVTranslator method)
(PyOpenWorm.data_trans.wormbase.WormbaseIonChannelCSVTranslator method)
(PyOpenWorm.data_trans.wormbase.WormbaseTextMatchCSVTranslator method)
(PyOpenWorm.datasource.BaseDataTranslator method)
Translation (class in PyOpenWorm.datasource)
translation_type (PyOpenWorm.data_trans.connections.NeuronConnectomeCSVTranslator attribute)
(PyOpenWorm.data_trans.wormatlas.WormAtlasCellListDataTranslator attribute)
(PyOpenWorm.datasource.BaseDataTranslator attribute)
(PyOpenWorm.datasource.DataTranslator attribute)
TrixSource (class in PyOpenWorm.data)
U
UnionProperty (class in PyOpenWorm.simpleProperty)
UnionProperty() (PyOpenWorm.dataObject.BaseDataObject class method)
UnreadableGraphException
update_from_wormbase() (PyOpenWorm.document.Document method)
uri (PyOpenWorm.document.Document attribute)
V
values (class in PyOpenWorm.dataObject)
variable() (PyOpenWorm.dataObject.BaseDataObject method)
W
wbid (PyOpenWorm.document.Document attribute)
Website (class in PyOpenWorm.website)
Worm (class in PyOpenWorm.worm)
WormAtlasCellListDataSource (class in PyOpenWorm.data_trans.wormatlas)
WormAtlasCellListDataTranslation (class in PyOpenWorm.data_trans.wormatlas)
WormAtlasCellListDataTranslator (class in PyOpenWorm.data_trans.wormatlas)
WormBaseCSVDataSource (class in PyOpenWorm.data_trans.wormbase)
wormbaseid (PyOpenWorm.document.Document attribute)
WormbaseIonChannelCSVDataSource (class in PyOpenWorm.data_trans.wormbase)
WormbaseIonChannelCSVTranslator (class in PyOpenWorm.data_trans.wormbase)
WormbaseRetrievalException
WormbaseTextMatchCSVDataSource (class in PyOpenWorm.data_trans.wormbase)
WormbaseTextMatchCSVTranslator (class in PyOpenWorm.data_trans.wormbase)
write() (PyOpenWorm.my_neuroml.NeuroML class method)
Y
year (PyOpenWorm.document.Document attribute)
Z
ZODBSource (class in PyOpenWorm.data)
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