PyOpenWorm API¶

Basic Classes¶

`Worm`¶

class PyOpenWorm.Worm(scientific_name=False, **kwargs)[source]¶

Bases: PyOpenWorm.dataObject.DataObject

A representation of the whole worm.

All worms with the same name are considered to be the same object.

Attributes

neuron_network	(ObjectProperty) The neuron network of the worm
muscle	(ObjectProperty) Muscles of the worm

add_reference(g, reference_iri)¶

Add a citation to a set of statements in the database

Parameters:	triples – A set of triples to annotate

get_neuron_network()[source]¶

Return the neuron network of the worm.

Example:

# Grabs the representation of the neuronal network
>>> net = P.Worm().get_neuron_network()

# Grab a specific neuron
>>> aval = net.aneuron('AVAL')

>>> aval.type()
set([u'interneuron'])

#show how many connections go out of AVAL
>>> aval.connection.count('pre')
77

Returns:	An object to work with the network of the worm
Return type:	PyOpenWorm.Network

get_semantic_net()[source]¶

Get the underlying semantic network as an RDFLib Graph

Returns:	A semantic network containing information about the worm
Return type:	rdflib.ConjunctiveGraph

load()¶

Load in data from the database. Derived classes should override this for their own data structures.

load() returns an iterable object which yields DataObjects which have the same class as the object and have, for the Properties set, the same values

Parameters:	self – An object which limits the set of objects which can be returned. Should have the configuration necessary to do the query

muscles()[source]¶

Get all Muscle objects attached to the Worm

Returns a set of all muscles:

Example:

>>> muscles = P.Worm().muscles()
>>> len(muscles)
96

Returns:	A set of all muscles
Return type:	set

retract()¶: Remove this object from the data store.

save()¶: Write in-memory data to the database. Derived classes should call this to update the store.

`Network`¶

class PyOpenWorm.Network(**kwargs)[source]¶

Bases: PyOpenWorm.dataObject.DataObject

A network of neurons

Attributes

neuron	Representation of neurons in the network
synapse	Representation of synapses in the network

add_reference(g, reference_iri)¶

Add a citation to a set of statements in the database

Parameters:	triples – A set of triples to annotate

aneuron(name)[source]¶

Get a neuron by name.

Example:

# Grabs the representation of the neuronal network
>>> net = P.Worm().get_neuron_network()

# Grab a specific neuron
>>> aval = net.aneuron('AVAL')

>>> aval.type()
set([u'interneuron'])

Parameters:	name – Name of a c. elegans neuron
Returns:	Neuron corresponding to the name given
Return type:	PyOpenWorm.Neuron

as_networkx()[source]¶

interneurons()[source]¶

Get all interneurons

Returns:	A iterable of all interneurons
Return type:	iter(Neuron)

load()¶

Load in data from the database. Derived classes should override this for their own data structures.

load() returns an iterable object which yields DataObjects which have the same class as the object and have, for the Properties set, the same values

Parameters:	self – An object which limits the set of objects which can be returned. Should have the configuration necessary to do the query

motor()[source]¶

Get all motor

Returns:	A iterable of all motor neurons
Return type:	iter(Neuron)

neurons()[source]¶

Gets the complete set of neurons in this network.

Example:

# Grabs the representation of the neuronal network
>>> net = P.Worm().get_neuron_network()

#NOTE: This is a VERY slow operation right now
>>> len(set(net.neurons()))
302
>>> set(net.neurons())
set(['VB4', 'PDEL', 'HSNL', 'SIBDR', ... 'RIAL', 'MCR', 'LUAL'])

retract()¶: Remove this object from the data store.

save()¶: Write in-memory data to the database. Derived classes should call this to update the store.

sensory()[source]¶

Get all sensory neurons

Returns:	A iterable of all sensory neurons
Return type:	iter(Neuron)

`Connection`¶

class PyOpenWorm.Connection(pre_cell=None, post_cell=None, number=None, syntype=None, synclass=None, **kwargs)[source]¶

Bases: PyOpenWorm.relationship.Relationship

Connection between neurons

Parameters:

pre_cell : string or Neuron, optional

The pre-synaptic cell

post_cell : string or Neuron, optional

The post-synaptic cell

number : int, optional

The weight of the connection

syntype : {‘gapJunction’, ‘send’}, optional

The kind of synaptic connection. ‘gapJunction’ indicates a gap junction and ‘send’ a chemical synapse

synclass : string, optional

The kind of Neurotransmitter (if any) sent between pre_cell and post_cell

add_reference(g, reference_iri)¶

Add a citation to a set of statements in the database

Parameters:	triples – A set of triples to annotate

load()¶

Load in data from the database. Derived classes should override this for their own data structures.

load() returns an iterable object which yields DataObjects which have the same class as the object and have, for the Properties set, the same values

Parameters:	self – An object which limits the set of objects which can be returned. Should have the configuration necessary to do the query

retract()¶: Remove this object from the data store.

save()¶: Write in-memory data to the database. Derived classes should call this to update the store.

`Cell`¶

class PyOpenWorm.Cell(name=False, lineageName=False, **kwargs)[source]¶

Bases: PyOpenWorm.dataObject.DataObject

A biological cell.

All cells with the same name are considered to be the same object.

Parameters:

name : string

The name of the cell

lineageName : string

The lineageName of the cell Example:

>>> c = Cell(name="ADAL")
>>> c.lineageName() # Returns ["AB plapaaaapp"]

Attributes

name	(DatatypeProperty) The ‘adult’ name of the cell typically used by biologists when discussing C. elegans
lineageName	(DatatypeProperty) The lineageName of the cell
description	(DatatypeProperty) A description of the cell
divisionVolume	(DatatypeProperty) When called with no argument, return the volume of the cell at division during development. When called with an argument, set the volume of the cell at division Example:: >>> v = Quantity(“600”,”(um)^3”) >>> c = Cell(lineageName=”AB plapaaaap”) >>> c.divisionVolume(v)

add_reference(g, reference_iri)¶

Add a citation to a set of statements in the database

Parameters:	triples – A set of triples to annotate

blast()[source]¶

Return the blast name.

Example:

>>> c = Cell(name="ADAL")
>>> c.blast() # Returns "AB"

Note that this isn’t a Property. It returns the blast extracted from the ‘’first’’ lineageName saved.

daughterOf()[source]¶

Return the parent(s) of the cell in terms of developmental lineage.

Example:

>>> c = Cell(lineageName="AB plapaaaap")
>>> c.daughterOf() # Returns [Cell(lineageName="AB plapaaaa")]

load()¶

Load in data from the database. Derived classes should override this for their own data structures.

load() returns an iterable object which yields DataObjects which have the same class as the object and have, for the Properties set, the same values

Parameters:	self – An object which limits the set of objects which can be returned. Should have the configuration necessary to do the query

parentOf()[source]¶

Return the direct daughters of the cell in terms of developmental lineage.

Example:

>>> c = Cell(lineageName="AB plapaaaap")
>>> c.parentOf() # Returns [Cell(lineageName="AB plapaaaapp"),Cell(lineageName="AB plapaaaapa")] 

retract()¶: Remove this object from the data store.

save()¶: Write in-memory data to the database. Derived classes should call this to update the store.

`Neuron`¶

class PyOpenWorm.Neuron(name=False, **kwargs)[source]¶

Bases: PyOpenWorm.cell.Cell

A neuron.

See what neurons express some neuropeptide

Example:

# Grabs the representation of the neuronal network
>>> net = P.Worm().get_neuron_network()

# Grab a specific neuron
>>> aval = net.aneuron('AVAL')

>>> aval.type()
set([u'interneuron'])

#show how many connections go out of AVAL
>>> aval.connection.count('pre')
77

>>> aval.name()
u'AVAL'

#list all known receptors
>>> sorted(aval.receptors())
[u'GGR-3', u'GLR-1', u'GLR-2', u'GLR-4', u'GLR-5', u'NMR-1', u'NMR-2', u'UNC-8']

#show how many chemical synapses go in and out of AVAL
>>> aval.Syn_degree()
90

Parameters:

name : string

The name of the neuron.

Attributes

type	(DatatypeProperty) The neuron type (i.e., sensory, interneuron, motor)
receptor	(DatatypeProperty) The receptor types associated with this neuron
innexin	(DatatypeProperty) Innexin types associated with this neuron
neurotransmitter	(DatatypeProperty) Neurotransmitters associated with this neuron
neuropeptide	(DatatypeProperty) Name of the gene corresponding to the neuropeptide produced by this neuron
neighbor	(Property) Get neurons connected to this neuron if called with no arguments, or with arguments, state that neuronName is a neighbor of this Neuron
connection	(Property) Get a set of Connection objects describing chemical synapses or gap junctions between this neuron and others

GJ_degree()[source]¶

Get the degree of this neuron for gap junction edges only

Returns:	total number of incoming and outgoing gap junctions
Return type:	int

Syn_degree()[source]¶

Get the degree of a this neuron for chemical synapse edges only

Returns:	total number of incoming and outgoing chemical synapses
Return type:	int

add_reference(g, reference_iri)¶

Add a citation to a set of statements in the database

Parameters:	triples – A set of triples to annotate

blast()¶

Return the blast name.

Example:

>>> c = Cell(name="ADAL")
>>> c.blast() # Returns "AB"

Note that this isn’t a Property. It returns the blast extracted from the ‘’first’’ lineageName saved.

daughterOf()¶

Return the parent(s) of the cell in terms of developmental lineage.

Example:

>>> c = Cell(lineageName="AB plapaaaap")
>>> c.daughterOf() # Returns [Cell(lineageName="AB plapaaaa")]

get_incidents(type=0)[source]¶: Get neurons which synapse at this neuron

load()¶

Load in data from the database. Derived classes should override this for their own data structures.

load() returns an iterable object which yields DataObjects which have the same class as the object and have, for the Properties set, the same values

Parameters:	self – An object which limits the set of objects which can be returned. Should have the configuration necessary to do the query

parentOf()¶

Return the direct daughters of the cell in terms of developmental lineage.

Example:

>>> c = Cell(lineageName="AB plapaaaap")
>>> c.parentOf() # Returns [Cell(lineageName="AB plapaaaapp"),Cell(lineageName="AB plapaaaapa")] 

retract()¶: Remove this object from the data store.

save()¶: Write in-memory data to the database. Derived classes should call this to update the store.

`Muscle`¶

class PyOpenWorm.Muscle(name=False, **kwargs)[source]¶

Bases: PyOpenWorm.cell.Cell

A single muscle cell.

See what neurons innervate a muscle:

Example:

>>> mdr21 = P.Muscle('MDR21')
>>> innervates_mdr21 = mdr21.innervatedBy()
>>> len(innervates_mdr21)
4

Attributes

neurons	(ObjectProperty) Neurons synapsing with this muscle
receptors	(DatatypeProperty) Get a list of receptors for this muscle if called with no arguments, or state that this muscle has the given receptor type if called with an argument

add_reference(g, reference_iri)¶

Add a citation to a set of statements in the database

Parameters:	triples – A set of triples to annotate

blast()¶

Return the blast name.

Example:

>>> c = Cell(name="ADAL")
>>> c.blast() # Returns "AB"

Note that this isn’t a Property. It returns the blast extracted from the ‘’first’’ lineageName saved.

daughterOf()¶

Return the parent(s) of the cell in terms of developmental lineage.

Example:

>>> c = Cell(lineageName="AB plapaaaap")
>>> c.daughterOf() # Returns [Cell(lineageName="AB plapaaaa")]

load()¶

Load in data from the database. Derived classes should override this for their own data structures.

load() returns an iterable object which yields DataObjects which have the same class as the object and have, for the Properties set, the same values

Parameters:	self – An object which limits the set of objects which can be returned. Should have the configuration necessary to do the query

parentOf()¶

Return the direct daughters of the cell in terms of developmental lineage.

Example:

>>> c = Cell(lineageName="AB plapaaaap")
>>> c.parentOf() # Returns [Cell(lineageName="AB plapaaaapp"),Cell(lineageName="AB plapaaaapa")] 

retract()¶: Remove this object from the data store.

save()¶: Write in-memory data to the database. Derived classes should call this to update the store.

`Channel`¶

class PyOpenWorm.Channel(subfamily=False, **kwargs)[source]¶

Bases: PyOpenWorm.dataObject.DataObject

An ion channel.

Channels are identified by subtype name.

Parameters:

subfamily : string

The subfamily to which the ion channel belongs

Attributes

subfamily	(DatatypeProperty) The subfamily to which the ion channel belongs
Models	(Property) Get experimental models of this ion channel

add_reference(g, reference_iri)¶

Add a citation to a set of statements in the database

Parameters:	triples – A set of triples to annotate

load()¶

Load in data from the database. Derived classes should override this for their own data structures.

load() returns an iterable object which yields DataObjects which have the same class as the object and have, for the Properties set, the same values

Parameters:	self – An object which limits the set of objects which can be returned. Should have the configuration necessary to do the query

retract()¶: Remove this object from the data store.

save()¶: Write in-memory data to the database. Derived classes should call this to update the store.

`Evidence`¶

class PyOpenWorm.Evidence(conf=False, **source)[source]¶

Bases: PyOpenWorm.dataObject.DataObject

A representation of some document which provides evidence like scholarly references, for other objects.

Possible keys include:

pmid,pubmed: a pubmed id or url (e.g., 24098140)
wbid,wormbase: a wormbase id or url (e.g., WBPaper00044287)
doi: a Digitial Object id or url (e.g., s00454-010-9273-0)

Parameters:

doi : string

A Digital Object Identifier (DOI) that provides evidence, optional

pmid : string

A PubMed ID (PMID) that point to a paper that provides evidence, optional

wormbaseid : string

An ID from WormBase that points to a record that provides evidence, optional

author : string

The author of the evidence

title : string

The title of the evidence

year : string or int

The date (e.g., publication date) of the evidence

uri : string

A URL that points to evidence

Attributes

asserts	(ObjectProperty (value_type=DataObject)) When used with an argument, state that this Evidence asserts that the relationship is true. Example:: import bibtex bt = bibtex.parse(“my.bib”) n1 = Neuron(“AVAL”) n2 = Neuron(“DA3”) c = Connection(pre=n1,post=n2,class=”synapse”) e = Evidence(bibtex=bt[‘white86’]) e.asserts(c) Other methods return objects which asserts accepts. Example:: n1 = Neuron(“AVAL”) r = n1.neighbor(“DA3”) e = Evidence(bibtex=bt[‘white86’]) e.asserts(r) When used without arguments, returns a sequence of statements asserted by this evidence Example:: import bibtex bt = bibtex.parse(“my.bib”) n1 = Neuron(“AVAL”) n2 = Neuron(“DA3”) c = Connection(pre=n1,post=n2,class=”synapse”) e = Evidence(bibtex=bt[‘white86’]) e.asserts(c) list(e.asserts()) # Returns a list [..., d, ...] such that d==c
doi	(DatatypeProperty) A Digital Object Identifier (DOI) that provides evidence, optional
pmid	(DatatypeProperty) A PubMed ID (PMID) that point to a paper that provides evidence, optional
wormbaseid	(DatatypeProperty) An ID from WormBase that points to a record that provides evidence, optional
author	(DatatypeProperty) The author of the evidence
title	(DatatypeProperty) The title of the evidence
year	(DatatypeProperty) The date (e.g., publication date) of the evidence
uri	(DatatypeProperty) A URL that points to evidence

add_data(k, v)[source]¶

Add a field

Parameters:

k : string

Field name

v : string

Field value

add_reference(g, reference_iri)¶

Add a citation to a set of statements in the database

Parameters:	triples – A set of triples to annotate

load()¶

Load in data from the database. Derived classes should override this for their own data structures.

load() returns an iterable object which yields DataObjects which have the same class as the object and have, for the Properties set, the same values

Parameters:	self – An object which limits the set of objects which can be returned. Should have the configuration necessary to do the query

retract()¶: Remove this object from the data store.

save()¶: Write in-memory data to the database. Derived classes should call this to update the store.