vfb_connect package
Subpackages
Submodules
vfb_connect.cross_server_tools module
- class vfb_connect.cross_server_tools.VfbConnect(neo_endpoint='http://pdb.virtualflybrain.org', neo_credentials=('neo4j', 'vfb'), owlery_endpoint='http://owl.virtualflybrain.org/kbs/vfb/', lookup_prefixes=('FBbt', 'VFBexp', 'VFBext'))[source]
Bases:
object
API wrapper class. By default this wraps connections to the more basal API endpoints (OWL, Neo4j).
Top level methods combined semantic queries that range across VFB content with neo4j queries, returning detailed metadata about anatomical classes and individuals that fulfill these queries.
Methods allowing direct queries cypher queries of the production Neo4j are available under nc
Methods for querying Neo4j with arbitrary lists of identifiers to return rich metadata or mappings to external IDs are available under neo_query_wrapper.
Direct access OWL queries, returning identifiers only, are available via methods under oc
Example semantic queries (OWL class expressions). Note quoting scheme (outer “ + single quotes for entities).
“‘GABAergic neuron’” “‘GABAeric neuron’ that ‘overlaps’ some ‘antennal lobe’”
- get_connected_neurons_by_type(upstream_type, downstream_type, weight, query_by_label=True, return_dataframe=True)[source]
Get all synaptic connections between individual neurons of upstream_type and dowstream_type where synapse count >= weight. Warning: Does not support Class Expressions.
- Parm upstream_type
The upstream neuron type (e.g. ‘GABAeric neuron’).
- Parameters
downstream_type – The upstream neuron type (e.g. ‘Descending neuron’).
query_by_label – specify neuron type by label if True (default) or by short_form id if False
return_dataframe – Returns pandas dataframe if true, otherwise returns list of dicts.
- get_images_by_type(class_expression, template, image_folder, image_type='swc', query_by_label=True, direct=False, stomp=False)[source]
Download all images of individuals specified by a class expression, e.g. all images of the nodulus or of MBON01.
- Parameters
class_expression – A valid OWL class expression, e.g. the name or symbol of a type of neuron (MBON01)
template – template name
image_folder – folder to save image files & manifest to.
image_type – image type (file extension)
stomp – Overwrite image_folder if already exists.
- Returns
Manifest as Pandas DataFrame
- get_instances(class_expression, query_by_label=True, summary=False)[source]
Generate JSON report of all instances of class_expression. Instances are specific examples of a type/class, e.g. a neuron of type DA1 adPN from the FAFB_catmaid database.
- Parameters
class_expression – A valid OWL class expression, e.g. the name of a class.
query_by_label – Optional. If false, class_expression takes IDs instead of labels Default True
summary – Optional. Returns summary reports if true. Default False
- Returns
Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
- Return type
list of VFB_json or summary_report_json
- get_instances_by_dataset(dataset, summary=False)[source]
Get JSON report of all individuals in a dataset
- Parameters
dataset – dataset ID
summary – Optional. Returns summary reports if true. Default False
- Returns
Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
- Return type
list of VFB_json or summary_report_json
- get_neurons_downstream_of(neuron, weight, classification=None, query_by_label=True, return_dataframe=True)[source]
Get all neurons downstream of individual neuron
- Parameters
neuron – the name or id of a particular neuron (dependent on query_by_label setting)
weight – limit returned neurons to those with connected by >= weight synapses
query_by_label – query neuron may be specified with a label if true
return_dataframe – Returns pandas dataframe if true, otherwise returns list of dicts.
- Classification
optionally specify classification of downstream neuron using a class expression e.g. MBON
- get_neurons_upstream_of(neuron, weight, classification=None, query_by_label=True, return_dataframe=True)[source]
“Get all neurons downstream of individual neuron
- Parameters
neuron – the name or id of a particular neuron (dependent on query_by_label setting)
weight – limit returned neurons to those with connected by >= weight synapses
query_by_label – query neuron may be specified with a label if true
return_dataframe – Returns pandas dataframe if true, otherwise returns list of dicts.
- Classification
optionally specify classification of upstream neuron using a class expression e.g. MBON
- get_similar_neurons(neuron, similarity_score='NBLAST_score', return_dataframe=True)[source]
Get JSON report of individual neurons similar to input neuron
- Parameters
neuron –
similarity_score – Optionally specify similarity score to chose
return_dataframe – Returns pandas dataframe if true, otherwise returns list of dicts.
- Returns
list of similar neurons (id, label, tags, source (db) id, accession_in_source) + similarity score.
- Return type
pandas.DataFrame or list of dicts
- get_subclasses(class_expression, query_by_label=True, direct=False, summary=False)[source]
Generate JSON report of all subclasses of class_expression.
- Parameters
class_expression – A valid OWL class expression, e.g. the name of a class.
query_by_label – Optional. If false, class_expression takes IDs instead of labels Default True
direct – Return direct subclasses only. Default False
summary – Optional. Returns summary reports if true. Default False
- Returns
Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
- Return type
list of VFB_json or summary_report_json
- get_superclasses(class_expression, query_by_label=True, direct=False, summary=False)[source]
Generate JSON report of all superclasses of class_expression.
- Parameters
class_expression – A valid OWL class expression, e.g. the name of a class.
query_by_label – Optional. If false, class_expression takes IDs instead of labels Default True
direct – Return direct superclass only. Default False
summary – Optional. Returns summary reports if true. Default False
- Returns
Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
- Return type
list of VFB_json or summary_report_json
- get_terms_by_region(region, cells_only=False, verbose=False, query_by_label=True, summary=False)[source]
Generate TermInfo reports for all terms relevant to annotating some specific region, optionally limited to cells.
- Parameters
region – The name (rdfs:label) of brain region (or CURIE style ID if query_by_label is False)
cells_only – Optional. Limits query to cell type if True. Defaults to False
verbose – Optional.
query_by_label – Optional (see region). Default True
summary – Optional. Returns summary reports if true. Default False
- Returns
Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
- Return type
list of VFB_json or summary_report_json
- get_vfb_link(short_forms, template)[source]
Takes a list of VFB IDs (short_forms) and the name (label) of a template. Returns a link to VFB loading all available images of neurons on that template.
- Parameters
short_forms (
iter
) – A list (or other iterable) of VFB short_form IDs for individuals with images- Returns
A url for viewing images and metadata for specified individuals on VFB.