VFB_connect output formats

VFB_JSON

A JSON representation of the information displayed in VFB term information reports.

The confirms to a standard JSON schema: raw schema docs; schema in browsable form.

Summary reports

Summary reports provide a high-level, tabular summary of VFB term information, provided as a list of dictionaries in JSON, which can be easily loaded into Python Pandas:

import pandas
df = pd.DataFrame.from_records(vc.<some method call>)  # Add example

…

Applies to	Column name	content
all	label	name of entity
all	symbol	short symbol for entity (if any)
all	id	VFB ID of entity
all	tags	tags associated with entity (gross class; data flags)
anatomical types & individuals	parents_label	parent class labels (`
anatomical types & individuals	parents_id	parent classes IDs (`
anatomical individuals	data_source	ID of data_source
anatomical individuals	accession	ID of individual in data_source
anatomical individuals	dataset	dataset(s) individual belongs to (`
anatomical individuals	templates	template(s) registered to (`
anatomical individuals	license	license data is available under
dataset	description	DataSet description, if present
dataset	miniref	minimal information for DataSet reference
dataset	FlyBase	FlyBase ID for DataSet reference
dataset	PMID	PMID for DataSet reference
dataset	DOI	DOI for DataSet reference

Image manifest

Image download methods save an image manifest to disk, consisting of a tsv with summary info for anatomical individuals depicted in the the downloaded images, with an addition column containing filenames.

ID Mappings

Mappings between VFB IDs and external IDs are provided as dictionaries with the form:

{ VFB_id : [{ db: <db> : acc : <acc> }]}
# OR
{ acc : [{ db: <db> : vfb_id : <VFB_id> }]}

This structure is necessary because the relationship of VFB_id and external identifier my not always be 1:1. ID mapping methods come with an option to switch between the two representations.

Connectomics & neuron similarity reports

type: type

column	content
upstream_neuron_id	VFB id (short_form) of upstream neuron
upstream_neuron_name	name of upstream neuron in VFB
weight	weight
downstream_neuron_id	VFB id (short_form) of downstream neuron
downstream_neuron_name	name of downstream neuron in VFB
upstream_class	upstream neuron type(s) (name; `
downstream_class	downstream neuron type(s) (name; `

Individual: type

column	content
query_neuron_id	VFB id (short_form) of query neuron
query_neuron_name	name of query neuron in VFB
weight	weight
target_neuron_id	VFB id (short_form) of target neuron
target_neuron_name	name of target neuron in VFB

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