Welcome to VFB_connect

[Robbie1977]

VFB Connect: Quickstart Guide

VFB Connect is a Python package for interacting with the Virtual Fly Brain (VFB) database. This guide will walk you through the basics of using VFB Connect, including installation, querying terms, and working with the results.

Installation

To install VFB Connect and its dependencies, run the following commands:

pip install vfb-connect --upgrade --quiet

Getting Started

Importing VFB Connect

Begin by importing the vfb object from the vfb_connect package. This object is your gateway to querying the VFB database.

from vfb_connect import vfb

Querying Terms

You can query the VFB database for specific terms using their IDs. The supported IDs include anatomical entities, dataset IDs, and ontology IDs (e.g., FBbt).

Single Term Query

Retrieve a term by its ID and get a summary of the term:

term = vfb.term('VFB_00010001')
print(term.summary)  # Prints the summary of the term

Multiple Term Query

Retrieve multiple terms and get their summaries in a pandas DataFrame:

terms = vfb.terms(['VFB_00010001', 'VFB_00000001'])
print(terms.get_summaries())  # Prints summaries in a DataFrame

Inspecting Term Properties

You can inspect the properties and methods available for a term object:

print(dir(vfb.terms(['VFB_00010001'])[0]))  # Prints available properties for the term
print(dir(vfb.terms(['VFB_00010001'])))     # Prints available methods for the VFBTerms object

Accessing Xrefs

Retrieve cross-references for a term:

print(vfb.term('VFB_00010001').xrefs)  # Prints xrefs for the term

Working with External IDs

You can query terms using external IDs from various databases:

# Query with an external ID from catmaid_l1em
term = vfb.term('catmaid_l1em:17545695')
print(term.summary)

# Get all xrefs by database
xrefs = vfb.xref_2_vfb_id(db='catmaid_fafb')
print(list(xrefs.items())[0:10])  # Prints first 10 xrefs

Exploring Terms

Explore terms for their subparts and related neuron types:

# Retrieve and explore a term
fsb = vfb.term('fan-shaped body')

print(fsb.subparts)  # Prints subparts of the term
print(f"{len(fsb.neuron_types_with_synaptic_terminals_here)} neuron_types_with_synaptic_terminals_here")
print(f"{len(fsb.neuron_types_that_overlap)} neuron_types_that_overlap")
print(fsb._subparts.get_names())  # Prints names of the subparts

Working with Instances

Retrieve and work with instances of a term:

# Retrieve instances and their summaries
cyp_neuron_images = vfb.term('larval subesophageal zone cypress neuron').instances
print(cyp_neuron_images.get_summaries())

# List available methods for loading images
print([attr for attr in dir(cyp_neuron_images) if attr.startswith('load')])

# Plot the images in 3D
cyp_neuron_images.plot3d(include_template=True)  # Include anatomical template in the plot

# Show an image thumbnail or open it in VFB 3D web browser
cyp_neuron_images[0].show()

Sorting and Filtering

Sort parent terms and query transcriptomic profiles:

# Example: Sort parent terms
dPAM = vfb.term('dopaminergic PAM neuron')
parents = set([instance.parents[0].name for instance in dPAM.instances])
print(sorted(parents))  # Prints sorted list of parent names

# Find single cell transcriptomics data for a given cell type
profile = vfb.get_transcriptomic_profile(cell_type='adult olfactory receptor neuron')
print(profile.head())

# Filter transcriptomic profiles by gene function
functions = vfb.get_gene_function_filters()
print(functions)  # Prints available gene functions
filtered_profile = vfb.get_transcriptomic_profile(cell_type='adult olfactory receptor neuron', gene_type='Olfactory_receptor')
print(filtered_profile.head())

Exploring VFB Connect Methods

To explore the available methods in VFB Connect, use the dir function:

print(dir(vfb))  # Prints available methods for the vfb object

You can also use the help function for detailed information on specific methods:

help(vfb.term)  # Prints detailed help on the term method

Conclusion

VFB Connect provides a robust set of tools for querying and interacting with the VFB database. This guide covers the basics, including installation, querying terms, and working with results. For more advanced usage and additional features, refer to the VFB Connect API Documentation and explore the methods available in the package. Happy querying!