Building a data pipeline

Overview

What you’ll build

• A pipeline demonstrating how to:
  • download data (e.g. morphologies) from a remote source (e.g. Allen Cell Types Database)
  • register the downloaded data in a knowledge graph within Blue Brain Nexus
  • register the dataset provenance in the knowledge graph
  • build a dataset made of entities of interest (e.g. a set of morphologies from a given species, brain region) and register it in Blue Brain Nexus with an immutable identifier
  • Run analysis on the build dataset (e.g. topological analysis of neuronal morphologies using Topological Morphology Descriptor )
  • Register the analysis results (plots, figures) in the Knowledge graph and record their provenance

What you’ll learn

• How to leverage a knowledge graph as part of a data anaylis pipeline to store and manage (meta)data, search for data and record data provenance

What you’ll need

• A Python 3.5 or higher with support of Jupyter notebook

Get the tutorial code

This tutorial code is available:

• at Github
• on Google Colab