owmeta - A data access layer for C. elegans anatomy and physiology.

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owmeta

A data access layer in Python which integrates disparate structures and representations for C. elegans anatomy and physiology. Enables a simple Python API for asking various questions about the cells of the C. elegans and enabling data sharing for the purpose of building a data-to-model pipeline for the OpenWorm project.

Overview

The data and models required to simulate C. elegans are highly heterogeneous. Consequently, from a software perspective, a variety of underlying representations are needed to store different aspects of the relevant anatomy and physiology. For example, a NetworkX representation of the connectome as a complex graph enables questions to be asked about nearest neighbors of a given neuron. An RDF semantic graph representation is useful for reading and writing annotations about multiple aspects of a neuron, such as what papers have been written about it, properties it may have such as ion channels and neurotransmitter receptors, etc. A NeuroML representation is useful for answering questions about model morphology and simulation parameters. A Blender representation is a full 3D shape definition that can be used for calculations in 3D space.

The diversity of underlying representations required for OpenWorm presents a challenge for data integration and consolidation. owmeta solves this challenge with a unified data access layer whereby different representations are encapsulated into an abstract view. This allows the user to work with objects related to the biological reality of the worm, and forget about which representation is being used under the hood. The worm itself has a unified sense of neurons, networks, muscles, ion channels, etc. and so should our code.