Introduction
SCKAN, a key component of the SPARC Program is a semantic store housing a comprehensive knowledge base of nerve to end organ connectivity in the autonomic nervous system (ANS) and peripheral nervous system (PNS). Connectivity information is derived from SPARC experts, SPARC data, literature and textbooks. It provides a machine-readable format that supports reasoning and offers powerful query and visualization capabilities.
SCKAN is a subset of the SPARC Knowledge Graph, which ultimately allows us to link connectivity information to SPARC data, models, flat maps, simulations, and other related information.
How is SCKAN organized?
SCKAN contains statements about neuronal connectivity at the neuron population level, in the form of: “Neurons with somas in structure A project to structure B via nerve C.” For some connections, we have detailed connections modeled with a specification of the locations of their somas and dendrites, axon segments and synapses. Connectivity information is available as RDF triples or via SciGraph, an OWL-based graph database.
SCKAN models connections at two levels of granularity:
Circuits:
A circuit represents a detailed model of ANS connectivity associated with a particular organ (e.g., bladder) or functional circuit (e.g., defensive breathing). These models are created and curated by experts in conjunction with the SPARC Anatomy Working Group (SAWG) using information from multiple sources such as data, literature, and ontologies. Each circuit contains detailed representations of neuron populations, including locations of cell bodies, dendrites, and the anatomical course of axons as they traverse anatomical structures and nerves to synapse with their targets (example). This knowledge is represented using the ApiNATOMY connectivity model, a sophisticated semantic model that represents multiscale connectivity [Kokash N and de Bono B (2021), Osanlouy M, et al. (2021) - for additional information see this video]. ApiNATOMY provides a method of chaining together axon segments to create a unified representation of tractography.
General knowledge about individual connections:
To provide a comprehensive overview of the state of knowledge about ANS and PNS connectivity, the circuit-based approach is supplemented with well-known connections derived from the literature and textbooks using a Natural Language Processing (NLP) pipeline [Menke J et al. (2020) - to learn more about this process, see this video]. These types of connectivity statements do not have detailed topological information associated with them and are represented using The Neuron Phenotype Ontology (NPO), [Gillespie TH, et al. (2020)].
Curating and contributing to the contents of SCKAN
The contents of SCKAN are primarily populated and curated by SPARC K-Core. The process is outlined in the SCKAN Curation Manual: https://doi.org/10.5281/zenodo.14774195. However, we encourage others to contribute by suggesting new connections, extensions of existing connections, or corrections. As shown in the figure below, modifications can be suggested by approved users in flatmaps and Composer.
How do I access the connectivity in SCKAN?
Several tools now allow users to explore the contents of SCKAN and users are encouraged to provide feedback on the contents of SCKAN through flatmaps or Composer.
- SCKAN NLI: A new web-based application that allows users to query SCKAN with a natural language interface (NLI).
- SCKANNER: A new visualization tool that allows users to quickly explore the contents of SCKAN.
- SPARC flatmaps (https://sparc.science/maps) shows connectivity from SCKAN in an anatomical context; logged in users can recommend modifications.
- SCKAN Composer: A specialized interface for authoring and quality-checking connectivity statements in SCKAN Contact us if you’d like an account.
Additional information can be found at “How do I access SCKAN.”
Who Created SCKAN?
SCKAN is a product of the Knowledge Management team of K-Core, a collaboration between the FAIR Data Informatics Lab at UCSD and Whitby et al, Inc. The connectivity knowledge contained in SCKAN has been contributed by a number of SPARC investigators and the SPARC Anatomy Working Group (SAWG).
To suggest a new SCKAN query, please fill out this form.
For additional information contact us at kcore@sparc.science
