Accessing SCKAN

How do I see what Connections are in SCKAN?

For those interested in exploring connections in SCKAN, interfaces include:

• SPARC maps show connectivity information in SCKAN
• SCKANNER is a new visualization tool, see documentation here
• SCKAN NLI is a new natural language interface tool, see information for testers here
• SCKAN Explorer is a bit more advanced and typically used more for curation, see documentation here

For those interested in authoring connectivity information for SCKAN, see SCKAN Composer . Contact us at [email protected] if you are interested in an account.

Connections in SCKAN:

• A circuit in SCKAN covers an anatomical or functional system. It contains detailed topological information about neuron populations and where they travel. It is bounded and aims to be comprehensive within that circuit. These are derived from expert input that are then encoded into ApiNATOMY models. The creation of these circuit models is overseen by the SPARC Anatomy Working Group (SAWG), for information about the process and an example image of such a circuit, learn more about SAWG's ApiNATOMY.

• Individual connections in SCKAN have been extracted from the literature or textbooks to fill in gaps that are not represented in the circuits. They are generally high level, reflecting general knowledge on ANS connectivity and in contrast to the circuits, they do not contain detailed topological information. These are modeled using The Neuron Phenotype Ontology (NPO).

Programmatically accessing SCKAN:

For programmatic access, the latest release of SCKAN can be found at GitHub or find the SCKAN release at Zenodo.

Querying the SPARC Connectivity Knowledge Base of the Autonomic Nervous system (SCKAN) can be done programmatically using Cypher or SPARQL. We have created a containerized version of SCKAN that can be downloaded and installed locally along with the necessary documentation. We highlight how to use SCKAN in some example queries, but you can access all the information in SCKAN using this package. See the SCKAN Release page for more information about what is contained in the package.

We continue to develop new queries and welcome the submission of new queries. If you would like to request an addition, please use the feedback form .

SCKAN releases will be available in Zenodo. Each release will include a Docker container with the body of connections in the first release along with new connections that have been added to meet the needs of SPARC over the past quarter. We will specify circuits and general connectivity in each release, as well as identify areas that are not included.

Example queries:

• SCKAN Query Examples, including examples in Jupyter Notebook
• SCKAN query examples

Feedback

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Provide feedback about SCKAN or the SCKAN Tools in this form, this includes requests for future queries you would like to have added to SCKAN.