Neural Activity Resource (NAR) Calcium Imaging Ontology (NARCI)

The need for semantic description of data sets as a metadata, specially those originating from neuroscience experiments are well established due to diversity of experimental procedures and modalities. NARCI, Neural Activity Resource (NAR) Calcium Imaging Ontology, provides a semantic graph schema for describing Calcium Imaging experiments based on the work Montijn et al., 2016, Cell Reports 16, 2486–2498 doi.

This is an RDF schema using OWL languge and should be used to expressmetadata from a calcium imaging experiment.

Programmatic Usage

• For short tutorial on how to use the ontology programmatically via rdflib see python notebook under tutorial.

narci release management

The versions of the persistent URL of the ontology, narci should be used in production. Note that once it is released, schema version move to dev of next release number, first minor in the repository, for development purpose. The schema persistent URLs versioning should match with the released version. Documentation and tutorial for each version can be found in the released versions, tagged versions or in released files, these should be linked in the below list of production URLs.

Ontology current development URL

Development is performed on ontology/narci file in Turtle syntax.

• http://www.purl.org/narci/v0.3dev/schema

Ontology in production URLs

• http://www.purl.org/narci/v0.2.1/schema
  tutorial | full graph | prov graph

Release procedure

• Continue using dev version (URL) pointing to master branch.
• Once it is released, if not yet updated, update tutorials README.md with the new version and create a persistent URL with the correct version pointing to corresponding tag, release version.
• Remove previous dev version persistent URL to avoid unreachable links. There should be only single development persistent URL at a time.

Versions

versions directory contains all production releases prior to dev version. It contains turtle syntax file in .tll extension and auto-converted HBP compatible JSON-LD format with .json extension.

Resources used

We have listed resources, including peer-review papers used in developing this schema ontology: RESOURCE.md. Please update this document for any additional resource.

How to cite

• Neural Activity Resource Calcium Imaging Ontology, M.Suezen, G.Meijer, X.Troncoso, J.S.Montijn, C.S.Lansink, A.P.Davison, M.Denker, T.Wachtler, S.Gruen, C.M.A.Pennartz (2017) http://www.purl.org/narci/v0.2.1/schema

License

This work is licensed under a Creative Commons Attribution 4.0 Generic License.

(c) 2017, 2018 University of Amsterdam
               Forschungszentrum Juelich GmbH
               The German Neuroinformatics Node (G-Node)
               Le Centre National de la Recherche Scientifique (CRNS)

        

Mailing list

There is a group/mailing list for narci called narci:Calcium Imaging Ontology, Group: narci-ontology.

References

• Population-Level Neural Codes Are Robust to Single-Neuron Variability from a Multidimensional Coding Perspective Montijn et al., 2016, Cell Reports 16, 2486–2498 doi.

Acknowledgements

narci is developed under the auspices of European Union (EU) Human Brain Project (HBP). Work package SP 5.7.2 named NAR within the Neuroinformatics Platform.