SenseLab Semantic Web Development

The Semantic Web development of SenseLab involves exporting data from NeuronDB, ModelDB, and BrainPharm to RDF and/or OWL format. The overall goal is to facilitate neuroscience data aggregation, integration, and reasoning using Semantic Web technologies.

This project is part of the current and ongoing SenseLab effort including the following SenseLab team members: Kei Cheung, Huajun Chen, Ernest Lim, Matthias Samwald, Peter Masiar, Luis Marenco, Tom Morse, Nian Liu, Chiquito Crasto, Perry Miller, and Gordon Shepherd.

SenseLab OWL ontologies

Right-click and select save as to download the following files. These ontologies can also be imported by OWL-enabled software. The links always point to the most recent version of each ontology. Ontologies are updated periodically and without further notice. Stable versions of each ontology can be downloaded / imported from the SVN repository.

NeuronDB OWL file -- NeuronDB contains descriptions of anatomic locations, cell architecture and physiologic parameters of neuronal cells based on compartmental models of neurons.
ModelDB OWL file -- ModelDB is a large repository of computational neuroscience models and simulations. The mathematical models in ModelDB are annotated with references to NeuronDB.
BrainPharm OWL file -- The pilot BrainPharm database is intended to support research on drugs for the treatment of neurological disorders. It enhances the descriptions in a portion of NeuronDB with descriptions of the actions of pathological and pharmacological agents.
NeuronDB - BFO mapping -- A mapping between NeuronDB and the Basic Formal Ontology (BFO).
NeuronDB - CCDB SAO mapping -- A mapping between NeuronDB an the CCDB Subcellular Anatomy Ontology.
OWL mapping of Senselab to Birnlex, BAMS, BFO, OBI
NeuronDB generalized classes OWL file

Some of above ontologies (e.g., NeuronDB) have been updated. These updated ontologies will be released in the future.

SPARQL endpoint

The ontologies can also be queried through a SPARQL endpoint at

http://neuroweb.med.yale.edu:8890/sparql

The graph names of the ontologies are identical with those of the OWL files, e.g., http://purl.org/ycmi/senselab/neuron_ontology.owl is the name of the graph for the NeuronDB ontology.

Related ontologies

OWL version of the PDSP Ki database

Subversion repository

Older versions of the ontologies can be downloaded / imported from the SVN repository at

http://neuroweb.med.yale.edu/svn

SenseLab Conversion into Access tables

MS Access version

Previous RDF conversions (outdated)

RDF and N-triple Version of NeuronDB

For any question regarding these files please contact:

Kei Cheung: Kei.Cheung (at) Yale.edu
Matthias Samwald: samwald (at) gmx.at
Ernest Lim: Ernest.Lim (at) Yale.edu