From W3C Wiki
BrainPharm is a database UNDER DEVELOPMENT to support research on drugs for the treatment of different neurological disorders. It contains agents that act on neuronal properties (e.g., transmitters, channels, and receptors) in the normal brain and in nervous disorders. It enables searches for drug actions at the level of key molecular constituents, cell compartments and individual cells. For more information, please visit http://senselab.med.yale.edu/BrainPharm/
Recently we have created an RDFS ontology for BrainPharm (Media:BrainPharm$brainpharm_ontology_rdfs.rdfs), which models information about the effect of drugs on pathological (or molecular) mechanisms (which involve neuronal properties such as receptors, currents, and neurotransmitters) mediating the pathological changes in various neurological disorders such as Alzheimer's Disease. The ontology diagram of BrainPharm is available here: Media:BrainPharm$brainpharm_ontology. The main classes include: disease (e.g., AD), drug (subclass of agent), pathological mechanism (which contains related pharmacological and pathological information), pathological change (which has a pathological agent and its effect and targets), neuron (e.g., CA1 pyramidal neuron), and neuron property (which has the following subclasses: transmitter, current, and receptor). There are also non-hierarchical relationships among these classes. For example, pathological mechanism relates to drug through the hasPharmacologicalAgent property. With such an ontology, we can model the following:
- the pathological changes caused by certain pathological agents (e.g., beta Amyloid) to the neuronal properties (e.g., beta Amyloid inhibits the I Calcium channel of CA1 pyramidal neuron),
- the drugs and their actions on the pathological changes (e.g., Nifedipine reduces the pathological effect of beta Amlyloid on the molecular properties such as the I Calcium channel of CA1 pyramidal neuron),
- stages of the disease (e.g., early, middle, and late stages), and
- literature sources (e.g., PubMed sources).
To download an example data set in RDF format, just click on: Media:BrainPharm$brainpharm_sample.rdf.