Unfortunately, I will not be able to participate in the BioRDF call today.
For the purposes of our W3C notes, I have extended one of the demo queries
so that it also includes references to receptors in the NeuronDB database of
SenseLab (http://neuroweb.med.yale.edu/senselab/). Based on the gene records
found in the original Banff query, this query also retrieves corresponding
receptor proteins from NeuronDB, if available. These references to NeuronDB
could then be used to retrieve further neuroanatomic and -physiologic
information, but this is not included in this query. This query spans (at
least) 5 different information sources.
The query requires a newer version of SenseLab than that of the original
HCLS KB. I have put this newer vesion into the graph
<http://purl.org/ycmi/senselab/neuron_ontology.owl> on the DERI server.
You can copy&past the query below into the SPARQL query form at
http://hcls.deri.ie/sparql
or you can run the query with a single click on
http://tinyurl.com/268rjf
"Query: Genes associated with CA1 Pyramidal Neurons and signal transduction
processes.
Signal transduction pathways are considered to be rich proteins that might
respond to chemical therapy. CA1 Pyramidal Neurons are known to be
particularly damaged in Alzheimer's disease.
Can we find candidate genes known to be involved in signal transduction and
active in Pyramidal Neurons?"
===============
prefix go: <http://purl.org/obo/owl/GO#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix mesh: <http://purl.org/commons/record/mesh/>
prefix sc: <http://purl.org/science/owl/sciencecommons/>
prefix ro: <http://www.obofoundry.org/ro/ro.owl#>
prefix senselab: <http://purl.org/ycmi/senselab/neuron_ontology.owl#>
SELECT ?paper ?gene_record_name ?process ?processname ?receptor_protein
?receptor_protein_name
WHERE
{
graph <http://purl.org/commons/hcls/pubmesh> {
?paper ?p mesh:D017966 .
?article sc:identified_by_pmid ?paper .
?gene_record sc:describes_gene_or_gene_product_mentioned_by ?article .
}
OPTIONAL {
graph <http://purl.org/ycmi/senselab/neuron_ontology.owl> {
?gene owl:equivalentClass ?restriction1 .
?restriction1 owl:onProperty
senselab:has_nucleotide_sequence_described_by .
?restriction1 owl:hasValue ?gene_record .
?receptor_protein rdfs:subClassOf ?restriction2 .
?restriction2 owl:onProperty senselab:proteinGeneProductOf .
?restriction2 owl:someValuesFrom ?gene .
?receptor_protein rdfs:label ?receptor_protein_name
}
}
graph <http://purl.org/commons/hcls/goa> {
?protein rdfs:subClassOf ?restriction3 .
?restriction3 owl:onProperty ro:has_function .
?restriction3 owl:someValuesFrom ?restriction4 .
?restriction4 owl:onProperty ro:realized_as .
?restriction4 owl:someValuesFrom ?process .
graph <http://purl.org/commons/hcls/20070416/classrelations> {
{
?process <http://purl.org/obo/owl/obo#part_of> go:GO_0007166 .
}
union
{
?process rdfs:subClassOf go:GO_0007166 .
}
}
?protein rdfs:subClassOf ?protein_superclass .
?protein_superclass owl:equivalentClass ?restriction5 .
?restriction5 owl:hasValue ?gene_record .
}
graph <http://purl.org/commons/hcls/gene> {
?gene_record rdfs:label ?gene_record_name .
}
graph <http://purl.org/commons/hcls/20070416> {
?process rdfs:label ?processname .
}
}
LIMIT 30
===============
The query could require some improvement, for example, the specifity for
pyramidal neurons is based on the MeSH annotation of the PubMed articles,
not on the information in NeuronDB.
cheers,
Matthias Samwald
P.S.: The [semweb-lifesci] tag is not a christmas present from the admins, I
just typed it myself.