All,
We've reloaded: NeuroCommons.
Added:
1. Freebase (this is the version used in the Billion Triples Challenge
for now; Freebase folks plan to make an up to data RDF dump available soon)
2. DBtune (*Yves please give this a look over*)
3. GeoSpecies
Quick Tests for NeuroCommons:
SPARQL:
# Banff 2007 Demo Query 1: GO Process Terms with "dendrite" in their names
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX go: <http://purl.org/obo/owl/GO#>
PREFIX obo: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select ?name ?class ?definition
where
{ ?class rdfs:subClassOf go:GO_0008150.
?class rdfs:label ?name.
?class obo:hasDefinition ?def.
?def rdfs:label ?definition
filter(regex(str(?name),"[Dd]endrite"))
}
# Banff 2007 Demo Query 2: CA1 Pyramidal Neuron related genes involved
in signal transduction processes
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#>
select distinct ?genename ?processname
where
{
?paper ?p mesh:D017966.
?article sc:identified_by_pmid ?paper.
?gene sc:describes_gene_or_gene_product_mentioned_by ?article.
?protein rdfs:subClassOf ?res.
?res owl:onProperty ro:has_function.
?res owl:someValuesFrom ?res2.
?res2 owl:onProperty ro:realized_as.
?res2 owl:someValuesFrom ?process.
{ ?process <http://purl.org/obo/owl/obo#part_of> go:GO_0007166 }
union
{ ?process rdfs:subClassOf go:GO_0007166 }
?protein rdfs:subClassOf ?parent.
?parent owl:equivalentClass ?res3.
?res3 owl:hasValue ?gene.
?gene sc:ggp_has_primary_description ?genename.
?process rdfs:label ?processname
}
Full Text Patterns:
1. ionotropic glutamate receptor signaling pathway
2. negative regulation of dendrite morphogenesis
Links:
1. http://lod.openlinksw.com/sparql -- SPARQL Endpoint
2. http://lod.openlinksw.com/fct/facet.vsp -- Server Hosted Faceted
Browser Interface delivering "Full Text Search" and/or "Property or Type
driven Find").
The loading effort continues :-)
--
Regards,
Kingsley Idehen Weblog: http://www.openlinksw.com/blog/~kidehen
President & CEO
OpenLink Software Web: http://www.openlinksw.com
