W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > December 2007

[semweb-lifesci] Extended HCLS demo query (including SenseLab)

From: Matthias Samwald <samwald@gmx.at>
Date: Mon, 17 Dec 2007 14:13:22 +0100
Message-ID: <631637CFD15A4B0D848AD0AEF515BB5B@tessellate>
To: <public-semweb-lifesci@w3.org>
Cc: "Kei Cheung" <kei.cheung@yale.edu>

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. 
Received on Monday, 17 December 2007 13:13:55 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:34 UTC