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

From: Eric Prud'hommeaux <eric@w3.org>
Date: Tue, 25 Dec 2007 09:34:43 -0500
To: Matthias Samwald <samwald@gmx.at>
Cc: public-semweb-lifesci@w3.org, Kei Cheung <kei.cheung@yale.edu>
Message-ID: <20071225143442.GA28779@w3.org>
[Lots of stuff @L115 (+105)]

* Matthias Samwald <samwald@gmx.at> [2007-12-17 14:13+0100]
>
> 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.

I didn't dig into this, but I did look for the intersection of the
SenseLab sequence data at DERI with that at Science Commons. I could
have chosen better than to unify on pmid, but it served the
purpose. The following records were linked by gene record to both GO
and NeuronDB:

http://purl.org/commons/record/pmid/8840028, Entrez Gene record for human GRM7, 2917, negative regulation of adenylate cyclase activity
http://purl.org/commons/record/pmid/8840028, Entrez Gene record for human GRM7, 2917, negative regulation of adenylate cyclase activity
http://purl.org/commons/record/pmid/8840028, Entrez Gene record for human GRM7, 2917, G-protein coupled receptor protein signaling pathway
http://purl.org/commons/record/pmid/8840028, Entrez Gene record for human GRM7, 2917, G-protein coupled receptor protein signaling pathway

http://purl.org/commons/record/pmid/10698743, Entrez Gene record for human DRD1, 1812, dopamine receptor, adenylate cyclase activating pathway
http://purl.org/commons/record/pmid/10698743, Entrez Gene record for human DRD1, 1812, G-protein signaling, coupled to cyclic nucleotide second messenger
http://purl.org/commons/record/pmid/10698743, Entrez Gene record for human DRD1, 1812, dopamine receptor, adenylate cyclase activating pathway
http://purl.org/commons/record/pmid/10698743, Entrez Gene record for human DRD1, 1812, G-protein signaling, coupled to cyclic nucleotide second messenger
http://purl.org/commons/record/pmid/10698743, Entrez Gene record for human DRD1IP, 50632, dopamine receptor signaling pathway
http://purl.org/commons/record/pmid/10698743, Entrez Gene record for human DRD1IP, 50632, dopamine receptor signaling pathway
http://purl.org/commons/record/pmid/10698743, Entrez Gene record for human DRD1IP, 50632, dopamine receptor signaling pathway
http://purl.org/commons/record/pmid/10698743, Entrez Gene record for human DRD1IP, 50632, dopamine receptor signaling pathway

http://purl.org/commons/record/pmid/10753124, Entrez Gene record for human SSTR5, 6755, G-protein signaling, coupled to cyclic nucleotide second messenger
http://purl.org/commons/record/pmid/10753124, Entrez Gene record for human SSTR5, 6755, G-protein signaling, coupled to cyclic nucleotide second messenger
http://purl.org/commons/record/pmid/10753124, Entrez Gene record for human DRD2, 1813, G-protein coupled receptor protein signaling pathway
http://purl.org/commons/record/pmid/10753124, Entrez Gene record for human DRD2, 1813, dopamine receptor, adenylate cyclase inhibiting pathway
http://purl.org/commons/record/pmid/10753124, Entrez Gene record for human DRD2, 1813, G-protein coupled receptor protein signaling pathway
http://purl.org/commons/record/pmid/10753124, Entrez Gene record for human DRD2, 1813, dopamine receptor, adenylate cyclase inhibiting pathway

http://purl.org/commons/record/pmid/11441182, Entrez Gene record for human ADRB2, 154, arrestin mediated desensitization of G-protein coupled receptor protein signaling pathway
http://purl.org/commons/record/pmid/11441182, Entrez Gene record for human ADRB2, 154, arrestin mediated desensitization of G-protein coupled receptor protein signaling pathway
http://purl.org/commons/record/pmid/11441182, Entrez Gene record for human ADRB2, 154, transmembrane receptor protein tyrosine kinase activation (dimerization)
http://purl.org/commons/record/pmid/11441182, Entrez Gene record for human ADRB2, 154, transmembrane receptor protein tyrosine kinase activation (dimerization)
http://purl.org/commons/record/pmid/11441182, Entrez Gene record for human ADRB2, 154, adenylate cyclase activation
http://purl.org/commons/record/pmid/11441182, Entrez Gene record for human ADRB2, 154, adenylate cyclase activation


Here's the set difference of papers involved in potential solutions to
the use case query:
http://purl.org/commons/record/pmid/7816096, sc
http://purl.org/commons/record/pmid/8783260, sc
http://purl.org/commons/record/pmid/9003074, sc
http://purl.org/commons/record/pmid/9502803, sc
http://purl.org/commons/record/pmid/10521598, sc
http://purl.org/commons/record/pmid/10749211, sc
http://purl.org/commons/record/pmid/11421580, sc
http://purl.org/commons/record/pmid/11841602, deri
http://purl.org/commons/record/pmid/14657172, deri
http://purl.org/commons/record/pmid/14707550, sc
http://purl.org/commons/record/pmid/16640790, deri

Should have used ?process, but I'm moving on now and wanted to
document my acquired intel. I have selected GO:0007190, though
I considered GO:0007187 as it has a simpler relationship to
GO:0007166

Incidentally, we say in our demos that we are interested in genes
"involved in signal transduction" while we are actually looking for
7166, cell surface receptor linked signal transduction, a
specialization of signal transduction. s/7166/7165/ drops these solns:
  ncbi_gene:1812, go:GO_0007187
  ncbi_gene:1812, go:GO_0007187
  ncbi_gene:1812, go:GO_0007191
  ncbi_gene:1812, go:GO_0007191
  ncbi_gene:1813, go:GO_0007186
  ncbi_gene:1813, go:GO_0007186
  ncbi_gene:1813, go:GO_0007195
  ncbi_gene:1813, go:GO_0007195
  ncbi_gene:2902, go:GO_0007215
  ncbi_gene:2902, go:GO_0007215
  ncbi_gene:2902, go:GO_0007215
  ncbi_gene:2902, go:GO_0007215
  ncbi_gene:6755, go:GO_0007187
  ncbi_gene:6755, go:GO_0007187
  ncbi_gene:50632, go:GO_0007212
  ncbi_gene:50632, go:GO_0007212
  ncbi_gene:50632, go:GO_0007212
  ncbi_gene:50632, go:GO_0007212
and adds these:
  ncbi_gene:154, go:GO_0000187
  ncbi_gene:154, go:GO_0000187
  ncbi_gene:154, go:GO_0043410
  ncbi_gene:154, go:GO_0043410
  ncbi_gene:2785, go:GO_0000187
  ncbi_gene:2785, go:GO_0000187
  ncbi_gene:3084, go:GO_0046579
  ncbi_gene:3084, go:GO_0046579
  ncbi_gene:5590, go:GO_0007242
  ncbi_gene:5590, go:GO_0007242
  ncbi_gene:5864, go:GO_0007264
  ncbi_gene:5864, go:GO_0007264
  ncbi_gene:8567, go:GO_0000187
  ncbi_gene:8567, go:GO_0000187
  ncbi_gene:1139, go:GO_0000187
  ncbi_gene:1139, go:GO_0000187
  ncbi_gene:22983, go:GO_0007243
  ncbi_gene:22983, go:GO_0007243

Intuitively, I wouldn't expect any to get dropped. I suspected these
were dropped due to a lack of transitivity through
  ?process (rdfs:subClassOf | obo:part_of)* go:GO_0007166
(i.e. a subClassOf a part_of ...) but inspection of 7195
  http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0007195&selected=GO:0007195&viz=graph
didn't back that up. I haven't poked at the SC KB to make sure that
it's triples reflect what I expect from the ebi site.


> cheers,
> Matthias Samwald
>
> P.S.: The [semweb-lifesci] tag is not a christmas present from the admins, 
> I just typed it myself. 

And this time was my christmas present to you.
-- 
-eric

office: +1.617.258.5741 NE43-344, MIT, Cambridge, MA 02144 USA
mobile: +1.617.599.3509

(eric@w3.org)
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Received on Tuesday, 25 December 2007 14:35:26 UTC

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