Neurondb

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This page contains some notes about queries against neurondb ontology and across some other related data sources.

Which neuron has I_K currents in what compartments, show me the evidences.

Without class relation: We first experiment the query without using the class level relation.

Issues remained:

  • Reasoning incapability of the query engine.


PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX scdef: <http://purl.org/science/owl/sciencecommons/>
PREFIX neurondb: <http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>

select ?neuron,?compartment, ?evidence
Where {
  ?a rdfs:subClassOf ?neuron.
  ?a scdef:has_supporting_evidence ?evidence . 
  ?a rdfs:subClassOf ?b.
  ?b rdf:type owl:Restriction.
  ?b owl:onProperty <http://www.obofoundry.org/ro/ro.owl#has_part>.
  ?b owl:someValuesFrom ?c.
  ?c rdfs:subClassOf ?compartment.
  ?compartment rdfs:subClassOf neurondb:Compartment.
  ?c rdfs:subClassOf ?d.
  ?d rdf:type owl:Restriction.
  ?d owl:onProperty neurondb:has_Current.
  ?d owl:someValuesFrom neurondb:I_K.
}

Results:
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Thalamic_relay_neuron http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_Thalamic_relay_neuron_with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Thalamic_relay_neuron http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Dep http://purl.org/science/evidence/Evidence_for_Thalamic_relay_neuron_with_I_K_current_in_Dep 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#CA1_pyramidal_neuron http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_CA1_pyramidal_neuron_with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Dentate_granule_cell http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_Dentate_granule_cell_with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Olfactory_receptor_neuron http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_Olfactory_receptor_neuron_with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Olfactory_bulb_mitral_cell http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_Olfactory_bulb_mitral_cell_with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Olfactory_bulb_mitral_cell http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#AH http://purl.org/science/evidence/Evidence_for_Olfactory_bulb_mitral_cell_with_I_K_current_in_AH 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#CA3_pyramidal_neuron http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_CA3_pyramidal_neuron_with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#CA3_pyramidal_neuron http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Dap http://purl.org/science/evidence/Evidence_for_CA3_pyramidal_neuron_with_I_K_current_in_Dap 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#CA3_pyramidal_neuron http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Dad http://purl.org/science/evidence/Evidence_for_CA3_pyramidal_neuron_with_I_K_current_in_Dad 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#CA3_pyramidal_neuron http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Dam http://purl.org/science/evidence/Evidence_for_CA3_pyramidal_neuron_with_I_K_current_in_Dam 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Neocortical_pyramidal_neuron__deep http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Dad http://purl.org/science/evidence/Evidence_for_Neocortical_pyramidal_neuron__deep_with_I_K_current_in_Dad 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Neocortical_pyramidal_neuron__deep http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Dam http://purl.org/science/evidence/Evidence_for_Neocortical_pyramidal_neuron__deep_with_I_K_current_in_Dam 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Neocortical_pyramidal_neuron__deep http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_Neocortical_pyramidal_neuron__deep_with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Neocortical_pyramidal_neuron__deep http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Dap http://purl.org/science/evidence/Evidence_for_Neocortical_pyramidal_neuron__deep_with_I_K_current_in_Dap 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#CN_bushy_cell http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_CN_bushy_cell_with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Hair_cell__auditory_ http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_Hair_cell__auditory__with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#CN_pyramidal__fusiform__cell http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_CN_pyramidal__fusiform__cell_with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Olfactory_projection_neuron http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_Olfactory_projection_neuron_with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Cerebellar_purkinje_cell http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Dem http://purl.org/science/evidence/Evidence_for_Cerebellar_purkinje_cell_with_I_K_current_in_Dem 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Cerebellar_purkinje_cell http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Soma http://purl.org/science/evidence/Evidence_for_Cerebellar_purkinje_cell_with_I_K_current_in_Soma 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Cerebellar_purkinje_cell http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Ded http://purl.org/science/evidence/Evidence_for_Cerebellar_purkinje_cell_with_I_K_current_in_Ded 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Cerebellar_purkinje_cell http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Dep http://purl.org/science/evidence/Evidence_for_Cerebellar_purkinje_cell_with_I_K_current_in_Dep


With class relation:

Step 1: Adding part_of class relation. 


PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

insert in graph <http://neuroweb.med.yale.edu/senselab/neuron_ontology_classrelation.owl> 
   {  ?whole <http://www.obofoundry.org/ro/ro.owl#has_part> ?part. }
FROM <http://neuroweb.med.yale.edu/senselab/neuron_ontology_0503.owl>
WHERE 
 {
   ?whole rdfs:subClassOf ?sub.
   ?sub rdf:type owl:Restriction.
   ?sub owl:onProperty <http://www.obofoundry.org/ro/ro.owl#has_part>.
   ?sub owl:someValuesFrom ?part.
 }

Results: Insert into , 887 triples -- done


Step 2 Adding has_current class relation. 


PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX neurondb: <http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
insert in graph <http://neuroweb.med.yale.edu/senselab/neuron_ontology_classrelation.owl> 
   {  ?whole neurondb:has_Current ?part. }
FROM <http://neuroweb.med.yale.edu/senselab/neuron_ontology_0503.owl>
WHERE 
 {
   ?whole rdfs:subClassOf ?sub.
   ?sub rdf:type owl:Restriction.
   ?sub owl:onProperty neurondb:has_Current .
   ?sub owl:someValuesFrom ?part.
 }

Results: Insert into , 426 triples -- donene


Step 3. Query by using class relation. 

PREFIX scdef: <http://purl.org/science/owl/sciencecommons/>
PREFIX neurondb: <http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#>
SELECT ?neuron, ?compartment, ?evidence
WHERE {
?a rdfs:subClassOf ?neuron.
?a rdfs:subClassOf ?b.
?a scdef:has_supporting_evidence ?evidence . 
?a <http://www.obofoundry.org/ro/ro.owl#has_part?> ?c.
?c rdfs:subClassOf ?compartment.
?compartment rdfs:subClassOf neurondb:Compartment.
?c neurondb:has_Current  "I_K".
}


Query the genes and proteins relating to CA1_pyramidal_neuron

Without class relations. 

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX scdef: <http://purl.org/science/owl/sciencecommons/>
PREFIX ro: <http://www.obofoundry.org/ro/ro.owl#>
PREFIX neurondb: <http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#>

SELECT ?gene, ?protein WHERE {
  ?a rdfs:subClassOf neurondb:CA1_pyramidal_neuron.
  ?a rdfs:subClassOf ?b.
  ?b rdf:type owl:Restriction.
  ?b owl:onProperty ro:has_part.
  ?b owl:someValuesFrom ?c.
 
  ?c rdfs:subClassOf ?d.
  ?d rdfs:subClassOf neurondb:Compartment.
  ?c rdfs:subClassOf ?e.
  ?e rdf:type owl:Restriction.
  ?e owl:onProperty neurondb:has_Receptor.
  ?e owl:someValuesFrom ?f.
  
  ?f rdfs:subClassOf ?g.
  ?g rdf:type owl:Restriction.
  ?g owl:onProperty neurondb:proteinGeneProductOf.
  ?g owl:someValuesFrom ?gene.
  
  ?f owl:equivalentClass ?h.
  ?h rdf:type owl:Restriction.
  ?h owl:onProperty scdef:has_peptide_sequence_described_by.
  ?h owl:hasValue ?protein.
}

Results:
 gene  protein ;
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Gabrg1_Gene  http://purl.org/commons/record/uniprotkb/Q8N1C3 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#GABBR1_Gene  http://purl.org/commons/record/uniprotkb/Q9UBS5 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Gabrg1_Gene  http://purl.org/commons/record/uniprotkb/Q8N1C3 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#GABBR1_Gene  http://purl.org/commons/record/uniprotkb/Q9UBS5 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#gria3_Gene  http://purl.org/commons/record/uniprotkb/P42263 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#gria3_Gene  http://purl.org/commons/record/uniprotkb/P42263 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Gabrg1_Gene http://purl.org/commons/record/uniprotkb/Q8N1C3 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#GABBR1_Gene  http://purl.org/commons/record/uniprotkb/Q9UBS5 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Gabrg1_Gene  http://purl.org/commons/record/uniprotkb/Q8N1C3 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#GABBR1_Gene  http://purl.org/commons/record/uniprotkb/Q9UBS5 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Gabrg1_Gene  http://purl.org/commons/record/uniprotkb/Q8N1C3 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#GABBR1_Gene  http://purl.org/commons/record/uniprotkb/Q9UBS5 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#gria3_Gene  http://purl.org/commons/record/uniprotkb/P42263 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#GABBR1_Gene  http://purl.org/commons/record/uniprotkb/Q9UBS5 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Gabrg1_Gene  http://purl.org/commons/record/uniprotkb/Q8N1C3 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#gria3_Gene  http://purl.org/commons/record/uniprotkb/P42263 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#GABBR1_Gene  http://purl.org/commons/record/uniprotkb/Q9UBS5 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#Gabrg1_Gene  http://purl.org/commons/record/uniprotkb/Q8N1C3


With class relation. 


PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX scdef: <http://purl.org/science/owl/sciencecommons/>
PREFIX ro: <http://www.obofoundry.org/ro/ro.owl#>
PREFIX neurondb: <http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#>
SELECT ?gene, ?protein
WHERE {
?a rdfs:subClassOf neurondb:CA1_pyramidal_neuron.
?a ro:has_part ?b.
?b neurondb:has_Receptor ?c.
?c neurondb:proteinGeneProductOf ?gene.
?c scdef:has_peptide_sequence_described_by ?protein.
}


List the Neurons found in the hippocampus region that express the “I_K” current or channel

Without class relation. 


PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX neurondb: <http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#>
PREFIX ro: <http://www.obofoundry.org/ro/ro.owl#>

SELECT distinct ?neuron
WHERE {
    neurondb:Hippocampus rdfs:subClassOf ?a.
    ?a rdf:type owl:Restriction.
    ?a owl:onProperty neurondb:has_part.
    ?a owl:someValuesFrom ?neuron.   

    ?b rdfs:subClassOf ?neuron.
    ?b rdfs:subClassOf ?c.
    ?c rdf:type owl:Restriction.
    ?c owl:onProperty ro:has_part.
    ?c owl:someValuesFrom ?d.
    
    ?d rdfs:subClassOf ?e.
    ?e rdfs:subClassOf neurondb:Compartment.
    ?d rdfs:subClassOf ?f.
    ?f rdf:type owl:Restriction.
    ?f owl:onProperty neurondb:has_Current.
    ?f owl:someValuesFrom neurondb:I_K.
}

Result:

http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#CA1_oriens_alveus_interneuron 
http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#CA1_pyramidal_neuron


With class relation. 

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX neurondb: <http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#>
PREFIX ro: <http://www.obofoundry.org/ro/ro.owl#>
SELECT ?neuron
WHERE {
   neurondb:Hippocampus ro:has_part ?neuron.
   ?a rdfs:subClassOf ?neuron.
   ?a ro:has_part ?b.
   ?b neurodb:hasCurrent neurondb:I_K.
 }


Query from different data sources

Semantic relation enables query across different data sources. This example showcases the query across Birnlex and neurondb. (To be tested.) 



PREFIX neurondb: <http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#>
PREFIX birnlex: <http://www.nbirn.net/birnlex/1.1/BIRNLex-OBO-UBO.owl#>

SELECT ?neuron
from http://www.nbirn.net/birnlex/1.1/BIRNLex-OBO-UBO.owl,
from http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl,
from http://neuroweb.med.yale.edu/senselab/senselab-bfo-obi-birnlex-bams-mapping-april-05-b.owl,
WHERE{
  ?neuron rdfs:subClassOf ?b.
  ?b rdfs:label "Purkinje_neuron".
}
Retrieved from "https://www.w3.org/wiki/index.php?title=Neurondb&oldid=2694"