HCLS/DemoScript/Senselab Notes

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Notes about querying the NeuronDB and Brainpharm.


Which Neurons have I_K currents

Asking which neurons have I_K currents in Media:HCLS$$DemoScript$$Senselab_Notes$neurondb-20070429.owl, without overstatements. Assuming that in LSW we have already executed

(setq kb (load-kb-jena "http://esw.w3.org/topic/HCLS/DemoScript/Senslab_Notes?action=[[AttachFile]]&do=get&target=neurondb-20070429.owl"))

First: Which classes of neurons have parts which have I_K currents.


(descendants (manch (some !oborel:has_part (some !neurondb:has_Currents !neurondb:I_K)))  kb)

=>

!neurondb:Olfactory_cortex_interneuron__superficial_with_I_K_current_in_A 
!neurondb:Neocortical_pyramidal_neuron__deep_with_I_K_current_in_Dad 
!neurondb:Nigral_dopaminergic_cell_with_I_K_current_in_AH 
!neurondb:Dentate_granule_cell_with_I_K_current_in_Soma 
...


These produce the evidence classes. We can ask about the evidence like this:

PREFIX scdef: <http://purl.org/science/owl/sciencecommons/>
PREFIX neurondb: <http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl#>
SELECT ?p ?v
WHERE { 
neurondb:Dentate_granule_cell_with_I_K_current_in_Soma scdef:has_supporting_evidence ?evidence . 
?evidence ?p ?v . } 
Results:
!rdf:type	!evidence:0000033
!scdef:cites_evidence_source	!science:article/pmid/8814103
!rdfs:comment	"
Properties of K+ outward currents were investigated in human DG cells from 11 specimens obtained from patients with temporal lobe epilepsy. An IK was observed in all cells. The average current density, the time-dependent decay, and the resting membrane characteristics were not significantly different between patients with and without Ammon Horn Sclerosis. The V1/2inact was shifted in a hyperpolarizing direction in AHS -67.7mV compared with that in hippocampi not showing AHS -47.7mV [207]. The properties of outward currents were investigated with patch-clamp in acutely isolated rat DGCs at various postnatal ages and at adulthood 2-3 mo. Kinetic analysis and pharmacological properties showed that IK and IA were present in these cells. IA and IK remained stable with respect to kinetic properties during ontogenesis, but the relative contribution and pharmacological properties varied with age. IA dominated in P5-7 cells whereas IK was prominent in most older cells [208]."


But we would like just upper level classes, for a summary. So we ask for all the superclasses of the above, and only take ones that are one level of subclass below Neuron.


(intersection 
  (mapcan (lambda(c) (children c kb)) (children !neurondb:Neuron kb))
  (mapcan (lambda(p) (ancestors p kb)) 
     (descendants (manch (some !oborel:has_part (some !neurondb:has_Currents !neurondb:I_K)))  kb)))
=>
!neurondb:Olfactory_cortex_interneuron__superficial 
!neurondb:Olfactory_bulb_periglomerular_cell 
!neurondb:CA1_oriens_alveus_interneuron 
!neurondb:Spinal_Ia_interneuron 
!neurondb:Neostriatal_spiny_neuron 
!neurondb:Hair_cell__auditory_ 
!neurondb:Olfactory_cortex_pyramidal_neuron 
!neurondb:Dentate_granule_cell 
!neurondb:Retinal_ganglion_cell 
!neurondb:CN_pyramidal__fusiform__cell 
!neurondb:CN_bushy_cell 
!neurondb:Cerebellar_purkinje_cell 
!neurondb:Olfactory_receptor_neuron 
!neurondb:Nigral_dopaminergic_cell 
!neurondb:CA1_pyramidal_neuron 
!neurondb:Thalamic_relay_neuron 
!neurondb:Spinal_motor_neuron 
!neurondb:Olfactory_projection_neuron 
!neurondb:Olfactory_bulb_mitral_cell 
!neurondb:CN_octopus_cell 
!neurondb:Neocortical_pyramidal_neuron__superficial 
!neurondb:CA3_pyramidal_neuron 
!neurondb:Neocortical_pyramidal_neuron__deep 


Which papers mention deep neocortical pyramidal neurons

We can also ask, which papers mention deep neocortical pyramidal neurons, though the simply expressed form of this depends on pellet to correctly answer subclasses. To test this in LSW, compare the query that generated the results below


(sparql
   '(:select (?article) () (?class !rdfs:subClassOf !neurondb:Neocortical_pyramidal_neuron__deep) 
		   (?class !scdef:has_supporting_evidence ?evidence)
		   (?evidence !scdef:cites_evidence_source ?article)) :use-reasoner :jena :kb kb :trace t)


which uses the "reasoner" :jena, which is Jena backed by a Pellet ontmodel, with the results you get if you change :jena to :none, which queries just the literal graph (none)


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#>
SELECT ?article
WHERE { 
?class rdfs:subClassOf neurondb:Neocortical_pyramidal_neuron__deep . 
?class scdef:has_supporting_evidence ?evidence . 
?evidence scdef:cites_evidence_source ?article . } 

Results:
!science:article/pmid/11160518
!science:article/pmid/11160518
!science:article/pmid/284423
!science:article/pmid/284423
!science:article/pmid/10856117
!science:article/pmid/10922009
!science:article/pmid/10856117
!science:article/pmid/11264682
!science:article/pmid/11264682
!science:article/pmid/7658365
!science:article/pmid/7658365
!science:article/pmid/12736335
!science:article/pmid/11264682
!science:article/pmid/10758340
!science:article/pmid/11264682
!science:article/pmid/7658365
!science:article/pmid/11535687
!science:article/pmid/10856117
!science:article/pmid/7791901
!science:article/pmid/11535687
!science:article/pmid/10758340
!science:article/pmid/11160518
!science:article/pmid/11160518
!science:article/pmid/11264682
!science:article/pmid/11312283
!science:article/pmid/7791901
!science:article/pmid/11134520
!science:article/pmid/11264682
!science:article/pmid/11264682
!science:article/pmid/7506757
!science:article/pmid/10856117
!science:article/pmid/871919
!science:article/pmid/9570781
!science:article/pmid/10634854
!science:article/pmid/7658365
!science:article/pmid/10856117
!science:article/pmid/10856117
!science:article/pmid/11160518
!science:article/pmid/12736335
!science:article/pmid/10758340
!science:article/pmid/11160518
!science:article/pmid/11264682
!science:article/pmid/10758340
!science:article/pmid/7791901
!science:article/pmid/284423
!science:article/pmid/7658365
!science:article/pmid/10856117
!science:article/pmid/11312283
!science:article/pmid/11535687
!science:article/pmid/10856117
!science:article/pmid/7658365
!science:article/pmid/14754998