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Add connectivity label to Individuals that have connectivity data #16

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dosumis opened this issue Nov 24, 2020 · 4 comments
Open

Add connectivity label to Individuals that have connectivity data #16

dosumis opened this issue Nov 24, 2020 · 4 comments

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@dosumis
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dosumis commented Nov 24, 2020

We have multiple use cases here and need to decide if/how to split:

  • label on individuals where we have connectivity assertions with weights to other individuals. There are 2 types: neuron: region; neuron:neuron.
  • label on classes where we have non-weighted connectivity assertions to other classes

(edits on branch: https://github.com/VirtualFlyBrain/vfb-pipeline-dumps/edit/connectivity_label/)
Test sparql queries here first: http://ts.p2.virtualflybrain.org/rdf4j-workbench/repositories/vfb/query
instructions for adding new queries here: https://github.com/VirtualFlyBrain/vfb-pipeline-dumps/blob/connectivity_label/dumps.Makefile#L63

@dosumis
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dosumis commented Nov 24, 2020

Queries we need to drive:

  • neuron - neuron connectivity query (Individuals)
  • neuron - region connectivity query (Individuals)
  • neuron - neuron connectomics browser query (Classes & Individuals)

Maybe separate labels on Inds are best if we don't know whether region and neuron connectivity will always go together.

=> neuron_neuron_connectivity (inds and classes)
neuron_region_connectivity (just inds?)

@Robbie1977
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Probably need three labels even though they may overlap as will ensure actual results improving user experience considerably.

@dosumis
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dosumis commented Nov 24, 2020

Maybe two would be OK as we can distinguish Individuals from Classes separately?

@dosumis
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dosumis commented Nov 24, 2020

Example SPARQL:

PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

CONSTRUCT {
	?x <http://n2o.neo/property/nodeLabel> "neuron_neuron_connectivity" .
}
WHERE {
  ?x <http://purl.obolibrary.org/obo/RO_0002120> ?y . # synapsed_to
  ?x rdf:type owl:NamedIndividual .
}
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

CONSTRUCT {
	?x <http://n2o.neo/property/nodeLabel> "neuron_region_connectivity" .
}
WHERE {
  ?x <http://purl.obolibrary.org/obo/RO_0002113>|<http://purl.obolibrary.org/obo/RO_0002110> ?y . 
  ?x rdf:type owl:NamedIndividual .
}

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