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cypher-resources.yaml
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cypher-resources.yaml
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cypherResources:
- path: /dynamic/prod/sparc/phenotypeAnatomy/{id}
operations: &phenotypeAnatomy-ops
- summary: Return anatomical entities associated with a given phenotype.
parameters:
- name: id
description: HPO id of the phenotype to search from
paramType: path
query: &phenotypeAnatomy |
MATCH (anatomical_entity:Class)
<-[part_of:BFO:0000050|RO:0002433*0..4]-
(subclass_part_ctmo)
<-[inheres_in:RO:0000052|RO:0002314!]-(intersection_of_quality_and_anatomy) // inheres in (anon intersection of)
<-[has_process_part:BFO:0000051]-() // has part (process)
<-[:subClassOf*0..]-(phenotype:Class{iri: $id}) // phenotype and all subclasses
WHERE phenotype.iri IN $id
RETURN part_of
- path: /dynamic/test/sparc/phenotypeAnatomy/{id}
operations: *phenotypeAnatomy-ops
query: *phenotypeAnatomy
- path: /dynamic/prod/sparc/anatomyPhenotypes/{id}
operations: &anatomyPhenotypes-ops
- summary: Return phenotypes that inhere in some part of an anatomical entity.
parameters:
- name: id
description: uberon id of the anatomical entity to search from
paramType: path
query: &anatomyPhenotypes |
MATCH (anatomical_entity:Class{iri: $id})
<-[part_of:subClassOf|BFO:0000050|RO:0002433*0..40]-(subclass_part_ctmo)
<-[inheres_in:RO:0000052|RO:0002314!]-(intersection_of_quality_and_anatomy) // inheres in (anon intersection of)
<-[has_process_part:BFO:0000051]-() // has part (process)
<-[:subClassOf*0..]-(phenotype) // phenotype and all subclasses
WHERE
// filter out partOf/hasPart cases that induce circularity
ALL(e IN part_of WHERE NOT EXISTS(e.owlType) OR e.owlType = "subClassOf" OR e.owlType = "operand")
RETURN phenotype
- path: /dynamic/test/sparc/anatomyPhenotypes/{id}
operations: *anatomyPhenotypes-ops
query: *anatomyPhenotypes
- path: /dynamic/prod/sparc/organParts/{id}
operations: &organParts-ops
- summary: Get the parts list for an organ including nerves and blood vessels
parameters:
- name: id
description: ontology id of the organ
paramType: path
query: &organParts |
// depth of 6 captures everything, 5 is too shallow, 40 is WAY too deep
MATCH path = (start:Class{iri: "${id}"})
<-[:subClassOf|ilxtr:includedForSPARCUnder|fma:regional_part_of|fma:constitutional_part_of|fma:related_part_of*0..6]-(part)
<-[:fma:arterial_supply_of|fma:nerve_supply_of|fma:venous_drainage_of|fma:continuous_with*0..1]-(sup)
<-[:subClassOf|fma:constitutional_part_of|fma:branch|fma:tributary|fma:branch_of*0..1]-(a_bit_more)
RETURN path
UNION // for this query UNION seems to be MUCH faster than using WITH
MATCH path = (start:Class{iri: "${id}"})
// this one does not need to be inverted ? except for the INCOMING flag
<-[:fma:arterial_supply_of|fma:venous_drainage_of]-(vessel)
<-[:fma:branch|fma:tributary]-(more_vessel)
<-[:fma:branch|fma:tributary|fma:regional_part]-(even_more_vessel)
RETURN path
- path: /dynamic/test/sparc/organParts/{id}
operations: *organParts-ops
query: *organParts
- path: /dynamic/prod/sparc/parcellationArtifacts
operations:
- summary: Get the graph of all parcellation artifacts for all species
query: |
MATCH path = (artifact)
-[:subClassOf*0..2]->(parent)
-[:ilxtr:isDefinedInTaxon]->(species)
WHERE artifact.iri <> "http://www.w3.org/2002/07/owl#Nothing"
RETURN path
- path: /dynamic/prod/sparc/parcellationArtifacts/{species-id}
operations:
- summary: Get the graph of all parcellation artifacts for a single species
parameters:
- name: species-id
description: ontology id of the species
paramType: path
query: |
MATCH path = (artifact)
-[:subClassOf*0..2]->(parent)
-[:ilxtr:isDefinedInTaxon]->(species:Class{iri: "${species-id}"})
WHERE artifact.iri <> "http://www.w3.org/2002/07/owl#Nothing"
RETURN path
- path: /dynamic/prod/sparc/artifactRoots/{artifact-id}
operations:
- summary: Get the graph of all parcellation label roots for a single artifact WARNING this can return no results
parameters:
- name: artifact-id
description: ontology id of the parcellation artifact
paramType: path
query: |
MATCH path = (root)
-[:ilxtr:isDefinedBy]->(a)<-[:subClassOf*0..2]
-(artifact:Class{iri: "${artifact-id}"})
RETURN path
- path: /dynamic/prod/sparc/artifactLabels/{artifact-id}
operations:
- summary: Get the graph of all parcellation labels for a single artifact WARNING this can return no results
parameters:
- name: artifact-id
description: ontology id of the parcellation artifact
paramType: path
query: |
MATCH path = (label)
-[:subClassOf]->(root)
-[:ilxtr:isDefinedBy]->(a)<-[:subClassOf*0..2]
-(artifact:Class{iri: "${artifact-id}"})
WHERE label.iri <> "http://www.w3.org/2002/07/owl#Nothing"
RETURN path
- path: /dynamic/prod/sparc/rootLabels/{root-id}
operations: &rootLabes-ops
- summary: Get the list of all parcellation labels for a single label root
parameters:
- name: root-id
description: ontology id of the parcellation label root
paramType: path
query: &rootLabels |
MATCH (label)-[:subClassOf]->(root:Class{iri: "${root-id}"})
, path = (label)-[relation*0..1]-(maybe)
WHERE NONE (r in relation WHERE type(r) IN ["isDefinedBy", "subClassOf", "filler"])
AND NOT (label.iri =~ ".*_:.*") AND NOT (maybe.iri =~ ".*_:.*")
AND label.iri <> "http://www.w3.org/2002/07/owl#Nothing"
RETURN path
- path: /dynamic/test/sparc/rootLabels/{root-id}
operations: *rootLabes-ops
query: *rootLabels
- path: /dynamic/prod/sparc/parcellationRoots
operations:
- summary: Get the graph of all parcellation label roots for all species
query: |
MATCH path = (artifact)
-[:subClassOf*0..2]->(parent)
-[:ilxtr:isDefinedInTaxon]->(species)
WHERE artifact.iri <> "http://www.w3.org/2002/07/owl#Nothing"
RETURN path
UNION
MATCH path = (root)
-[:ilxtr:isDefinedBy]->(artifact)
-[:subClassOf*0..2]->(parent)
-[:ilxtr:isDefinedInTaxon]->(species)
RETURN path
- path: /dynamic/prod/sparc/parcellationRoots/{species-id}
operations:
- summary: Get the graph of all parcellation label roots for a single species
parameters:
- name: species-id
description: ontology id of the species
paramType: path
query: |
MATCH path = (artifact)
-[:subClassOf*0..2]->(parent)
-[:ilxtr:isDefinedInTaxon]->(species:Class{iri: "${species-id}"})
WHERE artifact.iri <> "http://www.w3.org/2002/07/owl#Nothing"
return path
UNION
MATCH path = (root)
-[:ilxtr:isDefinedBy]->(artifact)
-[:subClassOf*0..2]->(parent)
-[:ilxtr:isDefinedInTaxon]->(species:Class{iri: "${species-id}"})
RETURN path
- path: /dynamic/prod/sparc/parcellationRoots/{species-id}/{region-id}
operations:
- summary: Get the graph of all parcellation label roots for a single species and anatomical region
parameters:
- name: species-id
description: ontology id of the species
paramType: path
- name: region-id
description: ontology id of the anatomical region
paramType: path
query: |
MATCH
(region:Class{iri: "${region-id}"})
<-[:ilxtr:isDefinedInRegion]-
(parent)
-[:ilxtr:isDefinedInTaxon]->
(species:Class{iri: "${species-id}"})
WITH parent
MATCH path = (artifact)
-[:subClassOf*0..2]->(parent)
WHERE artifact.iri <> "http://www.w3.org/2002/07/owl#Nothing"
RETURN path
UNION
MATCH
(region:Class{iri: "${region-id}"})
<-[:ilxtr:isDefinedInRegion]-
(parent)
-[:ilxtr:isDefinedInTaxon]->
(species:Class{iri: "${species-id}"})
WITH parent
MATCH path = (root)
-[:ilxtr:isDefinedBy]->(artifact)
-[:subClassOf*0..2]->(parent)
RETURN path
- path: /dynamic/prod/sparc/parcellationRootsFMA/{species-id}/{fma-id}
operations: &parcellationRootsFMA-ops
- summary: Get the graph of all parcellation label roots for a single species and anatomical region
parameters:
- name: species-id
description: ontology id of the species
paramType: path
- name: fma-id
description: ontology id of the anatomical region
paramType: path
query: &parcellationRootsFMA |
MATCH (fma:Class{iri: "${fma-id}"})
WITH "FMA:" + toString(fma.`http://purl.org/sig/ont/fma/FMAID`) AS curie
MATCH (region)
-[:subClassOf*]->(start:Class{iri: "http://purl.obolibrary.org/obo/UBERON_0001062"})
WHERE any(x IN
region.`http://www.geneontology.org/formats/oboInOwl#hasDbXref`
WHERE x =~ curie)
WITH region
MATCH
(region)
<-[:ilxtr:isDefinedInRegion]-
(parent)
-[:ilxtr:isDefinedInTaxon]->
(species:Class{iri: "${species-id}"})
WITH parent
MATCH path = (artifact)
-[:subClassOf*0..2]->(parent)
WHERE artifact.iri <> "http://www.w3.org/2002/07/owl#Nothing"
RETURN path
UNION
MATCH (fma:Class{iri: "${fma-id}"})
WITH "FMA:" + toString(fma.`http://purl.org/sig/ont/fma/FMAID`) AS curie
MATCH (region)
-[:subClassOf*]->(start:Class{iri: "http://purl.obolibrary.org/obo/UBERON_0001062"})
WHERE any(x IN
region.`http://www.geneontology.org/formats/oboInOwl#hasDbXref`
WHERE x =~ curie)
WITH region
MATCH
(region)
<-[:ilxtr:isDefinedInRegion]-
(parent)
-[:ilxtr:isDefinedInTaxon]->
(species:Class{iri: "${species-id}"})
WITH parent
MATCH path = (root)
-[:ilxtr:isDefinedBy]->(artifact)
-[:subClassOf*0..2]->(parent)
RETURN path
- path: /dynamic/test/sparc/parcellationRootsFMA/{species-id}/{fma-id}
operations: *parcellationRootsFMA-ops
query: *parcellationRootsFMA
- path: /dynamic/prod/sparc/parcellationGraph
operations:
- summary: Get the graph of all parcellation labels for all species
query: |
MATCH path = (artifact)
-[:subClassOf*0..2]->(parent)
-[:ilxtr:isDefinedInTaxon]->(species)
WHERE artifact.iri <> "http://www.w3.org/2002/07/owl#Nothing"
return path
UNION
MATCH path = (maybe)
-[relation*0..1]-(label)
-[:subClassOf]->(root)
-[:ilxtr:isDefinedBy]->(artifact)
-[:subClassOf*0..2]->(parent)
-[:ilxtr:isDefinedInTaxon]->(species)
WHERE NONE (r in relation WHERE type(r) IN ["isDefinedBy", "subClassOf", "filler"])
AND NOT (label.iri =~ ".*_:.*") AND NOT (maybe.iri =~ ".*_:.*")
AND label.iri <> "http://www.w3.org/2002/07/owl#Nothing"
RETURN path
- path: /dynamic/prod/sparc/organList
operations: &organList-ops
- summary: Get the list of all FMA organ identifiers relevant to SPARC
query: &organList |
MATCH (n)
WHERE n.iri IN [
"http://purl.org/sig/ont/fma/fma7195", // lung
"http://purl.org/sig/ont/fma/fma7088", // heart
"http://purl.org/sig/ont/fma/fma7197", // liver
"http://purl.org/sig/ont/fma/fma7198", // pancreas
"http://purl.org/sig/ont/fma/fma7203", // kidney
"http://purl.org/sig/ont/fma/fma7148", // stomach
"http://purl.org/sig/ont/fma/fma7196", // spleen
"http://purl.org/sig/ont/fma/fma14543", // colon
"http://purl.org/sig/ont/fma/fma7201", // large intestine
"http://purl.org/sig/ont/fma/fma7200", // small intestine
"http://purl.org/sig/ont/fma/fma7199", // intestine
"http://purl.org/sig/ont/fma/fma15900", // urinary bladder
"http://purl.org/sig/ont/fma/fma45659", // lower urinary tract
"http://purl.org/sig/ont/fma/fma7157", // nervous system
"http://purl.org/sig/ont/fma/fma9903", // peripheral nervous system
"http://purl.org/sig/ont/fma/fma9906", // sympathetic nervous system
"http://purl.org/sig/ont/fma/fma7647", // spinal cord
"http://purl.org/sig/ont/fma/fma50801", // brain
"http://purl.org/sig/ont/fma/fma5889", // autonomic ganglion
"http://purl.org/sig/ont/fma/fma19667", // urethra
"http://purl.org/sig/ont/fma/fma7131" // esophagus
]
RETURN n
- path: /dynamic/test/sparc/organList
operations: *organList-ops
query: *organList
- path: /dynamic/prod/sparc/speciesList
operations: &speciesList-ops
- summary: Get the list of all NCBITaxon species identifiers relevant to SPARC
query: &speciesList |
MATCH (n)
WHERE n.iri IN [
"http://purl.obolibrary.org/obo/NCBITaxon_9378", // Suncus murinus
"http://purl.obolibrary.org/obo/NCBITaxon_9606", // Homo sapiens
"http://purl.obolibrary.org/obo/NCBITaxon_9685", // Felis catus
"http://purl.obolibrary.org/obo/NCBITaxon_9823", // Sus scrofa
"http://purl.obolibrary.org/obo/NCBITaxon_10090", // Mus musculus
"http://purl.obolibrary.org/obo/NCBITaxon_10116" // Rattus norvegicus
]
RETURN n
- path: /dynamic/test/sparc/speciesList
operations: *speciesList-ops
query: *speciesList
- path: /dynamic/shortestSimple
query: |
MATCH (start:Class{iri: '${start_id}'})
WITH start
MATCH (end:Class{iri: '${end_id}'})
WITH start, end
MATCH path = shortestPath((start)-[:${relationship}*..${max_depth}]->(end))
RETURN path
operations:
- summary: Get the shortest path between two IDs
parameters:
- name: start_id
description: The starting node (ex UBERON:0005751)
paramType: query
- name: end_id
description: The ending node (ex UBERON:0001255)
paramType: query
- name: max_depth
description: the maximum depth to traverse
paramType: query
- name: relationship
description: The property to traverse (ex subClassOf or subClassOf|partOf|isA)
paramType: query
required: false
- path: /dynamic/neurons/connectivity
query: |
MATCH (blank)-
[entrytype:ilxtr:hasSomaLocatedIn|ilxtr:hasAxonLocatedIn|ilxtr:hasDendriteLocatedIn|ilxtr:hasPresynapticTerminalsIn]
->(location:Class{iri: '${start_id}'})
WITH location, entrytype, blank
MATCH (phenotype)<-[predicate]-(blank)<-[:equivalentClass]-(neuron)
WHERE NOT (phenotype.iri =~ ".*_:.*")
// RETURN phenotype, (phenotype)-[predicate]-(neuron) as e
// WITH location, predicate, phenotype, neuron
RETURN location, entrytype, neuron, predicate, phenotype
operations:
- summary: Get connected anatomical regions by neuron type
parameters:
- name: start_id
description: The starting location (eg UBERON:0001759)
paramType: query
- path: /dynamic/neurons/connectedRegions
query: |
MATCH (blank)-
[entrytype:ilxtr:hasSomaLocatedIn|ilxtr:hasAxonLocatedIn|ilxtr:hasDendriteLocatedIn|ilxtr:hasPresynapticTerminalsIn]
->(location:Class{iri: '${start_id}'})
WITH entrytype, blank
MATCH (phenotype)<-[:${target_predicate}]-(blank)
// WHERE NOT (phenotype.iri =~ ".*_:.*")
RETURN phenotype
operations:
- summary: Get connected anatomical regions by starting location and target relationship
parameters:
- name: start_id
description: The starting location (eg UBERON:0001759)
paramType: query
- name: target_predicate
description: The predicate for the type of connectivity (eg ilxtr:hasPresynapticTerminalsIn)
paramType: query
required: false
- path: /dynamic/demos/apinat/bundles/{start-id}
operations:
- summary: Return the paths to somas from an anatomical region (aka connected-somas)
parameters:
- name: start-id
description: ontology id of the starting point
paramType: path
query: |
MATCH path1 = (start:Class{iri: "${start-id}"})
-[:apinatomy:annotates]->(start_housing)
-[:apinatomy:subtypes*0..1]->()
-[:apinatomy:clones*0..1]->(layer_or_end)
-[:apinatomy:layers*0..1]->()
-[:apinatomy:bundles]->(linkStart)
-[:apinatomy:prevChainEndLevels|apinatomy:prev|apinatomy:source*1..]->(link)
-[:apinatomy:targetOf|apinatomy:sourceOf]->(linkSoma) // axon or dendrite root
-[:apinatomy:conveyingLyph]->()
-[:apinatomy:supertype*0..1]->(soma:NamedIndividual)
-[:apinatomy:ontologyTerms]->(c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
WITH path1, link
OPTIONAL MATCH path2 = (link)
-[:apinatomy:fasciculatesIn|apinatomy:endsIn]->(layer_or_end)
-[:apinatomy:layerIn*0..1]->(end)
-[:apinatomy:ontologyTerms]->(external)
RETURN path1, path2
- path: /dynamic/demos/apinat/old-bundles/{start-id}
operations:
- summary: Return the paths to somas from an anatomical region (aka connected-somas)
parameters:
- name: start-id
description: ontology id of the starting point
paramType: path
query: |
MATCH path1 = (start:Class{iri: '${start-id}'})
-[:apinatomy:annotates]->(start_housing)
-[:apinatomy:bundlesChains]->(chain)
-[:apinatomy:root]->(root)
-[:apinatomy:internalIn]->(layer_or_end) # this hits a cycle back to start_housing
-[:apinatomy:cloneOf*0..1]->()
-[:apinatomy:supertype*0..1]->()
-[:apinatomy:ontologyTerms]->(layer_or_end_external)
WITH path1, root, layer_or_end AS layer
OPTIONAL MATCH path2 = (layer)
-[:apinatomy:layerIn]->(end_housing)
-[:apinatomy:ontologyTerms]->(end_housing_external)
WITH path1, path2, root
MATCH path3 = (root) // in the layer case this hits an additional lyph
<-[:apinatomy:target|apinatomy:source]-(link)
<-[:apinatomy:conveys]-(soma)
<-[:apinatomy:annotates]-(soma_NLX)
RETURN path1, path2, path3
- path: /dynamic/demos/apinat/somas
operations:
- summary: List all the somas for a given graph (TODO on the given graph)
query: |
MATCH (c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
-[:apinatomy:annotates]->(soma:NamedIndividual)
RETURN soma
- path: /dynamic/demos/apinat/housing-lyphs
operations:
- summary: List all the housing lyphs (neuronal processes) for all starting points.
query: |
MATCH path = (c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
-[:apinatomy:annotates]->(soma:NamedIndividual) // soma lyph
-[:apinatomy:conveys]->(somaLink) // link connecting soma to axon and dendrite
-[:apinatomy:target|apinatomy:source]->(root) // axon or dendrite root
-[:apinatomy:controlNodes|apinatomy:rootOf*1..2]->(chain) // axon or dendrite tree
-[:apinatomy:housingLyphs]->(housing) // list of lyphs housing the trees
-[:apinatomy:ontologyTerms*0..1]->(external) // external ids for the housing lyphs
WHERE soma.`https://apinatomy.org/uris/readable/generated` IS NULL
RETURN path
- path: /dynamic/demos/apinat/housing-lyphs/{start-id}
operations:
- summary: List all the housing lyphs for a starting point.
parameters:
- name: start-id
description: ontology id of the starting point
paramType: path
query: |
MATCH path1 = (c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
-[:apinatomy:annotates]->(soma:NamedIndividual) // soma lyph
-[:apinatomy:conveys]->(somaLink) // link connecting soma to axon and dendrite
-[:apinatomy:target|apinatomy:source]->(root) // axon or dendrite root
-[:apinatomy:internalIn]->(layer_or_end)
-[:apinatomy:cloneOf*0..1]->()
-[:apinatomy:supertype*0..1]->()
-[:apinatomy:ontologyTerms]->(layer_or_end_external:Class{iri: '${start-id}'})
WHERE soma.`https://apinatomy.org/uris/readable/generated` IS NULL
WITH path1, root
MATCH path2 = (root)
-[:apinatomy:controlNodes|apinatomy:rootOf*1..2]->(chain) // axon or dendrite tree
-[:apinatomy:housingLyphs]->(housing) // list of lyphs housing the trees
-[:apinatomy:ontologyTerms*0..1]->(external) // external ids for the housing lyphs
RETURN path1, path2
UNION
MATCH path1 = (c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
-[:apinatomy:annotates]->(soma:NamedIndividual) // soma lyph
-[:apinatomy:conveys]->(somaLink) // link connecting soma to axon and dendrite
-[:apinatomy:target|apinatomy:source]->(root) // axon or dendrite root
-[:apinatomy:internalIn]->(layer)
-[:apinatomy:cloneOf*0..1]->()
-[:apinatomy:supertype*0..1]->()
-[:apinatomy:layerIn]->(end_housing)
-[:apinatomy:ontologyTerms]->(end_housing_external:Class{iri: '${start-id}'})
WHERE soma.`https://apinatomy.org/uris/readable/generated` IS NULL
WITH path1, root
MATCH path2 = (root)
-[:apinatomy:rootOf]->(chain) // axon or dendrite tree
-[:apinatomy:housingLyphs]->(housing) // list of lyphs housing the trees
-[:apinatomy:ontologyTerms*0..1]->(external) // external ids for the housing lyphs
RETURN path1, path2
- path: /dynamic/demos/apinat/soma-processes
operations:
- summary: List all the neuronal processes for all somas.
query: |
MATCH path1 = (c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
-[:apinatomy:annotates]->(soma:NamedIndividual) // soma lyph
-[:apinatomy:conveys]->(linkSoma) // link connecting soma to axon and dendrite
-[:apinatomy:target|apinatomy:source]->(nodeRoot) // axon or dendrite root
-[:apinatomy:sourceOf|apinatomy:nextChainStartLevels|apinatomy:next*1..]->(link) // sourceOf is first and only once
-[:apinatomy:fasciculatesIn|apinatomy:endsIn]->(layer_or_end)
-[:apinatomy:cloneOf*0..1]->()
-[:apinatomy:supertype*0..1]->()
-[:apinatomy:ontologyTerms]->(external)
WHERE soma.`https://apinatomy.org/uris/readable/generated` IS NULL
WITH path1, nodeRoot, layer_or_end AS layer
OPTIONAL MATCH path2 = (layer) // if we were in a layer, get the containing lyph as well
-[:apinatomy:layerIn]->(end_housing)
-[:apinatomy:ontologyTerms]->(end_housing_external)
WITH path1, path2, nodeRoot
MATCH path3 = (nodeRoot) // extract chain for axon vs dendrite
-[:apinatomy:rootOf]->(chain)
RETURN path1, path2, path3
- path: /dynamic/demos/apinat/soma-processes/{start-id}
operations:
- summary: List all the neuronal processes for somas located in start-id.
parameters:
- name: start-id
description: ontology id of the starting point
paramType: path
query: |
MATCH path1 = (c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
-[:apinatomy:annotates]->(soma:NamedIndividual) // soma lyph
-[:apinatomy:conveys]->(linkSoma) // link connecting soma to axon and dendrite
-[:apinatomy:target|apinatomy:source]->(nodeRoot) // axon or dendrite root
-[:apinatomy:internalIn]->(layer_or_end)
-[:apinatomy:cloneOf*0..1]->()
-[:apinatomy:supertype*0..1]->()
-[:apinatomy:layerIn*0..1]->(layerSoma) // don't need to see both layer and housing for soma
-[:apinatomy:ontologyTerms]->(externalEndSoma:Class{iri: '${start-id}'})
WHERE soma.`https://apinatomy.org/uris/readable/generated` IS NULL
WITH path1, nodeRoot
MATCH path3 = (chain)
<-[:apinatomy:rootOf]-(nodeRoot)
-[:apinatomy:sourceOf|apinatomy:nextChainStartLevels|apinatomy:next*1..]->(link)
-[:apinatomy:fasciculatesIn|apinatomy:endsIn]->(layer_or_end)
-[:apinatomy:cloneOf*0..1]->()
-[:apinatomy:supertype*0..1]->()
-[:apinatomy:ontologyTerms]->(external)
WITH path1, path3, nodeRoot, layer_or_end AS layer
OPTIONAL MATCH path2 = (layer) // if we were in a layer, get the containing lyph as well
-[:apinatomy:layerIn]->(end_housing)
-[:apinatomy:ontologyTerms]->(end_housing_external)
RETURN path1, path2, path3
- path: /dynamic/demos/apinat/weird-soma-processes/{process-id}
operations:
- summary: List all the neuronal processes for somas where some processes is in process-id.
parameters:
- name: process-id
description: ontology id of the starting point
paramType: path
query: |
MATCH path1 = (c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
-[:apinatomy:annotates]->(soma:NamedIndividual) // soma lyph
-[:apinatomy:conveys]->(linkSoma) // link connecting soma to axon and dendrite
-[:apinatomy:target|apinatomy:source]->(nodeRoot) // axon or dendrite root
-[:apinatomy:sourceOf|apinatomy:nextChainStartLevels|apinatomy:next*1..]->(link) // sourceOf is first and only once
-[:apinatomy:fasciculatesIn|apinatomy:endsIn]->(layer_or_end)
-[:apinatomy:cloneOf*0..1]->()
-[:apinatomy:supertype*0..1]->()
-[:apinatomy:ontologyTerms]->(external:Class{iri: '${process-id}'})
WHERE soma.`https://apinatomy.org/uris/readable/generated` IS NULL
WITH path1, nodeRoot, layer_or_end AS layer
OPTIONAL MATCH path2 = (layer) // if we were in a layer, get the containing lyph as well
-[:apinatomy:layerIn]->(end_housing)
-[:apinatomy:ontologyTerms]->(end_housing_external)
WITH path1, path2, nodeRoot
MATCH path3 = (nodeRoot) // extract chain for axon vs dendrite
-[:apinatomy:rootOf]->(chain)
RETURN path1, path2, path3
UNION
MATCH path1 = (c:Class{iri: "http://uri.neuinfo.org/nif/nifstd/nlx_154731"})
-[:apinatomy:annotates]->(soma:NamedIndividual) // soma lyph
-[:apinatomy:conveys]->(linkSoma) // link connecting soma to axon and dendrite
-[:apinatomy:target|apinatomy:source]->(nodeRoot) // axon or dendrite root
-[:apinatomy:sourceOf|apinatomy:nextChainStartLevels|apinatomy:next*1..]->(link) // sourceOf is first and only once
-[:apinatomy:fasciculatesIn|apinatomy:endsIn]->(layer_or_end)
-[:apinatomy:cloneOf*0..1]->()
-[:apinatomy:supertype*0..1]->()
-[:apinatomy:ontologyTerms]->(external)
WHERE soma.`https://apinatomy.org/uris/readable/generated` IS NULL
WITH path1, nodeRoot, layer_or_end AS layer
MATCH path2 = (layer) // if we were in a layer, get the containing lyph as well
-[:apinatomy:layerIn]->(end_housing)
-[:apinatomy:ontologyTerms]->(end_housing_external:Class{iri: '${process-id}'})
WITH path1, path2, nodeRoot
MATCH path3 = (nodeRoot) // extract chain for axon vs dendrite
-[:apinatomy:rootOf]->(chain)
RETURN path1, path2, path3
- path: /dynamic/demos/apinat/neru-1/{neupop-id}
operations: &neru-ops
- summary: Return the housing regions and publications for neurulated groups.
parameters:
- name: neupop-id
description: neuron population identifier
paramType: path
query: |
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
// publications
WITH neugrp, a
OPTIONAL MATCH path = (neugrp)
-[:apinatomy:references]->(pub)
-[:type]->(:Class{iri: "https://apinatomy.org/uris/elements/Publication"}) // cannot be curied, dynamic endpoints will not expand it
WITH neugrp, a, path
MATCH (neugrp)
-[b:apinatomy:links]->(link)
-[c:apinatomy:fasciculatesIn|apinatomy:endsIn*0..1]->(lyph_or_layer) // real lyphs convey things, layers do not
-[d:apinatomy:layerIn*0..1]->(lyph)
-[:apinatomy:conveys*0..1]->() // make sure we are at a real lyph
WITH lyph, a, b, c, d, path
MATCH (lyph)
-[e:apinatomy:ontologyTerms]->(region)
RETURN a, b, c, d, e, path
UNION
// this part usually only returns the soma housing lyph
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
-[b:apinatomy:lyphs]->(lyph)
-[c:apinatomy:internalIn]->(e) // e is a hack to get columns to match
-[d:apinatomy:ontologyTerms*0..1]->(region)
// this variant shows the dead end lyphs that correspond to the fasciculatesIn links above
//-[c:apinatomy:internalIn*0..1]->(e)
//-[d:apinatomy:ontologyTerms*0..1]->(region)
return a, b, c, d, null AS e, null AS path
- path: /dynamic/demos/apinat/neru-2/{neupop_id}
operations: *neru-ops
query: |
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
// publications
WITH neugrp, a
OPTIONAL MATCH path = (neugrp)
-[:apinatomy:references]->(pub)
-[:type]->(:Class{iri: "https://apinatomy.org/uris/elements/Publication"}) // cannot be curied, dynamic endpoints will not expand it
WITH neugrp, a, path
MATCH (neugrp)
-[b:apinatomy:links]->(link)
-[c:apinatomy:fasciculatesIn|apinatomy:endsIn*0..1]->(lyph_or_layer) // real lyphs convey things, layers do not
-[d:apinatomy:layerIn*0..1]->(lyph)
-[:apinatomy:conveys*0..1]->() // make sure we are at a real lyph
WITH neugrp, link, lyph, a, b, c, d, path
MATCH (lyph)
-[e:apinatomy:ontologyTerms]->(region)
// use apinatomy:next to extract ordering information
WITH neugrp, link, a, b, c, d, e, path
MATCH (link)
-[f:apinatomy:next*0..]->()
//-[f:apinatomy:next|apinatomy:nextChainStartLevels*0..]->()
// FIXME these should be collapsing into a single relationship
-[g:apinatomy:target*0..1]->()
-[h:apinatomy:rootOf*0..1]->()
-[i:apinatomy:levels*0..1]->()
<-[:apinatomy:links]-(neugrp)
RETURN a, b, c, d, e, f, g,h,i, path
UNION
// this part usually only returns the soma housing lyph
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
-[b:apinatomy:lyphs]->(lyph)
-[c:apinatomy:internalIn]->(e) // e is a hack to get columns to match
-[d:apinatomy:ontologyTerms*0..1]->(region)
// this variant shows the dead end lyphs that correspond to the fasciculatesIn links above
//-[c:apinatomy:internalIn*0..1]->(e)
//-[d:apinatomy:ontologyTerms*0..1]->(region)
RETURN a, b, c, d, null AS e, null AS f, null AS g, null AS h, null AS i, null AS path
- path: /dynamic/demos/apinat/neru-3/{neupop_id}
operations: *neru-ops
query: |
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
// publications
WITH neugrp, a
OPTIONAL MATCH path = (neugrp)
-[:apinatomy:references]->(pub)
-[:type]->(:Class{iri: "https://apinatomy.org/uris/elements/Publication"}) // cannot be curied, dynamic endpoints will not expand it
WITH neugrp, a, path
MATCH (neugrp)
-[b:apinatomy:links]->(link)
-[c:apinatomy:fasciculatesIn|apinatomy:endsIn*0..1]->(lyph_or_layer) // real lyphs convey things, layers do not
-[d:apinatomy:layerIn*0..1]->(lyph)
-[:apinatomy:conveys*0..1]->() // make sure we are at a real lyph
WITH neugrp, link, lyph, a, b, c, d, path // MATCH vs , not all things that match as lyphs have externals
MATCH (lyph)
-[e:apinatomy:ontologyTerms]->(region)
// use apinatomy:next to extract ordering information
WITH neugrp, link, a, b, c, d, e, path
MATCH p2 = (link)
-[:apinatomy:conveyingLyph]->(cl)
-[:apinatomy:topology]->()
WITH neugrp, link, a, b, c, d, e, path, p2, cl
MATCH (cl)
-[x:apinatomy:inheritedOntologyTerms*0..1]->()
WITH neugrp, link, a, b, c, d, e, path, p2, x
MATCH (link)
-[f:apinatomy:next*0..]->()
//-[f:apinatomy:next|apinatomy:nextChainStartLevels*0..]->()
// FIXME these should be collapsing into a single relationship
-[g:apinatomy:target*0..1]->()
-[h:apinatomy:rootOf*0..1]->()
-[i:apinatomy:levels*0..1]->()
<-[:apinatomy:links]-(neugrp)
RETURN a, b, c, d, e, f, g,h,i, path, p2, x
UNION
// this part usually only returns the soma housing lyph
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
-[b:apinatomy:lyphs]->(lyph)
-[c:apinatomy:internalIn]->()
-[d:apinatomy:ontologyTerms*0..1]->(region)
// this variant shows the dead end lyphs that correspond to the fasciculatesIn links above
//-[c:apinatomy:internalIn*0..1]->()
//-[d:apinatomy:ontologyTerms*0..1]->(region)
RETURN a, b, c, d, null AS e, null AS f, null AS g, null AS h, null AS i, null AS path, null as p2, null as x
- path: /dynamic/demos/apinat/neru-4/{neupop_id}
operations: *neru-ops
query: |
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
, (neugrp)
-[:apinatomy:links]->(link)
-[c:apinatomy:fasciculatesIn|apinatomy:endsIn*0..1]->(lyph_or_layer) // real lyphs convey things, layers do not
-[d:apinatomy:layerIn*0..1]->(lyph)
-[:apinatomy:conveys*0..1]->() // make sure we are at a real lyph
WITH neugrp, link, lyph, a, c, d
OPTIONAL MATCH layer_ext = (lyph)
<-[d*1]-(layer)-[:apinatomy:cloneOf]->()-[:apinatomy:inheritedOntologyTerms]->()
WITH neugrp, link, lyph, a, c, d, layer_ext // there is a difference here because the previous match does not require lyphs to have external ids
MATCH (lyph)
-[e:apinatomy:ontologyTerms]->(region)
, p2 = (link)
-[:apinatomy:conveyingLyph]->(cl)
-[:apinatomy:topology]->()
, (cl)
-[x:apinatomy:inheritedOntologyTerms*0..1]->()
// use apinatomy:next to extract ordering information
, (link)
-[f:apinatomy:next*0..]->()
-[g:apinatomy:target*0..1]->()
-[h:apinatomy:rootOf*0..1]->()
-[i:apinatomy:levels*0..1]->()
<-[:apinatomy:links]-(neugrp)
// publications
WITH neugrp, a, c, d, e, f, g,h,i, p2, x, layer_ext
OPTIONAL MATCH path = (neugrp)
-[:apinatomy:references]->(pub)
-[:type]->(:Class{iri: "https://apinatomy.org/uris/elements/Publication"}) // cannot be curied, dynamic endpoints will not expand it
RETURN a, null as b, c, d, e, f, g,h,i, path, p2, x, layer_ext
UNION
// this part usually only returns the soma housing lyph
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
-[b:apinatomy:lyphs]->(lyph)
-[c:apinatomy:internalIn]->()
-[d:apinatomy:ontologyTerms*0..1]->(region)
, p2 = (lyph)
-[:apinatomy:conveys]->(soma_link)
-[:apinatomy:source|apinatomy:target]->(soma_node)
-[:apinatomy:sourceOf]->(chain_link)
, (chain_link)
-[:apinatomy:levelIn]->(chain)
, (soma_node)
-[:apinatomy:rootOf]->(chain)
RETURN a, b, c, d, null AS e, null AS f, null AS g, null AS h, null AS i, null AS path, p2, null as x, null as layer_ext
- path: /dynamic/demos/apinat/neru-5/{neupop_id}
operations: *neru-ops
query: |
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
, (neugrp)
-[:apinatomy:links]->(link)
-[c:apinatomy:fasciculatesIn|apinatomy:endsIn*0..1]->(lyph_or_layer) // real lyphs convey things, layers do not
-[d:apinatomy:layerIn*0..1]->(lyph)
-[:apinatomy:conveys*0..1]->() // make sure we are at a real lyph
WITH neugrp, link, lyph, a, c, d
OPTIONAL MATCH layer_ext = (lyph)
<-[d*1]-(layer)-[:apinatomy:cloneOf*0..1]->()-[:apinatomy:inheritedExternal]->()
WITH neugrp, link, lyph, a, c, d, layer_ext
OPTIONAL MATCH more = (lyph)
-[:apinatomy:layerIn|apinatomy:endsIn|apinatomy:fasciculatesIn|apinatomy:internalIn|apinatomy:cloneOf*1..]->()
-[:apinatomy:ontologyTerms|apinatomy:inheritedExternal]->()
WITH neugrp, link, lyph, a, c, d, layer_ext, more // there is a difference here because the previous match does not require lyphs to have external ids
MATCH (lyph)
-[e:apinatomy:ontologyTerms]->(region)
, p2 = (link)
-[:apinatomy:conveyingLyph]->(cl)
-[:apinatomy:topology]->()
, (cl)
-[x:apinatomy:inheritedExternal*0..1]->()
// use apinatomy:next to extract ordering information
, (link)
-[f:apinatomy:next*0..]->()
-[g:apinatomy:target*0..1]->()
-[h:apinatomy:rootOf*0..1]->()
-[i:apinatomy:levels*0..1]->()
<-[:apinatomy:links]-(neugrp)
// publications
WITH neugrp, a, c, d, e, f, g,h,i, p2, x, layer_ext, more
OPTIONAL MATCH path = (neugrp)
-[:apinatomy:references]->(pub)
-[:type]->(:Class{iri: "https://apinatomy.org/uris/elements/Reference"}) // cannot be curied, dynamic endpoints will not expand it
RETURN a, null as b, c, d, e, f, g,h,i, path, p2, x, layer_ext, more
UNION
// this part usually only returns the soma housing lyph
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
-[b:apinatomy:lyphs]->(lyph)
-[c:apinatomy:internalIn]->()
-[d:apinatomy:ontologyTerms*0..1]->(region)
, p2 = (lyph)
-[:apinatomy:conveys]->(soma_link)
-[:apinatomy:source|apinatomy:target]->(soma_node)
-[:apinatomy:sourceOf]->(chain_link)
, (chain_link)
-[:apinatomy:levelIn]->(chain)
, (soma_node)
-[:apinatomy:rootOf]->(chain)
WITH lyph, a, b, c, d, p2
OPTIONAL MATCH more = (lyph)
-[:apinatomy:layerIn|apinatomy:endsIn|apinatomy:fasciculatesIn|apinatomy:internalIn|apinatomy:cloneOf*1..]->()
-[:apinatomy:ontologyTerms|apinatomy:inheritedExternal]->()
RETURN a, b, c, d, null AS e, null AS f, null AS g, null AS h, null AS i, null AS path, p2, null as x, null as layer_ext, more
- path: /dynamic/demos/apinat/neru-6/{neupop_id}
operations: *neru-ops
query: |
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
, (neugrp)
-[:apinatomy:links]->(link)
-[c:apinatomy:fasciculatesIn|apinatomy:endsIn*0..1]->(lyph_or_layer) // real lyphs convey things, layers do not
-[d:apinatomy:layerIn*0..1]->(lyph)
-[:apinatomy:conveys*0..1]->() // make sure we are at a real lyph
WITH neugrp, link, lyph, a, c, d
OPTIONAL MATCH layer_ext = (lyph)
<-[d*1]-(layer)-[:apinatomy:cloneOf*0..1]->()-[:apinatomy:inheritedExternal]->()
WITH neugrp, link, lyph, a, c, d, layer_ext
OPTIONAL MATCH more = (lyph)
-[:apinatomy:layerIn|apinatomy:endsIn|apinatomy:fasciculatesIn|apinatomy:internalIn|apinatomy:cloneOf*1..]->()
-[:apinatomy:ontologyTerms|apinatomy:inheritedExternal]->()
WITH neugrp, link, lyph, a, c, d, layer_ext, more // there is a difference here because the previous match does not require lyphs to have external ids
MATCH (lyph)
-[e:apinatomy:ontologyTerms]->(region)
, p2 = (link)
-[:apinatomy:conveyingLyph]->(cl)
-[:apinatomy:topology]->()
, (cl)
-[x:apinatomy:inheritedExternal*0..1]->()
// use apinatomy:next to extract ordering information
, (link)
-[f:apinatomy:next|apinatomy:nextChainStartLevels*0..]->()
-[g:apinatomy:target*0..1]->()
-[h:apinatomy:rootOf*0..1]->()
-[i:apinatomy:levels*0..1]->()
<-[:apinatomy:links]-(neugrp)
// publications
WITH neugrp, a, c, d, e, f, g,h,i, p2, x, layer_ext, more
OPTIONAL MATCH path = (neugrp)
-[:apinatomy:references]->(pub)
-[:type]->(:Class{iri: "https://apinatomy.org/uris/elements/Reference"}) // cannot be curied, dynamic endpoints will not expand it
RETURN a, null as b, c, d, e, f, g,h,i, path, p2, x, layer_ext, more
UNION
// this part usually only returns the soma housing lyph
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
-[b:apinatomy:lyphs]->(lyph)
-[c:apinatomy:internalIn]->()
-[d:apinatomy:ontologyTerms*0..1]->(region)
, p2 = (lyph)
-[:apinatomy:conveys]->(soma_link)
-[:apinatomy:source|apinatomy:target]->(soma_node)
-[:apinatomy:sourceOf]->(chain_link)
, (chain_link)
-[:apinatomy:levelIn]->(chain)
, (soma_node)
-[:apinatomy:rootOf]->(chain)
WITH lyph, a, b, c, d, p2
OPTIONAL MATCH more = (lyph)
-[:apinatomy:layerIn|apinatomy:endsIn|apinatomy:fasciculatesIn|apinatomy:internalIn|apinatomy:cloneOf*1..]->()
-[:apinatomy:ontologyTerms|apinatomy:inheritedExternal]->()
RETURN a, b, c, d, null AS e, null AS f, null AS g, null AS h, null AS i, null AS path, p2, null as x, null as layer_ext, more
- path: /dynamic/demos/apinat/neru-7/{neupop_id}
operations: *neru-ops
query: |
MATCH (neupop:Class{iri: $neupop_id})
-[a:apinatomy:annotates]->(neugrp:NamedIndividual{`https://apinatomy.org/uris/readable/description`: "dynamic"}) // FIXME HACK
, (neugrp)
-[:apinatomy:links]->(link)
-[c:apinatomy:fasciculatesIn|apinatomy:endsIn*0..1]->(lyph_or_layer) // real lyphs convey things, layers do not
-[d:apinatomy:layerIn*0..1]->(lyph)
-[:apinatomy:conveys*0..1]->() // make sure we are at a real lyph
WITH neugrp, link, lyph, a, c, d
OPTIONAL MATCH layer_ext = (lyph)
<-[d*1]-(layer)-[:apinatomy:cloneOf*0..1]->()-[:apinatomy:inheritedOntologyTerms]->()
WITH neugrp, link, lyph, a, c, d, layer_ext
OPTIONAL MATCH more = (lyph)
-[:apinatomy:layerIn|apinatomy:endsIn|apinatomy:fasciculatesIn|apinatomy:internalIn|apinatomy:cloneOf*1..]->()