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Update cell_by_location.rq #135

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Update cell_by_location.rq #135

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8076bc0
Update cell_by_location.rq
dosumis Dec 16, 2023
ba3f96c
Update cell_by_location.rq
dosumis Dec 21, 2023
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21 changes: 13 additions & 8 deletions sparql/cell_by_location.rq
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Original file line number Diff line number Diff line change
@@ -1,19 +1,24 @@
#+ summary: Find cells by location
#+ description: Enter an anatomical location, get back a list of cell type IRIs and labels
#+ summary: Find cells by type and location
#+ description: Args: cell: the iri or a cell type; location: the iri of an anatomical location. All args are optional. With no args returns all cells with an anatomical location. Location is a union of part_of (suitable for location of most cells) and has_soma_location (used for neurons). This pattern is designed for safe grouping of cell annotations. Returns: a 2 column table: cell (type) IRIs and cell (type) labels.
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#+ description: Args: cell: the iri or a cell type; location: the iri of an anatomical location. All args are optional. With no args returns all cells with an anatomical location. Location is a union of part_of (suitable for location of most cells) and has_soma_location (used for neurons). This pattern is designed for safe grouping of cell annotations. Returns: a 2 column table: cell (type) IRIs and cell (type) labels.
#+ description: Args: cell: the iri of a cell type; location: the iri of an anatomical location. All args are optional. With no args returns all cells with an anatomical location. Location is a union of part_of (suitable for location of most cells) and has_soma_location (used for neurons). This pattern is designed for safe grouping of cell annotations. Returns: a 2 column table: cell (type) IRIs and cell (type) labels.


#+ defaults:
#+ - location: http://purl.obolibrary.org/obo/UBERON_0002113
#+ - location: http://purl.obolibrary.org/obo/UBERON_0001062 # Anatomical Entity
#+ - cell: http://purl.obolibrary.org/obo/CL_0000000 # Cell

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX overlaps: <http://purl.obolibrary.org/obo/RO_0002131>
PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050>
PREFIX cell: <http://purl.obolibrary.org/obo/CL_0000000>
PREFIX has_soma_location: <http://purl.obolibrary.org/obo/RO_0002100>

SELECT DISTINCT ?cell_iri (STR(?qlabel) as ?cell_label)
WHERE {
?cell_iri overlaps: ?_location_iri .
?cell_iri rdfs:subClassOf cell: .
?cell_iri rdfs:label ?qlabel .
{
?cell_iri part_of: ?_location_iri .
} UNION {
?cell_iri has_soma_location: ?someValue .
}
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{
?cell_iri part_of: ?_location_iri .
} UNION {
?cell_iri has_soma_location: ?someValue .
}
?cell_iri part_of:|has_soma_location: ?_location_iri .


?cell_iri rdfs:subClassOf ?_cell_iri .
?cell_iri rdfs:label ?qlabel .
}