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Added ‘has soma location’ RO:0002100 to get_scope_query method #2174

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Oct 11, 2023
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Added ‘has soma location’ RO:0002100 to get_scope_query method #2174

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16 changes: 10 additions & 6 deletions src/scripts/generic_coverage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -92,10 +92,12 @@ def get_scope_query(scope_term: str) -> str:
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
PREFIX BFO: <http://purl.obolibrary.org/obo/BFO_>
PREFIX RO: <http://purl.obolibrary.org/obo/RO_>
SELECT ?scope_member ?label
WHERE
{{
?scope_member <http://www.w3.org/2000/01/rdf-schema#subClassOf>|<http://purl.obolibrary.org/obo/BFO_0000050> {_scope} .
?scope_member rdfs:subClassOf|BFO:0000050|RO:0002100 {_scope} .
?scope_member rdfs:isDefinedBy <http://purl.obolibrary.org/obo/cl.owl> .
?scope_member rdfs:label ?label.
}}
Expand All @@ -116,14 +118,15 @@ def get_superclass_value_query(term_iri_list: List[str], _scope: str) -> str:
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
PREFIX BFO: <http://purl.obolibrary.org/obo/BFO_>
SELECT DISTINCT ?super ?label
WHERE
{{
?term <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super. ?super rdfs:label ?label.
?super <http://www.w3.org/2000/01/rdf-schema#subClassOf>|<http://purl.obolibrary.org/obo/BFO_0000050> {_scope}.
?term rdfs:subClassOf ?super. ?super rdfs:label ?label.
?super rdfs:subClassOf|BFO:0000050 {_scope}.
?super rdfs:isDefinedBy <http://purl.obolibrary.org/obo/cl.owl> .
VALUES ?term {{{' '.join(term_iri_list)}}}
FILTER(?term != ?super)
FILTER(?term != ?super)
}}
"""

Expand All @@ -143,12 +146,13 @@ def get_term_leaves_list_query(term_iri_list: List[str], scope_term: str) -> str
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
PREFIX BFO: <http://purl.obolibrary.org/obo/BFO_>
SELECT ?term_label ?term_leaf ?term_leaf_label
WHERE
{{
?term_leaf <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?term.
?term_leaf rdfs:subClassOf ?term.
?term_leaf rdfs:label ?term_leaf_label. ?term_leaf rdfs:isDefinedBy <http://purl.obolibrary.org/obo/cl.owl> .
?term_leaf <http://www.w3.org/2000/01/rdf-schema#subClassOf>|<http://purl.obolibrary.org/obo/BFO_0000050> {_scope}.
?term_leaf rdfs:subClassOf|BFO:0000050 {_scope}.
?term rdfs:label ?term_label.
VALUES ?term {{{' '.join(term_iri_list)}}}
}}
Expand Down