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Some changes I need to check #42

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Some changes I need to check #42

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Empty file added src/ontology/pheno_q_bp.csv
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6 changes: 6 additions & 0 deletions src/ontology/zp.Makefile
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Expand Up @@ -223,3 +223,9 @@ mass_obsolete: $(TMPDIR)/old_labels.txt $(TMPDIR)/new_labels.txt
qc:
$(ROBOT) report -i ../../zp.owl --fail-on None --print 5 -o zp_owl_report.owl
$(ROBOT) merge --input ../../zp.owl reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --output test.owl && rm test.owl && echo "Success"


pheno_q_bp.csv:
$(ROBOT) query -f csv -i zp.owl --use-graphs true --query ../sparql/zp_phenotype_q_bp.sparql $@


23 changes: 23 additions & 0 deletions src/sparql/zp_phenotype_q_bp.sparql
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@@ -0,0 +1,23 @@
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT ?s ?lab ?quality ?bearer WHERE
{
?s rdfs:subClassOf* <http://purl.obolibrary.org/obo/ZP_0000000> .
?s owl:equivalentClass [
rdf:type owl:Restriction ;
owl:onProperty <http://purl.obolibrary.org/obo/BFO_0000051> ;
owl:someValuesFrom [
owl:intersectionOf ( ?quality
[ rdf:type owl:Restriction ;
owl:onProperty <http://purl.obolibrary.org/obo/RO_0000052> ;
owl:someValuesFrom ?bearer ]
[ rdf:type owl:Restriction ;
owl:onProperty <http://purl.obolibrary.org/obo/RO_0002573> ;
owl:someValuesFrom <http://purl.obolibrary.org/obo/PATO_0000460> ]
)
]
] .
OPTIONAL { ?s rdfs:label ?lab }
}
27 changes: 5 additions & 22 deletions src/templates/df_obsolete_candidates.txt
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@@ -1,22 +1,5 @@
Ontology ID ZFIN Annotation Obsolete Label
http://purl.obolibrary.org/obo/ZP_0002061 GO:0005623-BFO:0000050-ZFA:0000152-PATO:0001997-0-0-0 true obsolete cell retina decreased amount, abnormal
http://purl.obolibrary.org/obo/ZP_0004217 0-0-ZFA:0001288-PATO:0001478-0-0-0 true obsolete renal glomerulus collapsed, abnormal
http://purl.obolibrary.org/obo/ZP_0004219 GO:0005604-BFO:0000050-ZFA:0001288-PATO:0000937-0-0-0 true obsolete basement membrane renal glomerulus disorganized, abnormal
http://purl.obolibrary.org/obo/ZP_0004688 GO:0005913-BFO:0000050-ZFA:0000040-PATO:0000025-0-0-0 true obsolete http://purl.obolibrary.org/obo/GO_0005913 median fin fold composition, abnormal
http://purl.obolibrary.org/obo/ZP_0005458 GO:0005913-BFO:0000050-ZFA:0000086-PATO:0000141-0-0-0 true obsolete http://purl.obolibrary.org/obo/GO_0005913 EVL structure, abnormal
http://purl.obolibrary.org/obo/ZP_0005992 GO:0005623-BFO:0000050-ZFA:0000119-PATO:0001997-0-0-0 true obsolete cell retinal inner nuclear layer decreased amount, abnormal
http://purl.obolibrary.org/obo/ZP_0007542 GO:0005623-BFO:0000050-ZFA:0001114-PATO:0000638-0-0-0 true obsolete cell head apoptotic, abnormal
http://purl.obolibrary.org/obo/ZP_0008256 GO:0005623-BFO:0000050-ZFA:0000086-PATO:0000051-0-0-0 true obsolete cell EVL morphology, abnormal
http://purl.obolibrary.org/obo/ZP_0008631 GO:0005913-BFO:0000050-ZFA:0001205-PATO:0000470-0-0-0 true obsolete http://purl.obolibrary.org/obo/GO_0005913 Meckel's cartilage increased amount, abnormal
http://purl.obolibrary.org/obo/ZP_0008642 GO:0005913-BFO:0000050-ZFA:0009084-PATO:0000470-0-0-0 true obsolete http://purl.obolibrary.org/obo/GO_0005913 chondrocyte increased amount, abnormal
http://purl.obolibrary.org/obo/ZP_0008777 GO:0005623-BFO:0000050-ZFA:0005124-PATO:0001453-0-0-ZFA:0005124 true obsolete intestinal epithelium detached from cell intestinal epithelium, abnormal
http://purl.obolibrary.org/obo/ZP_0010624 GO:0005623-BFO:0000050-ZFA:0001360-PATO:0000628-0-0-0 true obsolete cell parapineal organ mislocalised, abnormal
http://purl.obolibrary.org/obo/ZP_0014564 0-0-ZFA:0001315-PATO:0002001-GO:0005623-BFO:0000050-ZFA:0001320 true obsolete atrioventricular canal has fewer parts of type cell endocardium, abnormal
http://purl.obolibrary.org/obo/ZP_0015083 GO:0005913-BFO:0000050-ZFA:0001157-PATO:0002303-0-0-0 true obsolete http://purl.obolibrary.org/obo/GO_0005913 posterior lateral line primordium decreased object quality, abnormal
http://purl.obolibrary.org/obo/ZP_0018128 GO:0005623-BFO:0000050-ZFA:0000144-PATO:0000051-0-0-0 true obsolete cell retinal pigmented epithelium morphology, abnormal
http://purl.obolibrary.org/obo/ZP_0018659 GO:0005623-BFO:0000050-ZFA:0000023-PATO:0001997-0-0-0 true obsolete cell forerunner cell group decreased amount, abnormal
http://purl.obolibrary.org/obo/ZP_0022274 GO:0005623-BFO:0000050-ZFA:0005057-PATO:0000060-0-0-0 true obsolete cell epicardium spatial pattern, abnormal
http://purl.obolibrary.org/obo/ZP_0100125 GO:0098858-BFO:0000050-ZFA:0009041-PATO:0000122-0-0-0 true obsolete actin-based cell projection peridermal cell length, abnormal
http://purl.obolibrary.org/obo/ZP_0103459 GO:0005623-BFO:0000050-ZFA:0000035-PATO:0000937-0-0-0 true obsolete cell lens disorganized, abnormal
http://purl.obolibrary.org/obo/ZP_0104120 GO:0005623-BFO:0000050-ZFA:0000135-PATO:0001872-0-0-0 true obsolete cell notochord cuboid, abnormal
http://purl.obolibrary.org/obo/ZP_0105661 GO:0005913-BFO:0000050-ZFA:0001135-PATO:0000051-0-0-0 true obsolete http://purl.obolibrary.org/obo/GO_0005913 neural tube morphology, abnormal
Ontology ID ZFIN Annotation Obsolete Label
http://purl.obolibrary.org/obo/ZP_0004217 0-0-ZFA:0001288-PATO:0001478-0-0-0 TRUE "obsolete renal glomerulus collapsed, abnormal"
http://purl.obolibrary.org/obo/ZP_0014564 0-0-ZFA:0001315-PATO:0002001-GO:0005623-BFO:0000050-ZFA:0001320 TRUE "obsolete atrioventricular canal has fewer parts of type cell endocardium, abnormal"
http://purl.obolibrary.org/obo/ZP_0004219 GO:0005604-BFO:0000050-ZFA:0001288-PATO:0000937-0-0-0 TRUE "obsolete basement membrane renal glomerulus disorganized, abnormal"
http://purl.obolibrary.org/obo/ZP_0100125 GO:0098858-BFO:0000050-ZFA:0009041-PATO:0000122-0-0-0 TRUE "obsolete actin-based cell projection peridermal cell length, abnormal"
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