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authorMunyoki Kilyungi2023-08-14 18:05:44 +0300
committerMunyoki Kilyungi2023-08-15 19:32:48 +0300
commit877906dc164add37bfff07ebc1d0684ab6a3a333 (patch)
tree21329eb8a8ff92c5f0ef1b803b024e875c8b4d59
parent6e4359319695a6d93de55339b758b6ec6926c5ca (diff)
downloadgn-transform-databases-877906dc164add37bfff07ebc1d0684ab6a3a333.tar.gz
Update how genotypes are dumped
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
-rwxr-xr-xexamples/dump-genotype.scm91
1 files changed, 64 insertions, 27 deletions
diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm
index 50cafb6..4ac836d 100755
--- a/examples/dump-genotype.scm
+++ b/examples/dump-genotype.scm
@@ -25,10 +25,6 @@
(left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")
(left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId"))
"WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL")
- (schema-triples
- (gnt:datasetOfInbredSet rdfs:subPropertyOf gnc:inbredSet)
- (gnc:genotypeDataset rdfs:subPropertyOf gnc:dataset)
- (gnt:shortName rdfs:subPropertyOf gnc:genotypeDataset))
(triples
(string->identifier
""
@@ -41,59 +37,98 @@
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
- (set rdf:type 'gnc:genotypeDataset)
- (set gnt:name (field GenoFreeze Name))
- (set gnt:fullName (field GenoFreeze FullName))
- (set gnt:shortName (field GenoFreeze ShortName))
+ (set rdf:type 'gnc:genotype)
+ (set rdfs:label (field GenoFreeze Name))
+ (set skos:prefLabel (field GenoFreeze FullName))
+ (set skos:altLabel (field GenoFreeze ShortName))
(set dct:created (annotate-field
(field GenoFreeze CreateTime)
'^^xsd:date))
- (set gnt:datasetOfInbredSet
+ (set gnt:belongsToInbredSet
(string->identifier "" (field InbredSet Name InbredSetName)))))
(define-dump dump-genotypes
(tables (Geno
(left-join GenoXRef "ON Geno.Id = GenoXRef.GenoId")
(left-join GenoFreeze "ON GenoFreeze.Id = GenoXRef.GenoFreezeId")
+ (left-join InbredSet "ON InbredSet.InbredSetId = GenoFreeze.InbredSetId")
(left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")))
(schema-triples
- (gnc:genotype rdfs:range rdfs:Literal)
- (gnt:genotypeDataset rdfs:subPropertyOf gn:dataset))
+ (gnt:chr a owl:ObjectProperty)
+ (gnt:chr skos:description "This resource is located on a given chromosome")
+ (gnt:chr rdfs:domain gnc:genotype)
+ (gnt:mb a owl:ObjectProperty)
+ (gnt:mb skos:definition "The size of this resource in Mb")
+ (gnt:mb rdfs:domain gnc:genotype)
+ (gnt:mbMm8 a owl:ObjectProperty)
+ (gnt:mbMm8 skos:definition "TODO")
+ (gnt:mbMm8 rdfs:domain gnc:genotype)
+ (gnt:mb2016 a owl:ObjectProperty)
+ (gnt:mb2016 skos:definition "TODO")
+ (gnt:mb2016 rdfs:domain gnc:genotype)
+ (gnt:hasSequence a owl:ObjectProperty)
+ (gnt:hasSequence skos:definition "This resource has a given sequence")
+ (gnt:hasSequence rdfs:domain gnc:genotype)
+ (gnt:hasSource a owl:ObjectProperty)
+ (gnt:hasSource rdfs:domain gnc:genotype)
+ (gnt:hasSource skos:definition "This resource was obtained from this given source")
+ (gnt:hasAltSourceName a owl:ObjectProperty)
+ (gnt:hasAltSourceName rdfs:domain gnc:genotype)
+ (gnt:hasAltSourceName
+ skos:definition
+ "The alternative name this resource was obtained from")
+ (gnt:chrNum a owl:ObjectProperty)
+ (gnt:chrNum rdfs:domain gnc:genotype)
+ (gnt:chrNum skos:definition "The chromosome number for this resource")
+ (gnt:cM a owl:ObjectProperty)
+ (gnt:cM rdfs:domain gnc:genotype)
+ (gnt:cM skos:definition "The centimorgan for this resource")
+ (gnt:usedForMapping a owl:ObjectProperty)
+ (gnt:usedForMapping rdfs:domain gnc:genotype)
+ (gnt:usedForMapping
+ skos:definition "This indicates whether this resource is used for mapping"))
(triples
(string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
- (field ("CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, ':')), Geno.Name)" abbrev))
+ (field ("CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, '_')), Geno.Name)" abbrev))
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gnc:genotype)
- (set gnt:name (sanitize-rdf-string (field Geno Name)))
- (set gnt:markerName (sanitize-rdf-string (field Geno Marker_Name)))
+ (set skos:prefLabel (sanitize-rdf-string (field Geno Name)))
(set gnt:chr (field Geno Chr))
- (set gnt:mb (annotate-field (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double))
- (set gnt:sequence (field Geno Sequence))
- (set gnt:source (field Geno Source))
- (set gnt:source2 (field Geno Source2))
- (set gnt:genotypeOfDataset
+ (set gnt:mb (annotate-field
+ (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double))
+ (set gnt:mbMm8 (annotate-field (field ("IFNULL(Geno.Mb_mm8, '')" Mb_mm8))
+ '^^xsd:double))
+ (set gnt:mb2016
+ (annotate-field (field ("IFNULL(Geno.Mb_2016, '')" Mb_2016))
+ '^^xsd:double))
+ (set gnt:hasSequence (field Geno Sequence))
+ (set gnt:hasSource (field Geno Source))
+ ;; Only dump Source2 if it differs from Source
+ (set gnt:hasAltSourceName
+ (field ("IF((Source2 = Source), NULL, Source2)"
+ Source2)))
+ (set gnt:belongsToDataset
(string->identifier
""
(regexp-substitute/global
- #f "[^A-Za-z0-9:]"
- (field ("IFNULL(GenoFreeze.Name, '')" DatasetName))
- 'pre "_" 'post)
+ #f "[^A-Za-z0-9:]"
+ (field ("IFNULL(GenoFreeze.Name, '')" DatasetName))
+ 'pre "_" 'post)
#:separator ""
- #:proc string-capitalize-first)
- )
+ #:proc string-capitalize-first))
(set gnt:chrNum
(annotate-field
- (field ("IFNULL(Geno.chr_num, '')" chr_num))
+ (field Geno chr_num)
'^^xsd:int))
- (set gn:comments (field ("CAST(CONVERT(BINARY CONVERT(Geno.Comments USING latin1) USING utf8) AS VARCHAR(255))" Comments)))
+ (set rdfs:comments (field Geno Comments))
(set gnt:cM
(annotate-field
- (field ("IFNULL(GenoXRef.cM, '')" Chr_mm8))
+ (field GenoXRef cM)
'^^xsd:int))))
@@ -109,6 +144,8 @@
("gnt:" "<http://genenetwork.org/term/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+ ("owl:" "<http://www.w3.org/2002/07/owl#>")
+ ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
(inputs
(list dump-genofreeze