diff options
Diffstat (limited to 'examples/dump-genotype.scm')
| -rwxr-xr-x | examples/dump-genotype.scm | 36 |
1 files changed, 18 insertions, 18 deletions
diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm index d97b7e5..88125fa 100755 --- a/examples/dump-genotype.scm +++ b/examples/dump-genotype.scm @@ -26,9 +26,9 @@ (left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId")) "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL") (schema-triples - (gn-term:datasetOfInbredSet rdfs:range gn:inbredSet) + (gnt:datasetOfInbredSet rdfs:range gn:inbredSet) (gn:genotypeDataset rdfs:subPropertyOf gn:dataset) - (gn-term:shortName rdfs:range rdfs:Literal)) + (gnt:shortName rdfs:range rdfs:Literal)) (triples (string->identifier "" @@ -42,13 +42,13 @@ #:separator "" #:proc string-capitalize-first) (set rdf:type 'gn:genotypeDataset) - (set gn-term:name (field GenoFreeze Name)) - (set gn-term:fullName (field GenoFreeze FullName)) - (set gn-term:shortName (field GenoFreeze ShortName)) + (set gnt:name (field GenoFreeze Name)) + (set gnt:fullName (field GenoFreeze FullName)) + (set gnt:shortName (field GenoFreeze ShortName)) (set dct:created (annotate-field (field GenoFreeze CreateTime) '^^xsd:date)) - (set gn-term:datasetOfInbredSet + (set gnt:datasetOfInbredSet (string->identifier "" (field InbredSet Name InbredSetName))))) (define-dump dump-genotypes @@ -58,7 +58,7 @@ (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name"))) (schema-triples (gn:genotype rdfs:range rdfs:Literal) - (gn-term:genotypeDataset rdfs:subPropertyOf gn:dataset)) + (gnt:genotypeDataset rdfs:subPropertyOf gn:dataset)) (triples (string->identifier "" @@ -69,14 +69,14 @@ #:separator "" #:proc string-capitalize-first) (set rdf:type 'gn:genotype) - (set gn-term:name (sanitize-rdf-string (field Geno Name))) - (set gn-term:markerName (sanitize-rdf-string (field Geno Marker_Name))) - (set gn-term:chr (field Geno Chr)) - (set gn-term:mb (annotate-field (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double)) - (set gn-term:sequence (field Geno Sequence)) - (set gn-term:source (field Geno Source)) - (set gn-term:source2 (field Geno Source2)) - (set gn-term:genotypeOfDataset + (set gnt:name (sanitize-rdf-string (field Geno Name))) + (set gnt:markerName (sanitize-rdf-string (field Geno Marker_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 (string->identifier "" (regexp-substitute/global @@ -86,12 +86,12 @@ #:separator "" #:proc string-capitalize-first) ) - (set gn-term:chrNum + (set gnt:chrNum (annotate-field (field ("IFNULL(Geno.chr_num, '')" chr_num)) '^^xsd:int)) (set gn:comments (field ("CAST(CONVERT(BINARY CONVERT(Geno.Comments USING latin1) USING utf8) AS VARCHAR(255))" Comments))) - (set gn-term:cM + (set gnt:cM (annotate-field (field ("IFNULL(GenoXRef.cM, '')" Chr_mm8)) '^^xsd:int)))) @@ -105,7 +105,7 @@ (prefixes '(("dct:" "<http://purl.org/dc/terms/>") ("gn:" "<http://genenetwork.org/id/>") - ("gn-term:" "<http://genenetwork.org/term/>") + ("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#>") ("xsd:" "<http://www.w3.org/2001/XMLSchema#>"))) |