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-rwxr-xr-xexamples/dump-dataset-metadata.scm138
-rwxr-xr-xexamples/dump-genotype.scm36
-rwxr-xr-xexamples/dump-phenotype.scm76
-rwxr-xr-xexamples/dump-probeset-metadata.scm20
-rwxr-xr-xexamples/dump-probeset.scm22
-rwxr-xr-xexamples/dump-probesetfreeze.scm25
-rwxr-xr-xexamples/dump-publication.scm34
-rwxr-xr-xexamples/dump-species-metadata.scm35
-rwxr-xr-xexamples/dump-tissue.scm6
9 files changed, 197 insertions, 195 deletions
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm
index c51364a..33e72fe 100755
--- a/examples/dump-dataset-metadata.scm
+++ b/examples/dump-dataset-metadata.scm
@@ -52,11 +52,11 @@
(foaf:givenName rdfs:range rdfs:Literal)
(foaf:familyName rdfs:range rdfs:Literal)
(foaf:homepage rdfs:range rdfs:Literal)
- (gn-term:address rdfs:range rdfs:Literal)
- (gn-term:city rdfs:range rdfs:Literal)
- (gn-term:state rdfs:range rdfs:Literal)
- (gn-term:zipCode rdfs:range rdfs:Literal)
- (gn-term:country rdfs:range rdfs:Literal))
+ (gnt:address rdfs:range rdfs:Literal)
+ (gnt:city rdfs:range rdfs:Literal)
+ (gnt:state rdfs:range rdfs:Literal)
+ (gnt:zipCode rdfs:range rdfs:Literal)
+ (gnt:country rdfs:range rdfs:Literal))
(triples (investigator-attributes->id (field Investigators FirstName)
(field Investigators LastName)
(field Investigators Email))
@@ -70,11 +70,11 @@
(set foaf:familyName
(field ("CAST(CONVERT(BINARY CONVERT(LastName USING latin1) USING utf8) AS VARCHAR(100))" LastName)))
(set foaf:homepage (field Investigators Url))
- (set gn-term:address (field Investigators Address))
- (set gn-term:city (field Investigators City))
- (set gn-term:state (field Investigators State))
- (set gn-term:zipCode (field Investigators ZipCode))
- (set gn-term:country (field Investigators Country))))
+ (set gnt:address (field Investigators Address))
+ (set gnt:city (field Investigators City))
+ (set gnt:state (field Investigators State))
+ (set gnt:zipCode (field Investigators ZipCode))
+ (set gnt:country (field Investigators Country))))
(define-dump dump-info-files
(tables (InfoFiles
@@ -92,38 +92,38 @@
(left-join GeneChip "USING (GeneChipId)"))
"WHERE GN_AccesionId IS NOT NULL")
(schema-triples
- (gn-term:dataset rdfs:range rdfs:Literal)
- (gn-term:datasetOfInvestigator rdfs:domain gn:dataset)
- (gn-term:datasetOfOrganization rdfs:domain gn:dataset)
- (gn-term:datasetOfInvestigator rdfs:range foaf:Person)
- (gn-term:datasetOfInbredSet rdfs:domain gn:dataset)
- (gn-term:datasetOfInbredSet rdfs:range gn:inbredSet)
- (gn-term:datasetOfSpecies rdfs:domain gn:dataset)
- (gn-term:datasetOfSpecies rdfs:range gn:inbredSet)
- (gn-term:datasetOfTissue rdfs:domain gn:dataset)
- (gn-term:datasetOfTissue rdfs:range gn:tissue)
- (gn-term:normalization rdfs:domain gn:dataset)
- (gn-term:normalization rdfs:range gn:avgMethod)
- (gn-term:datasetOfPlatform rdfs:domain gn:dataset)
- (gn-term:datasetOfPlatform rdfs:range gn:geneChip)
- (gn-term:accessionId rdfs:range rdfs:Literal)
- (gn-term:datasetStatusName rdfs:range rdfs:Literal)
- (gn-term:summary rdfs:range rdfs:Literal)
- (gn-term:aboutTissue rdfs:range rdfs:Literal)
- (gn-term:geoSeries rdfs:range rdfs:Literal)
- (gn-term:name rdfs:range rdfs:Literal)
- (gn-term:title rdfs:range rdfs:Literal)
- (gn-term:publicationTitle rdfs:range rdfs:Literal)
- (gn-term:specifics rdfs:range rdfs:Literal)
- (gn-term:datasetGroup rdfs:range rdfs:Literal)
- (gn-term:aboutCases rdfs:range rdfs:Literal)
- (gn-term:aboutPlatform rdfs:range rdfs:Literal)
- (gn-term:aboutDataProcessing rdfs:range rdfs:Literal)
- (gn-term:notes rdfs:range rdfs:Literal)
- (gn-term:experimentDesign rdfs:range rdfs:Literal)
- (gn-term:contributors rdfs:range rdfs:Literal)
- (gn-term:citation rdfs:range rdfs:Literal)
- (gn-term:acknowledgment rdfs:range rdfs:Literal))
+ (gnt:dataset rdfs:range rdfs:Literal)
+ (gnt:datasetOfInvestigator rdfs:domain gn:dataset)
+ (gnt:datasetOfOrganization rdfs:domain gn:dataset)
+ (gnt:datasetOfInvestigator rdfs:range foaf:Person)
+ (gnt:datasetOfInbredSet rdfs:domain gn:dataset)
+ (gnt:datasetOfInbredSet rdfs:range gn:inbredSet)
+ (gnt:datasetOfSpecies rdfs:domain gn:dataset)
+ (gnt:datasetOfSpecies rdfs:range gn:inbredSet)
+ (gnt:datasetOfTissue rdfs:domain gn:dataset)
+ (gnt:datasetOfTissue rdfs:range gn:tissue)
+ (gnt:normalization rdfs:domain gn:dataset)
+ (gnt:normalization rdfs:range gn:avgMethod)
+ (gnt:datasetOfPlatform rdfs:domain gn:dataset)
+ (gnt:datasetOfPlatform rdfs:range gn:geneChip)
+ (gnt:accessionId rdfs:range rdfs:Literal)
+ (gnt:datasetStatusName rdfs:range rdfs:Literal)
+ (gnt:summary rdfs:range rdfs:Literal)
+ (gnt:aboutTissue rdfs:range rdfs:Literal)
+ (gnt:geoSeries rdfs:range rdfs:Literal)
+ (gnt:name rdfs:range rdfs:Literal)
+ (gnt:title rdfs:range rdfs:Literal)
+ (gnt:publicationTitle rdfs:range rdfs:Literal)
+ (gnt:specifics rdfs:range rdfs:Literal)
+ (gnt:datasetGroup rdfs:range rdfs:Literal)
+ (gnt:aboutCases rdfs:range rdfs:Literal)
+ (gnt:aboutPlatform rdfs:range rdfs:Literal)
+ (gnt:aboutDataProcessing rdfs:range rdfs:Literal)
+ (gnt:notes rdfs:range rdfs:Literal)
+ (gnt:experimentDesign rdfs:range rdfs:Literal)
+ (gnt:contributors rdfs:range rdfs:Literal)
+ (gnt:citation rdfs:range rdfs:Literal)
+ (gnt:acknowledgment rdfs:range rdfs:Literal))
(triples (string->identifier
"" (regexp-substitute/global #f "[^A-Za-z0-9:]"
(field InfoFiles InfoPageName)
@@ -133,84 +133,84 @@
(set rdf:type (string->symbol
(field ("IF(GenoFreeze.Id IS NOT NULL, 'gn:genotypeDataset', IF(PublishFreeze.Id IS NOT NULL, 'gn:phenotypeDataset', 'gn:dataset'))"
rdfType))))
- (set gn-term:name (regexp-substitute/global
+ (set gnt:name (regexp-substitute/global
#f "^[Nn]one$"
(field InfoFiles InfoPageName)
""))
- (set gn-term:fullName
+ (set gnt:fullName
(field ("IFNULL(GenoFreeze.FullName, IFNULL(PublishFreeze.FullName, ''))"
DatasetFullName)))
(set dct:created
(field ("IFNULL(GenoFreeze.CreateTime, IFNULL(PublishFreeze.CreateTime, IFNULL(ProbeSetFreeze.CreateTime, '')))"
createTimeGenoFreeze)))
- (set gn-term:datasetOfInvestigator
+ (set gnt:datasetOfInvestigator
(investigator-attributes->id (field Investigators FirstName)
(field Investigators LastName)
(field Investigators Email)))
- (set gn-term:datasetOfOrganization
+ (set gnt:datasetOfOrganization
(field ("CAST(CONVERT(BINARY CONVERT(Organizations.OrganizationName USING latin1) USING utf8) AS VARCHAR(1500))" Organizations)))
- (set gn-term:accessionId (format #f "GN~a" (field InfoFiles GN_AccesionId)))
- (set gn-term:datasetStatusName (string-downcase
+ (set gnt:accessionId (format #f "GN~a" (field InfoFiles GN_AccesionId)))
+ (set gnt:datasetStatusName (string-downcase
(field DatasetStatus DatasetStatusName)))
- (set gn-term:datasetOfInbredSet
+ (set gnt:datasetOfInbredSet
(string->identifier "inbredSet" (field InbredSet Name InbredSetName)))
- (set gn-term:datasetOfTissue (string->identifier "tissue"
+ (set gnt:datasetOfTissue (string->identifier "tissue"
(field Tissue Short_Name)))
- (set gn-term:normalization
+ (set gnt:normalization
(string->identifier "avgmethod"
;; If AvgMethodName is NULL, assume N/A.
(if (string-blank? (field AvgMethod Name AvgMethodName))
"N/A" (field AvgMethod Name AvgMethodName))))
- (set gn-term:datasetOfPlatform
+ (set gnt:datasetOfPlatform
(string->identifier "platform"
(field GeneChip Name GeneChip)))
- (set gn-term:summary
+ (set gnt:summary
(sanitize-rdf-string (field Datasets Summary)))
- (set gn-term:aboutTissue
+ (set gnt:aboutTissue
(sanitize-rdf-string (field Datasets AboutTissue)))
- (set gn-term:geoSeries
+ (set gnt:geoSeries
(let ((s
(string-match "GSE[0-9]*"
(field ("IFNULL(Datasets.GeoSeries, '')" GeoSeries)))))
(if s (ontology
'geoSeries: (match:substring s))
"")))
- (set gn-term:title
+ (set gnt:title
(regexp-substitute/global
#f "^[Nn]one$"
(field InfoFiles InfoFileTitle)
""))
- (set gn-term:publicationTitle
+ (set gnt:publicationTitle
(regexp-substitute/global
#f "^[Nn]one$"
(field Datasets PublicationTitle)
""))
- (set gn-term:specifics (sanitize-rdf-string (field InfoFiles Specifics)))
- (set gn-term:datasetGroup (field Datasets DatasetName DatasetGroup))
- (set gn-term:aboutCases
+ (set gnt:specifics (sanitize-rdf-string (field InfoFiles Specifics)))
+ (set gnt:datasetGroup (field Datasets DatasetName DatasetGroup))
+ (set gnt:aboutCases
(sanitize-rdf-string
(field ("CAST(CONVERT(BINARY CONVERT(Datasets.AboutCases USING latin1) USING utf8) AS VARCHAR(10000))" AboutCases))))
- (set gn-term:aboutPlatform
+ (set gnt:aboutPlatform
(sanitize-rdf-string
(field ("CAST(CONVERT(BINARY CONVERT(Datasets.AboutPlatform USING latin1) USING utf8) AS VARCHAR(1500))"
AboutPlatform))))
- (set gn-term:aboutDataProcessing
+ (set gnt:aboutDataProcessing
(sanitize-rdf-string
(field ("CAST(CONVERT(BINARY CONVERT(Datasets.AboutDataProcessing USING latin1) USING utf8) AS VARCHAR(1500))"
AboutDataProcessing))))
- (set gn-term:notes
+ (set gnt:notes
(sanitize-rdf-string
(field ("CAST(CONVERT(BINARY CONVERT(Datasets.Notes USING latin1) USING utf8) AS VARCHAR(1500))"
GNNotes))))
- (set gn-term:experimentDesign
+ (set gnt:experimentDesign
(sanitize-rdf-string
(field ("CAST(CONVERT(BINARY CONVERT(Datasets.ExperimentDesign USING latin1) USING utf8) AS VARCHAR(1500))"
ExperimentDesign))))
- (set gn-term:contributors
+ (set gnt:contributors
(sanitize-rdf-string
(field ("CAST(CONVERT(BINARY CONVERT(Datasets.Contributors USING latin1) USING utf8) AS VARCHAR(1500))"
Contributors))))
- (set gn-term:citation
+ (set gnt:citation
(sanitize-rdf-string
(regexp-substitute/global
#f "^[Nn]one$"
@@ -218,7 +218,7 @@
("CAST(CONVERT(BINARY CONVERT(Datasets.Citation USING latin1) USING utf8) AS VARCHAR(1500))"
Citation))
"")))
- (set gn-term:dataSourceAcknowledgment
+ (set gnt:dataSourceAcknowledgment
(sanitize-rdf-string
(string-trim-both
(regexp-substitute/global
@@ -226,7 +226,7 @@
(field ("CAST(CONVERT(BINARY CONVERT(InfoFiles.Data_Source_Acknowledge USING latin1) USING utf8) AS VARCHAR(1500))"
Data_Source_Acknowledge))
""))))
- (set gn-term:acknowledgment (sanitize-rdf-string
+ (set gnt:acknowledgment (sanitize-rdf-string
(field Datasets Acknowledgment)))))
@@ -239,7 +239,7 @@
(prefixes
'(("foaf:" "<http://xmlns.com/foaf/0.1/>")
("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
- ("gn-term:" "<http://genenetwork.org/term/>")
+ ("gnt:" "<http://genenetwork.org/term/>")
("gn:" "<http://genenetwork.org/id/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
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#>")))
diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm
index 1ef498d..00f99d2 100755
--- a/examples/dump-phenotype.scm
+++ b/examples/dump-phenotype.scm
@@ -27,10 +27,10 @@
(left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId"))
"WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL")
(schema-triples
- (gn-term:datasetOfInbredSet rdfs:range gn:inbredSet)
- (gn-term:name rdfs:range rdfs:Literal)
- (gn-term:fullName rdfs:range rdfs:Literal)
- (gn-term:shortName rdfs:range rdfs:Literal)
+ (gnt:datasetOfInbredSet rdfs:range gn:inbredSet)
+ (gnt:name rdfs:range rdfs:Literal)
+ (gnt:fullName rdfs:range rdfs:Literal)
+ (gnt:shortName rdfs:range rdfs:Literal)
(gn:phenotypeDataset rdf:subClassOf gn:dataset))
(triples
(string->identifier
@@ -41,13 +41,13 @@
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gn:phenotypeDataset)
- (set gn-term:name (field PublishFreeze Name))
- (set gn-term:fullName (field PublishFreeze FullName))
- (set gn-term:shortName (field PublishFreeze ShortName))
+ (set gnt:name (field PublishFreeze Name))
+ (set gnt:fullName (field PublishFreeze FullName))
+ (set gnt:shortName (field PublishFreeze ShortName))
(set dct:created (annotate-field
(field PublishFreeze CreateTime)
'^^xsd:date))
- (set gn-term:datasetOfInbredSet
+ (set gnt:datasetOfInbredSet
(string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
(define-dump dump-phenotypes
@@ -58,19 +58,19 @@
(left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")))
(schema-triples
(gn:phenotypeDataset rdfs:subPropertyOf gn:dataset)
- (gn-term:publicationDescription rdfs:range rdfs:Literal)
- (gn-term:originalDescription rdfs:range rdfs:Literal)
- (gn-term:prePublicationDescription rdfs:range rdfs:Literal)
- (gn-term:postPublicationAbbreviation rdfs:range rdfs:Literal)
- (gn-term:labCode rdfs:range rdfs:Literal)
- (gn-term:submitter rdfs:range rdfs:Literal)
- (gn-term:owner rdfs:range rdfs:Literal)
- (gn-term:mean rdfs:range xsd:double)
- (gn-term:LRS rdfs:range xsd:float)
- (gn-term:locus rdfs:range rdfs:Literal)
- (gn-term:additive rdfs:range xsd:decimal)
- (gn-term:sequence rdfs:range rdfs:Literal)
- (gn-term:phenotypeOfPublication rdfs:range gn-term:pubMedId))
+ (gnt:publicationDescription rdfs:range rdfs:Literal)
+ (gnt:originalDescription rdfs:range rdfs:Literal)
+ (gnt:prePublicationDescription rdfs:range rdfs:Literal)
+ (gnt:postPublicationAbbreviation rdfs:range rdfs:Literal)
+ (gnt:labCode rdfs:range rdfs:Literal)
+ (gnt:submitter rdfs:range rdfs:Literal)
+ (gnt:owner rdfs:range rdfs:Literal)
+ (gnt:mean rdfs:range xsd:double)
+ (gnt:LRS rdfs:range xsd:float)
+ (gnt:locus rdfs:range rdfs:Literal)
+ (gnt:additive rdfs:range xsd:decimal)
+ (gnt:sequence rdfs:range rdfs:Literal)
+ (gnt:phenotypeOfPublication rdfs:range gn-term:pubMedId))
(triples (string->identifier
""
(regexp-substitute/global #f "[^A-Za-z0-9:]"
@@ -79,44 +79,44 @@
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gn:phenotype)
- (set gn-term:name (sanitize-rdf-string
+ (set gnt:name (sanitize-rdf-string
(field
("CAST(CONVERT(BINARY CONVERT(IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation) USING latin1) USING utf8) AS VARCHAR(100))"
PhenotypeName))))
;; There is no row with an empty post-publication description so
;; use this field as the main publication description
- (set gn-term:publicationDescription
+ (set gnt:publicationDescription
(sanitize-rdf-string
(field ("CAST(CONVERT(BINARY CONVERT(Phenotype.Post_publication_description USING latin1) USING utf8) AS CHAR(10000))"
postPubDescr))))
- (set gn-term:originalDescription (sanitize-rdf-string
+ (set gnt:originalDescription (sanitize-rdf-string
(delete-substrings
(field Phenotype Original_description)
"Original post publication description: ")))
- (set gn-term:prePublicationDescription
+ (set gnt:prePublicationDescription
(sanitize-rdf-string
(field
("CAST(CONVERT(BINARY CONVERT(Phenotype.Pre_publication_description USING latin1) USING utf8) AS VARCHAR(15000))"
prePubDesc))))
- (set gn-term:prePublicationAbbreviation (sanitize-rdf-string (field Phenotype Pre_publication_abbreviation)))
- (set gn-term:postPublicationAbbreviation (sanitize-rdf-string (field Phenotype Post_publication_abbreviation)))
- (set gn-term:labCode (field Phenotype Lab_code))
- (set gn-term:submitter (sanitize-rdf-string (field Phenotype Submitter)))
- (set gn-term:owner (sanitize-rdf-string (field Phenotype Owner)))
- (set gn-term:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
+ (set gnt:prePublicationAbbreviation (sanitize-rdf-string (field Phenotype Pre_publication_abbreviation)))
+ (set gnt:postPublicationAbbreviation (sanitize-rdf-string (field Phenotype Post_publication_abbreviation)))
+ (set gnt:labCode (field Phenotype Lab_code))
+ (set gnt:submitter (sanitize-rdf-string (field Phenotype Submitter)))
+ (set gnt:owner (sanitize-rdf-string (field Phenotype Owner)))
+ (set gnt:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
'^^xsd:double))
- (set gn-term:locus (field PublishXRef Locus))
- (set gn-term:LRS (annotate-field (field ("IFNULL(PublishXRef.LRS, '')" lrs)) '^^xsd:float))
- (set gn-term:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:decimal))
- (set gn-term:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:int))
- (set gn-term:phenotypeOfDataset
+ (set gnt:locus (field PublishXRef Locus))
+ (set gnt:LRS (annotate-field (field ("IFNULL(PublishXRef.LRS, '')" lrs)) '^^xsd:float))
+ (set gnt:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:decimal))
+ (set gnt:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:int))
+ (set gnt:phenotypeOfDataset
(string->identifier
""
(field
("IFNULL(InfoFiles.InfoPageName, IFNULL(PublishFreeze.Name, ''))" DatasetName))
#:separator ""
#:proc string-capitalize-first))
- (set gn-term:phenotypeOfPublication
+ (set gnt:phenotypeOfPublication
(let ((pmid (field
("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
pmid)))
@@ -134,7 +134,7 @@
(prefixes
'(("dct:" "<http://purl.org/dc/terms/>")
("gn:" "<http://genenetwork.org/id/>")
- ("gn-term:" "<http://genenetwork.org/terms/>")
+ ("gnt:" "<http://genenetwork.org/terms/>")
("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#>")
diff --git a/examples/dump-probeset-metadata.scm b/examples/dump-probeset-metadata.scm
index 6da1eb0..ddbea5e 100755
--- a/examples/dump-probeset-metadata.scm
+++ b/examples/dump-probeset-metadata.scm
@@ -24,14 +24,14 @@
"WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1")
(schema-triples
(gn:probesetData rdfs:range gn:probeset)
- (gn-term:hasProbeset rdfs:range rdfs:Literal))
+ (gnt:hasProbeset rdfs:range rdfs:Literal))
(triples
(string->identifier
"probesetData"
(field ("CONCAT(ProbeSetFreeze.Name,':',IFNULL(ProbeSet.Name, ProbeSet.Id))"
ProbeSetName)))
(set rdf:type 'gn:probesetData)
- (set gn-term:hasProbeset
+ (set gnt:hasProbeset
(ontology
'probeset:
(regexp-substitute/global
@@ -39,34 +39,34 @@
(field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
name))
'pre "_" 'post)))
- (set gn-term:probesetOfDataset
+ (set gnt:probesetOfDataset
(ontology
'probeset:
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field ProbeSetFreeze Name)
'pre "_" 'post)))
- (set gn-term:mean
+ (set gnt:mean
(annotate-field
(field ("IFNULL(ProbeSetXRef.mean, '')" mean))
'^^xsd:double))
- (set gn-term:se
+ (set gnt:se
(annotate-field
(field ("IFNULL(ProbeSetXRef.se, '')" se))
'^^xsd:double))
- (set gn-term:locus (field ProbeSetXRef Locus))
+ (set gnt:locus (field ProbeSetXRef Locus))
(set gn:LRS
(annotate-field
(field ("IFNULL(ProbeSetXRef.LRS, '')" LRS))
'^^xsd:double))
- (set gn-term:pValue
+ (set gnt:pValue
(annotate-field
(field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
'^^xsd:double))
- (set gn-term:additive
+ (set gnt:additive
(annotate-field
(field ("IFNULL(ProbeSetXRef.additive, '')" additive))
'^^xsd:double))
- (set gn-term:h2
+ (set gnt:h2
(annotate-field
(field ("IFNULL(ProbeSetXRef.h2, '')" h2))
'^^xsd:float))))
@@ -79,7 +79,7 @@
(table-metadata? #f)
(prefixes
'(("gn:" "<http://genenetwork.org/id/>")
- ("gn-term:" "<http://genenetwork.org/id/>")
+ ("gnt:" "<http://genenetwork.org/id/>")
("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#>")))
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm
index be09b48..4d5f9a5 100755
--- a/examples/dump-probeset.scm
+++ b/examples/dump-probeset.scm
@@ -21,8 +21,8 @@
(tables (ProbeSet
(left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")))
(schema-triples
- (gn-term:name rdfs:range rdfs:Literal)
- (gn-term:probeset rdfs:range rdfs:Literal))
+ (gnt:name rdfs:range rdfs:Literal)
+ (gnt:probeset rdfs:range rdfs:Literal))
(triples (ontology
'probeset:
(string-trim-both
@@ -32,17 +32,17 @@
name))
'pre "_" 'post)))
(set rdf:type 'gn-id:probeset)
- (set gn-term:chipOf (string->identifier "platform" (field GeneChip Name)))
- (set gn-term:name (field ProbeSet Name))
- (set gn-term:symbol (delete-substrings (field ProbeSet Symbol) "\""))
- (set gn-term:description (sanitize-rdf-string
+ (set gnt:chipOf (string->identifier "platform" (field GeneChip Name)))
+ (set gnt:name (field ProbeSet Name))
+ (set gnt:symbol (delete-substrings (field ProbeSet Symbol) "\""))
+ (set gnt:description (sanitize-rdf-string
(field ProbeSet description)))
- (set gn-term:chr (field ProbeSet Chr))
- (set gn-term:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
- (set gn-term:blatSeq (sanitize-rdf-string
+ (set gnt:chr (field ProbeSet Chr))
+ (set gnt:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
+ (set gnt:blatSeq (sanitize-rdf-string
(string-trim-both (field ProbeSet BlatSeq))))
- (set gn-term:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq)))
- (set gn-term:uniProtReference (ontology 'uniprot:
+ (set gnt:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq)))
+ (set gnt:uniProtReference (ontology 'uniprot:
(field ProbeSet UniProtID)))))
diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm
index a45fd0a..828ab00 100755
--- a/examples/dump-probesetfreeze.scm
+++ b/examples/dump-probesetfreeze.scm
@@ -20,11 +20,11 @@
(define-dump dump-gene-chip
(tables (GeneChip))
(schema-triples
- (gn-term:name rdfs:range rdfs:Literal))
+ (gnt:name rdfs:range rdfs:Literal))
(triples (string->identifier "platform" (field GeneChip Name))
(set rdf:type 'gn:platform)
- (set gn-term:name (field GeneChip GeneChipName))
- (set gn-term:geoPlatform
+ (set gnt:name (field GeneChip GeneChipName))
+ (set gnt:geoPlatform
(ontology 'geoSeries:
(string-trim-both (field GeneChip GeoPlatform))))))
@@ -38,8 +38,8 @@
(left-join Tissue "ON ProbeFreeze.TissueId = Tissue.TissueId"))
"WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
(schema-triples
- (gn-term:avgMethod rdfs:range rdfs:Literal)
- (gn-term:dataScale rdfs:range rdfs:Literal)
+ (gnt:avgMethod rdfs:range rdfs:Literal)
+ (gnt:dataScale rdfs:range rdfs:Literal)
(gn:probesetDataset rdf:subClassOf gn:dataset))
(triples
(string->identifier
@@ -51,15 +51,15 @@
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gn:probesetDataset)
- (set gn-term:avgMethod (string->identifier "avgmethod" (field AvgMethod Name)))
- (set gn-term:fullName (field ProbeSetFreeze FullName))
- (set gn-term:shortName (field ProbeSetFreeze ShortName))
+ (set gnt:avgMethod (string->identifier "avgmethod" (field AvgMethod Name)))
+ (set gnt:fullName (field ProbeSetFreeze FullName))
+ (set gnt:shortName (field ProbeSetFreeze ShortName))
(set dct:created (annotate-field
(field ProbeSetFreeze CreateTime)
'^^xsd:datetime))
- (set gn-term:dataScale (field ProbeSetFreeze DataScale))
- (set gn-term:tissueName (string->identifier "tissue" (field Tissue Short_Name)))
- (set gn-term:datasetOfInbredSet
+ (set gnt:dataScale (field ProbeSetFreeze DataScale))
+ (set gnt:tissueName (string->identifier "tissue" (field Tissue Short_Name)))
+ (set gnt:datasetOfInbredSet
(string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
@@ -71,7 +71,8 @@
(prefixes
'(("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
("gn:" "<http://genenetwork.org/id/>")
- ("gn-term:" "<http://genenetwork.org/term/>")
+ ("dct:" "<>")
+ ("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#>")))
diff --git a/examples/dump-publication.scm b/examples/dump-publication.scm
index f79696e..1384261 100755
--- a/examples/dump-publication.scm
+++ b/examples/dump-publication.scm
@@ -21,15 +21,15 @@
(define-dump dump-publication
(tables (Publication))
(schema-triples
- (gn-term:pubMedId rdfs:range rdfs:Literal)
- (gn-term:title rdfs:range rdfs:Literal)
- (gn-term:journal rdfs:range rdfs:Literal)
- (gn-term:volume rdfs:range rdfs:Literal)
- (gn-term:pages rdfs:range rdfs:Literal)
- (gn-term:month rdfs:range rdfs:Literal)
- (gn-term:year rdfs:range rdfs:Literal)
- (gn-term:author rdfs:range rdfs:Literal)
- (gn-term:abstract rdfs:range rdfs:Literal))
+ (gnt:pubMedId rdfs:range rdfs:Literal)
+ (gnt:title rdfs:range rdfs:Literal)
+ (gnt:journal rdfs:range rdfs:Literal)
+ (gnt:volume rdfs:range rdfs:Literal)
+ (gnt:pages rdfs:range rdfs:Literal)
+ (gnt:month rdfs:range rdfs:Literal)
+ (gnt:year rdfs:range rdfs:Literal)
+ (gnt:author rdfs:range rdfs:Literal)
+ (gnt:abstract rdfs:range rdfs:Literal))
(triples
(let ((pmid (field
("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
@@ -40,19 +40,19 @@
(number->string publication-id))
(ontology 'pubmed: pmid)))
(set rdf:type 'gn:publication)
- (set gn-term:pubMedId
+ (set gnt:pubMedId
(ontology 'pubmed: (field ("IFNULL(PubMed_ID, '')" pubmedId))))
- (set gn-term:title (delete-substrings (field Publication Title)
+ (set gnt:title (delete-substrings (field Publication Title)
"Unknown"))
- (set gn-term:journal (delete-substrings (field Publication Journal)
+ (set gnt:journal (delete-substrings (field Publication Journal)
"Unknown"))
- (set gn-term:volume (delete-substrings (field Publication Volume)
+ (set gnt:volume (delete-substrings (field Publication Volume)
"Unknown"))
- (set gn-term:pages (delete-substrings (field Publication Pages)
+ (set gnt:pages (delete-substrings (field Publication Pages)
"Unknown"))
- (set gn-term:month (delete-substrings (field Publication Month)
+ (set gnt:month (delete-substrings (field Publication Month)
"Unknown"))
- (set gn-term:year (field Publication Year))
+ (set gnt:year (field Publication Year))
(multiset gn:author
;; The authors field is a comma
;; separated list. Split it.
@@ -68,7 +68,7 @@
(connection %connection-settings)
(table-metadata? #f)
(prefixes
- '(("gn-term:" "<http://genenetwork.org/terms/>")
+ '(("gnt:" "<http://genenetwork.org/terms/>")
("gn:" "<http://genenetwork.org/id/>")
("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm
index 77db764..39f7147 100755
--- a/examples/dump-species-metadata.scm
+++ b/examples/dump-species-metadata.scm
@@ -21,25 +21,25 @@
(define-dump dump-species
(tables (Species))
(schema-triples
- (gn-term:name rdfs:range rdfs:Literal)
- (gn-term:displayName rdfs:range rdfs:Literal)
- (gn-term:binomialName rdfs:range rdfs:Literal)
- (gn-term:family rdfs:range rdfs:Literal))
+ (gnt:name rdfs:range rdfs:Literal)
+ (gnt:displayName rdfs:range rdfs:Literal)
+ (gnt:binomialName rdfs:range rdfs:Literal)
+ (gnt:family rdfs:range rdfs:Literal))
(triples
(string->binomial-name (field Species FullName))
- (set rdf:type 'gn:species)
- (set gn-term:name (field Species SpeciesName))
- (set gn-term:displayName (field Species MenuName))
- (set gn-term:binomialName (field Species FullName))
- (set gn-term:family (field Species Family))
- (set gn-term:organism (ontology 'taxon: (field Species TaxonomyId)))))
+ (set rdf:type 'gnc:species)
+ (set gnt:name (field Species SpeciesName))
+ (set gnt:displayName (field Species MenuName))
+ (set gnt:binomialName (field Species FullName))
+ (set gnt:family (field Species Family))
+ (set gnt:organism (ontology 'taxon: (field Species TaxonomyId)))))
(define-dump dump-strain
(tables (Strain
(left-join Species "ON Strain.SpeciesId = Species.SpeciesId")))
(schema-triples
- (gn-term:strainOfSpecies rdfs:domain gn-term:strain)
- (gn-term:strainOfSpecies rdfs:range gn-term:species)
+ (gnt:strainOfSpecies rdfs:domain gnt:strain)
+ (gnt:strainOfSpecies rdfs:range gn-term:species)
(gn-term:name rdfs:range rdfs:Literal)
(gn-term:alias rdfs:range rdfs:Literal)
(gn-term:symbol rdfs:range rdfs:Literal))
@@ -51,7 +51,7 @@
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
- (set rdf:type 'gn:strain)
+ (set rdf:type 'gnc:strain)
(set gn-term:strainOfSpecies
(string->binomial-name (field Species FullName)))
;; Name, and maybe a second name
@@ -64,7 +64,7 @@
(tables (MappingMethod))
(triples
(string->identifier "mappingMethod" (field MappingMethod Name))
- (set rdf:type 'gn:mappingMethod)))
+ (set rdf:type 'gnc:mappingMethod)))
(define-dump dump-inbred-set
(tables (InbredSet
@@ -85,7 +85,7 @@
"" (field InbredSet Name)
#:separator ""
#:proc string-capitalize-first)
- (set rdf:type 'gn:inbredSet)
+ (set rdf:type 'gnc:inbredSet)
(set gn-term:binomialName (field InbredSet FullName))
(set gn-term:geneticType (field InbredSet GeneticType))
(set gn-term:inbredFamily (field InbredSet Family))
@@ -106,7 +106,7 @@
(schema-triples
(gn-term:normalization rdfs:range rdfs:Literal))
(triples (string->identifier "avgmethod" (field AvgMethod Name))
- (set rdf:type 'gn:avgMethod)
+ (set rdf:type 'gnc:avgMethod)
(set gn-term:normalization (field AvgMethod Normalization))))
@@ -117,7 +117,8 @@
(table-metadata? #f)
(prefixes
'(("gn:" "<http://genenetwork.org/id/>")
- ("gn-term:" "<http://genenetwork.org/term/>")
+ ("gnc:" "<http://genenetwork.org/category/>")
+ ("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#>")
("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
diff --git a/examples/dump-tissue.scm b/examples/dump-tissue.scm
index ff6792e..a9a50f3 100755
--- a/examples/dump-tissue.scm
+++ b/examples/dump-tissue.scm
@@ -23,12 +23,12 @@
;; and BIRN_lex_Name are mostly NULL.
(tables (Tissue))
(schema-triples
- (gn-term:name rdfs:range rdfs:Literal))
+ (gnt:name rdfs:range rdfs:Literal))
;; Hopefully the Short_Name field is distinct and can be used as an
;; identifier.
(triples (string->identifier "tissue" (field Tissue Short_Name))
(set rdf:type 'gn:tissue)
- (set gn-term:name (field Tissue Name))))
+ (set gnt:name (field Tissue Name))))
@@ -38,7 +38,7 @@
(table-metadata? #f)
(prefixes
'(("gn:" "<http://genenetwork.org/id/>")
- ("gn-term:" "<http://genenetwork.org/terms/>")
+ ("gnt:" "<http://genenetwork.org/terms/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
(inputs