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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.scm39
-rwxr-xr-xexamples/dump-tissue.scm6
9 files changed, 198 insertions, 198 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 a6be89a..5c9ef49 100755
--- a/examples/dump-species-metadata.scm
+++ b/examples/dump-species-metadata.scm
@@ -31,27 +31,25 @@
 (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->identifier "" (remap-species-identifiers (field Species Fullname))
-                             #:separator ""
-                             #:proc string-capitalize-first)
-    (set rdf:type 'gn:species)
-    (set gn-term:name (field Species SpeciesName))
-    (set gn-term:displayName (field Species MenuName))
-    (set gn-term:binomialName (remap-species-identifiers (field Species FullName)))
-    (set gn-term:family (field Species Family))
-    (set gn-term:organism (ontology 'taxon: (field Species TaxonomyId)))))
+      (string->binomial-name (field Species FullName))
+    (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))
@@ -63,7 +61,7 @@
              'pre "_" 'post)
             #:separator ""
             #:proc string-capitalize-first)
-    (set rdf:type 'gn:strain)
+    (set rdf:type 'gnc:strain)
     (set gn-term:strainOfSpecies
          (string->identifier "" (remap-species-identifiers (field Species FullName))
                           #:separator ""
@@ -78,7 +76,7 @@
   (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
@@ -99,7 +97,7 @@
             "" (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))
@@ -120,7 +118,7 @@
   (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))))
 
 
@@ -131,7 +129,8 @@
  (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
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-09-14 06:25:45 +0000