Replace dump.scm with separete dumps for several tables

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

8 files changed, 1020 insertions, 702 deletions

diff --git a/dump.scm b/dump.scm
deleted file mode 100755
index 0b2318c..0000000
--- a/dump.scm
+++ /dev/null
@@ -1,702 +0,0 @@
-#! /usr/bin/env guile
-!#
-
-(use-modules (rnrs programs)
-             (rnrs io ports)
-             (srfi srfi-1)
-             (srfi srfi-26)
-             (ice-9 match)
-             (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
-
-
-;;; GeneNetwork database connection parameters and dump path
-
-(define %connection-settings
-  (call-with-input-file (list-ref (command-line) 1)
-    read))
-
-(define %dump-directory
-  (list-ref (command-line) 2))
-
-
-;;; Dump tables
-
-(define binomial-name->species-id
-  (cut string->identifier "species" <>))
-
-(define-dump dump-species
-  (tables (Species))
-  (schema-triples
-   (gn:name rdfs:range rdfs:Literal)
-   (gn:displayName rdfs:range rdfs:Literal)
-   (gn:binomialName rdfs:range rdfs:Literal)
-   (gn:family rdfs:range rdfs:Literal))
-  (triples (binomial-name->species-id (field Species FullName))
-    (set rdf:type 'gn:species)
-    (set gn:name (field Species SpeciesName))
-    (set gn:displayName (field Species MenuName))
-    (set gn:binomialName (field Species FullName))
-    (set gn:family (field Species Family))
-    (set up:organism (ontology 'taxon: (field Species TaxonomyId)))))
-
-(define-dump dump-strain
-  (tables (Strain
-           (join Species "ON Strain.SpeciesId = Species.SpeciesId")))
-  (schema-triples
-   (gn:strainOfSpecies rdfs:domain gn:strain)
-   (gn:strainOfSpecies rdfs:range gn:species)
-   (gn:name rdfs:range rdfs:Literal)
-   (gn:alias rdfs:range rdfs:Literal)
-   (gn:symbol rdfs:range rdfs:Literal))
-  (triples (string->identifier "strain" (field Strain Name))
-    (set rdf:type 'gn:strain)
-    (set gn:strainOfSpecies
-         (binomial-name->species-id (field Species FullName)))
-    ;; Name, and maybe a second name
-    (set gn:name (field Strain Name))
-    (set gn:name (field Strain Name2))
-    (set gn:alias (field Strain Alias))
-    (set gn:symbol (field Strain Symbol))))
-
-;; TODO: This function is unused. Remove if not required.
-(define mapping-method-name->id
-  (cut string->identifier "mappingMethod" <>))
-
-;; TODO: This function is unused. Remove if not required.
-(define-dump dump-mapping-method
-  (tables (MappingMethod))
-  (triples (string->identifier "mappingMethod" (field MappingMethod Name))
-    (set rdf:type 'gn:mappingMethod)))
-
-(define inbred-set-name->id
-  (cut string->identifier "inbredSet" <>))
-
-(define-dump dump-inbred-set
-  (tables (InbredSet
-           (left-join Species "ON InbredSet.SpeciesId=Species.Id")
-           (left-join MappingMethod
-                       "ON InbredSet.MappingMethodId=MappingMethod.Id")))
-  (schema-triples
-   (gn:fullName rdfs:range rdfs:Literal)
-   (gn:geneticType rdfs:range rdfs:Literal)
-   (gn:inbredSetCode rdfs:range rdfs:Literal)
-   (gn:inbredFamily rdfs:range rdfs:Literal)
-   (gn:inbredSetOfSpecies rdfs:range gn:species)
-   (gn:inbredSetType rdfs:range rdfs:Literal)
-   (gn:phenotype rdfs:range gn:inbredSetType)
-   (gn:genotype rdfs:range gn:inbredSetType)
-   (gn:inbredSetOfMappingMethod rdfs:range gn:mappingMethod))
-  (triples (inbred-set-name->id (field InbredSet Name))
-    (set rdf:type 'gn:inbredSet)
-    (set gn:fullName (field InbredSet FullName))
-    (set gn:geneticType (field InbredSet GeneticType))
-    (set gn:inbredFamily (field InbredSet Family))
-    (set gn:inbredSetOfMappingMethod (field MappingMethod Name))
-    (set gn:inbredSetCode (field InbredSet InbredSetCode))
-    (set gn:inbredSetOfSpecies
-         (binomial-name->species-id (field Species FullName BinomialName)))
-    (set gn:genotype
-         (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP)))
-    (set gn:phenotype
-         (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP)))))
-
-(define-dump dump-molecular-traits
-  (tables (ProbeFreeze
-           (left-join ProbeSetFreeze "USING (ProbeFreezeId)")
-           (left-join InbredSet "USING (InbredSetId)")
-           (left-join Tissue "USING (TissueId)")
-           (left-join Species "USING (SpeciesId)"))
-          "GROUP BY InbredSet.Name")
-  (schema-triples
-   (gn:molecularTrait rdfs:range rdfs:Literal))
-  (triples (inbred-set-name->id (field InbredSet Name))
-    (set gn:molecularTrait (field Tissue TissueName))))
-
-;; Metadata for published datasets
-(define-dump dump-publishfreeze
-  (tables (PublishFreeze
-           (left-join InbredSet "USING (InbredSetId)")))
-  (schema-triples
-   (gn:datasetOfInbredSet rdfs:range gn:inbredSet)
-   (gn:name rdfs:range rdfs:Literal)
-   (gn:fullName rdfs:range rdfs:Literal)
-   (gn:shortName rdfs:range rdfs:Literal)
-   (gn:createTime rdfs:range rdfs:Literal))
-  (triples (string->identifier "dataset" (field PublishFreeze Name))
-    (set rdf:type 'gn:dataset)
-    (set gn:name (field PublishFreeze Name))
-    (set gn:fullName (field PublishFreeze FullName))
-    (set gn:shortName (field PublishFreeze ShortName))
-    (set gn:createTime (field PublishFreeze CreateTime))
-    (set gn:datasetOfInbredSet
-         (inbred-set-name->id (field InbredSet Name InbredSetName)))))
-
-(define-dump dump-publication
-  (tables (Publication))
-  (schema-triples
-   (gn:pubMedId rdfs:range rdfs:Literal)
-   (gn:title rdfs:range rdfs:Literal)
-   (gn:journal rdfs:range rdfs:Literal)
-   (gn:volume rdfs:range rdfs:Literal)
-   (gn:pages rdfs:range rdfs:Literal)
-   (gn:month rdfs:range rdfs:Literal)
-   (gn:year rdfs:range rdfs:Literal)
-   (gn:author rdfs:range rdfs:Literal)
-   (gn:abstract rdfs:range rdfs:Literal))
-  (triples
-      (let ((pmid (field
-                   ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
-                    pmid)))
-            (publication-id (field Publication Id)))
-        (if (string-null? pmid)
-            (string->identifier "publication"
-                                (number->string publication-id))
-            (ontology 'pubmed: pmid)))
-    (set rdf:type 'gn:publication)
-    (set gn:pubMedId (field ("IFNULL(PubMed_ID, '')" pubmedId)))
-    (set gn:title (field Publication Title))
-    (set gn:journal (field Publication Journal))
-    (set gn:volume (field Publication Volume))
-    (set gn:pages (field Publication Pages))
-    (set gn:month (field Publication Month))
-    (set gn:year (field Publication Year))
-    (multiset gn:author
-              ;; The authors field is a comma
-              ;; separated list. Split it.
-              (map string-trim (string-split (sanitize-rdf-string (field Publication Authors)) #\,)))
-    (set gn:abstract
-         (sanitize-rdf-string (field Publication Abstract)))))
-
-(define tissue-short-name->id
-  (cut string->identifier "tissue" <>))
-
-(define-dump dump-tissue
-  ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
-  ;; and BIRN_lex_Name are mostly NULL.
-  (tables (Tissue))
-  (schema-triples
-   (gn:name rdfs:range rdfs:Literal))
-  ;; Hopefully the Short_Name field is distinct and can be used as an
-  ;; identifier.
-  (triples (tissue-short-name->id (field Tissue Short_Name))
-    (set rdf:type 'gn:tissue)
-    (set gn:name (field Tissue Name))))
-
-;; One email ID in the Investigators table has spaces in it. This
-;; function fixes that.
-(define (fix-email-id email)
-  (string-delete #\space email))
-
-(define (investigator-attributes->id first-name last-name email)
-  ;; There is just one record corresponding to "Evan Williams" which
-  ;; does not have an email ID. To accommodate that record, we
-  ;; construct the investigator ID from not just the email ID, but
-  ;; also the first and the last names. It would be preferable to just
-  ;; find Evan Williams' email ID and insert it into the database.
-  (string->identifier "investigator"
-                      (string-join
-                       ;; Add special case for Yohan Bossé whose name
-                       ;; has unprintable characters.
-                       ;; TODO: Fix Yohan Bossé's name in the database.
-                       (let ((last-name (if (string=? first-name "Yohan")
-                                            "Bosse"
-                                            last-name)))
-                         (list first-name last-name (fix-email-id email)))
-                       "_")))
-
-(define-dump dump-investigators
-  ;; There are a few duplicate entries. We group by email to
-  ;; deduplicate.
-  (tables (Investigators)
-          "GROUP BY Email")
-  (schema-triples
-   ;; TODO: Are ranges required for FOAF predicates? Can they not be
-   ;; obtained from the FOAF spec?
-   (foaf:name rdfs:range rdfs:Literal)
-   (foaf:givenName rdfs:range rdfs:Literal)
-   (foaf:familyName rdfs:range rdfs:Literal)
-   (foaf:phone rdfs:range rdfs:Literal)
-   (foaf:mbox rdfs:range rdfs:Literal)
-   (foaf:homepage rdfs:range rdfs:Literal)
-   (gn:address rdfs:range rdfs:Literal)
-   (gn:city rdfs:range rdfs:Literal)
-   (gn:state rdfs:range rdfs:Literal)
-   (gn:zipCode rdfs:range rdfs:Literal)
-   (gn:country rdfs:range rdfs:Literal))
-  (triples (investigator-attributes->id (field Investigators FirstName)
-                                        (field Investigators LastName)
-                                        (field Investigators Email))
-    (set rdf:type 'foaf:Person)
-    ;; Special case Yohan Bossé's name since the last name has
-    ;; unprintable characters.
-    (set foaf:name (string-append (field Investigators FirstName) " "
-                                  (if (string=? (field Investigators FirstName) "Yohan")
-                                      "Bossé"
-                                      (field Investigators LastName))))
-    (set foaf:givenName (field Investigators FirstName))
-    ;; Special case Yohan Bossé's name since the last name has
-    ;; unprintable characters.
-    (set foaf:familyName (if (string=? (field Investigators FirstName) "Yohan")
-                             "Bossé"
-                             (field Investigators LastName)))
-    (set foaf:phone (field Investigators Phone))
-    (set foaf:mbox (fix-email-id (field Investigators Email)))
-    (set foaf:homepage (field Investigators Url))
-    (set gn:address (field Investigators Address))
-    (set gn:city (field Investigators City))
-    (set gn:state (field Investigators State))
-    (set gn:zipCode (field Investigators ZipCode))
-    (set gn:country (field Investigators Country))))
-
-(define avg-method-name->id
-  (cut string->identifier "avgmethod" <>))
-
-(define-dump dump-avg-method
-  ;; The Name and Normalization fields seem to be the same. Dump only
-  ;; the Name field.
-  (tables (AvgMethod))
-  (schema-triples
-   (gn:name rdfs:range rdfs:Literal))
-  (triples (avg-method-name->id (field AvgMethod Name))
-    (set rdf:type 'gn:avgMethod)
-    (set gn:name (field AvgMethod Name))))
-
-(define gene-chip-name->id
-  (cut string->identifier "platform" <>))
-
-(define-dump dump-gene-chip
-  (tables (GeneChip))
-  (schema-triples
-   (gn:name rdfs:range rdfs:Literal))
-  (triples (gene-chip-name->id (field GeneChip Name))
-    (set rdf:type 'gn:platform)
-    (set gn:name (field GeneChip GeneChipName))))
-
-;; Dumping Datasets from InfoFiles that don't exist in PublishFreeze and GenoFreeze
-(define-dump dump-info-files
-  (tables (InfoFiles
-           (left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name")
-           (left-join GenoFreeze "ON InfoFiles.InfoPageName = GenoFreeze.Name")
-           (left-join Datasets "USING (DatasetId)")
-           (left-join DatasetStatus "USING (DatasetStatusId)")
-           (left-join Species "USING (SpeciesId)")
-           (left-join Tissue "USING (TissueId)")
-           (left-join Investigators "USING (InvestigatorId)")
-           (left-join AvgMethod "USING (AvgMethodId)")
-           (left-join GeneChip "USING (GeneChipId)"))
-          "WHERE GN_AccesionId IS NOT NULL")
-  (schema-triples
-   (gn:datasetOfInvestigator rdfs:domain gn:dataset)
-   (gn:datasetOfInvestigator rdfs:range foaf:Person)
-   (gn:datasetOfSpecies rdfs:domain gn:dataset)
-   (gn:datasetOfSpecies rdfs:range gn:species)
-   (gn:datasetOfInbredSet rdfs:domain gn:dataset)
-   (gn:datasetOfInbredSet rdfs:range gn:inbredSet)
-   (gn:datasetOfTissue rdfs:domain gn:dataset)
-   (gn:datasetOfTissue rdfs:range gn:tissue)
-   (gn:normalization rdfs:domain gn:dataset)
-   (gn:normalization rdfs:range gn:avgMethod)
-   (gn:datasetOfPlatform rdfs:domain gn:dataset)
-   (gn:datasetOfPlatform rdfs:range gn:geneChip)
-   (gn:accessionId rdfs:range rdfs:Literal)
-   (gn:datasetStatusName rdfs:range rdfs:Literal)
-   (gn:summary rdfs:range rdfs:Literal)
-   (gn:aboutTissue rdfs:range rdfs:Literal)
-   (gn:geoSeries rdfs:range rdfs:Literal)
-   (gn:name rdfs:range rdfs:Literal)
-   (gn:title rdfs:range rdfs:Literal)
-   (gn:specifics rdfs:range rdfs:Literal)
-   (gn:datasetGroup rdfs:range rdfs:Literal)
-   (gn:aboutCases rdfs:range rdfs:Literal)
-   (gn:aboutPlatform rdfs:range rdfs:Literal)
-   (gn:aboutDataProcessing rdfs:range rdfs:Literal)
-   (gn:notes rdfs:range rdfs:Literal)
-   (gn:experimentDesign rdfs:range rdfs:Literal)
-   (gn:contributors rdfs:range rdfs:Literal)
-   (gn:citation rdfs:range rdfs:Literal)
-   (gn:acknowledgment rdfs:range rdfs:Literal))
-  (triples (string->identifier "dataset"
-                               (field InfoFiles InfoPageName))
-    (set rdf:type 'gn:dataset)
-    (set gn:name (field InfoFiles InfoPageName))
-    (set dct:created
-         (let* ((genotype-create-time
-                 (field ("IFNULL(GenoFreeze.CreateTime, '')"
-                         createTimeGenoFreeze)))
-                (phenotype-create-time
-                 (field ("IFNULL(PublishFreeze.CreateTime, '')"
-                         createTimePublishFreeze)))
-                (create-time
-                 (if (string-null? genotype-create-time)
-                     phenotype-create-time genotype-create-time)))
-           (annotate-field
-                create-time
-                '^^xsd:datetime)))
-    (set gn:datasetOfInvestigator
-         (investigator-attributes->id (field Investigators FirstName)
-                                      (field Investigators LastName)
-                                      (field Investigators Email)))
-    (set gn:accessionId (string-append "GN" (number->string
-                                             (field InfoFiles GN_AccesionId))))
-    (set gn:datasetStatusName (string-downcase
-                               (field DatasetStatus DatasetStatusName)))
-    (set gn:datasetOfSpecies (binomial-name->species-id
-                              (field Species FullName BinomialName)))
-    (set gn:datasetOfTissue (tissue-short-name->id (field Tissue Short_Name)))
-    (set gn:normalization
-         (avg-method-name->id
-          ;; If AvgMethodName is NULL, assume N/A.
-          (if (string-blank? (field AvgMethod Name AvgMethodName))
-              "N/A" (field AvgMethod Name AvgMethodName))))
-    (set gn:datasetOfPlatform (gene-chip-name->id (field GeneChip Name GeneChip)))
-    (set gn:summary
-         (sanitize-rdf-string (field Datasets Summary)))
-    (set gn:aboutTissue
-         (sanitize-rdf-string (field Datasets AboutTissue)))
-    (set gn:geoSeries
-         (and (not (string-prefix-ci? "no geo series"
-                                      (field Datasets GeoSeries)))
-              (field Datasets GeoSeries)))
-    (set gn:title (field InfoFiles Title))
-    (set gn:specifics (sanitize-rdf-string (field InfoFiles Specifics)))
-    (set gn:datasetGroup (field Datasets DatasetName DatasetGroup))
-    (set gn:aboutCases (sanitize-rdf-string (field Datasets AboutCases)))
-    (set gn:aboutPlatform (sanitize-rdf-string (field Datasets AboutPlatform)))
-    (set gn:aboutDataProcessing (sanitize-rdf-string
-                                 (field Datasets AboutDataProcessing)))
-    (set gn:notes (sanitize-rdf-string (field Datasets Notes)))
-    (set gn:experimentDesign (sanitize-rdf-string
-                              (field Datasets ExperimentDesign)))
-    (set gn:contributors (sanitize-rdf-string (field Datasets Contributors)))
-    (set gn:citation (sanitize-rdf-string (field Datasets Citation)))
-    (set gn:acknowledgment (sanitize-rdf-string
-                            (field Datasets Acknowledgment)))))
-
-;; Dumping Phenotypes from PublishFreeze that are not present in the InfoFiles tables
-(define-dump dump-phenotypes
-  (tables (Phenotype
-           (left-join PublishXRef "ON Phenotype.Id = PublishXRef.PhenotypeId")
-           (left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
-           (left-join PublishFreeze "ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId")
-           (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")))
-  (schema-triples
-   (gn:phenotypeDataset rdfs:subPropertyOf gn:dataset))
-  (triples (ontology 'phenotype:
-                     (regexp-substitute/global #f "[^A-Za-z0-9:]"
-                                               (field ("CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, ':')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation))" abbrev))
-                                               'pre "_" 'post))
-    (set rdf:type 'gn:phenotype)
-    (set gn:name (sanitize-rdf-string
-                  (field
-                   ("CAST(CONVERT(BINARY CONVERT(CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '-')), 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(10000))"
-                    abbrev))))
-    ;; There is no row with an empty post-publication description so
-    ;; use this field as the main publication description
-    (set gn:publicationDescription
-         (sanitize-rdf-string
-          (field ("CAST(CONVERT(BINARY CONVERT(Phenotype.Post_publication_description USING latin1) USING utf8) AS CHAR(10000))"
-                  postPubDescr))))
-    (set gn:originalDescription (sanitize-rdf-string
-                                 (delete-substrings
-                                  (field Phenotype Original_description)
-                                  "Original post publication description: ")))
-    (set gn:prePublicationDescription
-         (sanitize-rdf-string
-          (field
-           ("CAST(CONVERT(BINARY CONVERT(Phenotype.Pre_publication_description USING latin1) USING utf8) AS VARCHAR(15000))"
-            prePubDesc))))
-    (set gn:prePublicationAbbreviation (sanitize-rdf-string (field Phenotype Pre_publication_abbreviation)))
-    (set gn:postPublicationAbbreviation (sanitize-rdf-string (field Phenotype Post_publication_abbreviation)))
-    (set gn:labCode (field Phenotype Lab_code))
-    (set gn:submitter (sanitize-rdf-string (field Phenotype Submitter)))
-    (set gn:owner (sanitize-rdf-string (field Phenotype Owner)))
-    (set gn:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
-                                 '^^xsd:float))
-    (set gn:locus (field PublishXRef Locus))
-    (set gn:LRS (annotate-field (field ("IFNULL(PublishXRef.LRS, '')" lrs)) '^^xsd:float))
-    (set gn:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:decimal))
-    (set gn:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:int))
-    (set gn:phenotypeOfDataset (string->identifier "dataset" (field PublishFreeze Name)))
-    (set gn:phenotypeOfPublication
-         (let ((pmid (field
-                      ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
-                       pmid)))
-               (publication-id (field Publication Id)))
-           (if (string-null? pmid)
-               (string->identifier "publication"
-                                   (number->string publication-id))
-               (ontology 'pubmed: pmid))))))
-
-(define-dump dump-genotypes
-  (tables (GenoFreeze
-           (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name"))
-          "WHERE GenoFreeze.Name NOT IN (SELECT DISTINCT InfoFiles.InfoPageName FROM InfoFiles)")
-  (schema-triples
-   (gn:phenotypeDataset rdfs:subPropertyOf gn:dataset))
-  (triples (string->identifier "dataset"
-                               (field GenoFreeze Name))
-    (set rdf:type 'gn:genotypeDataset)
-    (set gn:name (field GenoFreeze FullName))
-    (set dct:created (annotate-field
-                      (field GenoFreeze CreateTime)
-                      '^^xsd:datetime))))
-
-
-(define (dump-data-table db table-name data-field)
-  (let ((dump-directory (string-append %dump-directory "/" table-name))
-        (port #f)
-        (current-strain-id #f))
-    (unless (file-exists? dump-directory)
-      (mkdir dump-directory))
-    (sql-for-each (match-lambda
-                    (((_ . strain-id)
-                      (_ . value))
-                     ;; Close file if new strain.
-                     (when (and port
-                                (not (= current-strain-id strain-id)))
-                       (close-port port)
-                       (set! port #f))
-                     ;; If no file is open, open new file.
-                     (unless port
-                       (set! current-strain-id strain-id)
-                       (let ((filename (string-append dump-directory
-                                                      "/" (number->string strain-id))))
-                         (display filename (current-error-port))
-                         (newline (current-error-port))
-                         (set! port (open-output-file filename))))
-                     (display value port)
-                     (newline port)))
-                  db
-                  (format #f "SELECT StrainId, ~a FROM ~a ORDER BY StrainId"
-                          data-field table-name))
-    (close-port port)))
-
-
-;;; Dump schema
-
-(define (tables db)
-  "Return list of all tables in DB. Each element of the returned list
-is a <table> object."
-  (map (lambda (table)
-         (set-table-columns table
-           (sql-map (lambda (row)
-                      (make-column (assoc-ref row "Field")
-                                   (assoc-ref row "Type")))
-                    db
-                    (format #f "SHOW COLUMNS FROM ~a" (table-name table)))))
-       (sql-map (lambda (row)
-                  (make-table (assoc-ref row "table_name")
-                              ;; FIXME: This is probably correct only for
-                              ;; MyISAM tables.
-                              (assoc-ref row "data_length")
-                              #f))
-                db
-                (select-query ((information_schema.tables table_name)
-                               (information_schema.tables data_length))
-                              (information_schema.tables)
-                              (format #f "WHERE table_schema = '~a'"
-                                      (assq-ref %connection-settings 'sql-database))))))
-
-(define (dump-schema db)
-  (let ((tables (tables db)))
-    (for-each (lambda (table)
-                (let ((table-id (string->identifier
-                                 "table"
-                                 ;; We downcase table names in
-                                 ;; identifiers. So, we distinguish
-                                 ;; between the user and User tables.
-                                 (if (string=? (table-name table) "User")
-                                     "user2"
-                                     (table-name table)))))
-                  (triple table-id 'rdf:type 'gn:sqlTable)
-                  (triple table-id 'gn:name (table-name table))
-                  (triple table-id 'gn:hasSize (table-size table))
-                  (for-each (lambda (column)
-                              (let ((column-id (column-id (table-name table)
-                                                          (column-name column))))
-                                (triple column-id 'rdf:type 'gn:sqlTableField)
-                                (triple column-id 'gn:name (column-name column))
-                                (triple column-id 'gn:sqlFieldType (column-type column))
-                                (triple table-id 'gn:hasField column-id)))
-                            (table-columns table))))
-              tables)))
-
-(define-dump dump-groups
-  (tables (InbredSet
-           (left-join Species "USING (SpeciesId)"))
-          (string-join
-           '("WHERE Species.Name IN "
-             "(SELECT Name FROM Species ORDER BY OrderId) "
-             "GROUP BY InbredSet.Name "
-             "ORDER BY "
-             "IFNULL(InbredSet.FamilyOrder, InbredSet.FullName) "
-             "ASC, IFNULL(InbredSet.Family, InbredSet.FullName) "
-             "ASC, InbredSet.FullName ASC, InbredSet.MenuOrderId ASC")))
-  (schema-triples
-   (gn:name rdfs:range rdfs:Literal)
-   (gn:binomialName rdfs:range rdfs:Literal)
-   (gn:species rdfs:range gn:species))
-  (triples (string->identifier "inbredSet" (field InbredSet Name))
-    (set gn:name (field InbredSet Name))
-    (set gn:binomialName (field InbredSet fullName))
-    (set gn:species (field Species Name))))
-
-(define-dump dump-genewiki-symbols
-  (tables (GeneRIF_BASIC
-           (left-join Species "USING (SpeciesId)"))
-          "GROUP BY GeneId ORDER BY BINARY symbol")
-  (schema-triples
-   (gn:symbol rdfs:domain gn:geneWikiEntry)
-   (gn:wikiEntryOfSpecies rdfs:range gn:species)
-   (gn:taxid rdfs:domain gn:geneWikiEntry))
-  (triples (ontology 'generif: (field GeneRIF_BASIC GeneId))
-    (multiset gn:symbol (string-split (field ("GROUP_CONCAT(DISTINCT symbol)" symbol))
-                                      #\,))
-    (multiset gn:wikiEntryOfSpecies
-              (string-split
-               (field ("GROUP_CONCAT(DISTINCT Species.SpeciesName)" species))
-               #\,))
-    (multiset gn:taxId (map (cut ontology 'taxon: <>)
-                            (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId))
-                                          #\,)))))
-;; GeneRIF metadata
-(define-dump dump-gn-genewiki-entries
-  (tables (GeneRIF
-           (left-join GeneRIF_BASIC "USING (symbol)")
-           (left-join Species "ON Species.SpeciesId = GeneRIF.SpeciesId")
-           (left-join GeneRIFXRef "ON GeneRIFXRef.GeneRIFId = GeneRIF.Id")
-           (left-join GeneCategory "ON GeneRIFXRef.GeneCategoryId = GeneCategory.Id"))
-          "WHERE GeneRIF.display > 0 AND GeneRIF.VersionId = 0 GROUP BY GeneRIF.symbol")
-  (schema-triples
-   (gn:geneWikiEntry a rdfs:Class)
-   (gn:geneWikiEntry a owl:Class)
-   (gn:geneWikiEntry rdfs:comment "Represents GeneRIF Entries")
-   (gn:geneCategory rdfs:domain gn:geneWikiEntry)
-   (gn:geneWikiEntryOfGn rdfs:domain gn:geneWikiEntry)
-   (gn:geneWikiEntry rdfs:domain gn:geneWikiEntry))
-  (triples
-      (let ([geneid (field GeneRIF_BASIC GeneId)])
-        (if (eq? geneid 0)
-            (ontology 'gn:anonSymbol_
-                      (field GeneRIF symbol))
-            (ontology 'generif:
-                      geneid)))
-    (set rdf:type (if (eq? (field GeneRIF_BASIC GeneId) 0)
-                        'gn:geneWikiEntry
-                        ""))
-    (set gn:wikiEntryOfSpecies (if (eq? (field GeneRIF_BASIC GeneId) 0)
-                                   (field Species SpeciesName)
-                                   ""))
-    ;; This only dumps symbols not present in the GeneRIF_BASIC table
-    (set gn:symbol (let ([geneid (field GeneRIF_BASIC GeneId)])
-                     (if (eq? geneid 0)
-                         (field GeneRIF symbol)
-                         "")))
-    (multiset gn:geneWikiEntryOfGn
-              (let* ([entries
-                      (replace-substrings
-                       (field
-                        ("GROUP_CONCAT(DISTINCT CONCAT_WS('::::', IFNULL(GeneCategory.Name, ''), IFNULL(GeneRIF.PubMed_ID, ''), GeneRIF.email, GeneRIF.comment, GeneRIF.createtime, IFNULL(weburl, '')) SEPARATOR';;;;;')"
-                         wikientry))
-                       '(("\x28" . "")
-                         ("\x29" . "")
-                         ("\xa0" . " ")
-                         ("â\x81„" . "/")
-                         ("â€\x9d" . #\")
-                         ("’" . #\')
-                         ("\x02" . "")
-                         ("\x01" . "")
-                         ("β" . "β")
-                         ("α-Â\xad" . "α")
-                         ("Â\xad" . "")
-                         ("α" . "α")
-                         ("–" . "-")))]
-                     [comments (string-split-substring entries ";;;;;")])
-                (map
-                 (match-lambda
-                   ((genecategory pmid email text createtime weburl)
-                    (blank-node
-                     (set gn:geneCategory genecategory)
-                     (multiset dct:source
-                               (map (lambda (el) (if (string-null? el)
-                                                     ""
-                                                     (ontology 'pubmed: el)))
-                                    (string-split pmid #\space)))
-                     (set dct:creator (regexp-substitute/global #f "@.*$"
-                                                                email
-                                                                'pre
-                                                                ""
-                                                                'post))
-                     (set gn:geneWikiEntry
-                          (annotate-field text '^^xsd:string))
-                     (set dct:created (annotate-field
-                                       createtime
-                                       '^^xsd:datetime))
-                     (set foaf:homepage weburl))))
-                 (map
-                  (cut string-split-substring <> "::::")
-                  comments))))))
-
-(define-dump dump-ncbi-genewiki-entries
-  (tables (GeneRIF_BASIC)
-          "GROUP BY GeneId, comment, createtime")
-  (schema-triples
-   (gn:geneWikiEntryofNCBI rdfs:domain gn:geneWikiEntry))
-  (triples (ontology 'generif:
-                     (field GeneRIF_BASIC GeneId))
-    (set gn:geneWikiEntryOfNCBI
-         (blank-node
-          (set gn:geneWikiEntry
-               (annotate-field (field GeneRIF_BASIC comment)
-                               '^^xsd:string))
-          (multiset dct:source (map (lambda (el) (if (string-null? el)
-                                                     ""
-                                                     (ontology 'pubmed: el)))
-                                    (string-split (field ("GROUP_CONCAT(PubMed_ID)" pmids))
-                                                  #\,)))
-          (set dct:created (annotate-field (time-unix->string
-                                            (field GeneRIF_BASIC createtime) "~5")
-                                           '^^xsd:datetime))))))
-
-
-;; Main function
-
-(call-with-genenetwork-database
- (lambda (db)
-   (with-output-to-file (string-append %dump-directory "/dump.ttl")
-     (lambda ()
-       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-       (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
-       (prefix "gn:" "<http://genenetwork.org/>")
-       (prefix "dct:" "<http://purl.org/dc/terms/>")
-       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
-       (prefix "up:" "<http://purl.uniprot.org/core/>")
-       (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
-       (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
-       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
-       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
-       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
-       (newline)
-       (dump-genewiki-symbols db)
-       (dump-gn-genewiki-entries db)
-       (dump-ncbi-genewiki-entries db)
-       (dump-species db)
-       (dump-strain db)
-       (dump-mapping-method db)
-       (dump-inbred-set db)
-       (dump-publishfreeze db)
-       (dump-publication db)
-       (dump-tissue db)
-       (dump-investigators db)
-       (dump-avg-method db)
-       (dump-gene-chip db)
-       (dump-info-files db)
-       (dump-schema db)
-       (dump-groups db)
-       (dump-published-phenotypes db)))))
-
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm
new file mode 100755
index 0000000..aa7a5f2
--- /dev/null
+++ b/examples/dump-dataset-metadata.scm
@@ -0,0 +1,220 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 match)
+             (ice-9 regex)
+             (dump strings)
+             (dump sql)
+             (dump triples)
+             (dump special-forms))
+
+
+
+(define %connection-settings
+  (call-with-input-file (list-ref (command-line) 1)
+    read))
+
+(define %dump-directory
+  (list-ref (command-line) 2))
+
+
+
+;; One email ID in the Investigators table has spaces in it. This
+;; function fixes that.
+(define (fix-email-id email)
+  (string-delete #\space email))
+
+(define (investigator-attributes->id first-name last-name email)
+  ;; There is just one record corresponding to "Evan Williams" which
+  ;; does not have an email ID. To accommodate that record, we
+  ;; construct the investigator ID from not just the email ID, but
+  ;; also the first and the last names. It would be preferable to just
+  ;; find Evan Williams' email ID and insert it into the database.
+  (string->identifier "investigator"
+                      (string-join
+                       ;; Add special case for Yohan Bossé whose name
+                       ;; has unprintable characters.
+                       ;; TODO: Fix Yohan Bossé's name in the database.
+                       (let ((last-name (if (string=? first-name "Yohan")
+                                            "Bosse"
+                                            last-name)))
+                         (list first-name last-name (fix-email-id email)))
+                       "_")))
+
+(define-dump dump-investigators
+  ;; There are a few duplicate entries. We group by email to
+  ;; deduplicate.
+  (tables (Investigators)
+          "GROUP BY Email")
+  (schema-triples
+   ;; TODO: Are ranges required for FOAF predicates? Can they not be
+   ;; obtained from the FOAF spec?
+   (foaf:name rdfs:range rdfs:Literal)
+   (foaf:givenName rdfs:range rdfs:Literal)
+   (foaf:familyName rdfs:range rdfs:Literal)
+   (foaf:phone rdfs:range rdfs:Literal)
+   (foaf:mbox rdfs:range rdfs:Literal)
+   (foaf:homepage rdfs:range rdfs:Literal)
+   (gn:address rdfs:range rdfs:Literal)
+   (gn:city rdfs:range rdfs:Literal)
+   (gn:state rdfs:range rdfs:Literal)
+   (gn:zipCode rdfs:range rdfs:Literal)
+   (gn:country rdfs:range rdfs:Literal))
+  (triples (investigator-attributes->id (field Investigators FirstName)
+                                        (field Investigators LastName)
+                                        (field Investigators Email))
+    (set rdf:type 'foaf:Person)
+    ;; Special case Yohan Bossé's name since the last name has
+    ;; unprintable characters.
+    (set foaf:name (string-append (field Investigators FirstName) " "
+                                  (if (string=? (field Investigators FirstName) "Yohan")
+                                      "Bossé"
+                                      (field Investigators LastName))))
+    (set foaf:givenName (field Investigators FirstName))
+    ;; Special case Yohan Bossé's name since the last name has
+    ;; unprintable characters.
+    (set foaf:familyName (if (string=? (field Investigators FirstName) "Yohan")
+                             "Bossé"
+                             (field Investigators LastName)))
+    (set foaf:phone (field Investigators Phone))
+    (set foaf:mbox (fix-email-id (field Investigators Email)))
+    (set foaf:homepage (field Investigators Url))
+    (set gn:address (field Investigators Address))
+    (set gn:city (field Investigators City))
+    (set gn:state (field Investigators State))
+    (set gn:zipCode (field Investigators ZipCode))
+    (set gn:country (field Investigators Country))))
+
+(define-dump dump-info-files
+  (tables (InfoFiles
+           (left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name")
+           (left-join GenoFreeze "ON InfoFiles.InfoPageName = GenoFreeze.Name")
+           (left-join ProbeSetFreeze "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
+           (left-join Datasets "USING (DatasetId)")
+           (left-join DatasetStatus "USING (DatasetStatusId)")
+           (left-join Species "USING (SpeciesId)")
+           (left-join Tissue "USING (TissueId)")
+           (left-join Investigators "USING (InvestigatorId)")
+           (left-join AvgMethod "USING (AvgMethodId)")
+           (left-join GeneChip "USING (GeneChipId)"))
+          "WHERE GN_AccesionId IS NOT NULL")
+  (schema-triples
+   (gn:datasetOfInvestigator rdfs:domain gn:dataset)
+   (gn:datasetOfInvestigator rdfs:range foaf:Person)
+   (gn:datasetOfSpecies rdfs:domain gn:dataset)
+   (gn:datasetOfSpecies rdfs:range gn:species)
+   (gn:datasetOfInbredSet rdfs:domain gn:dataset)
+   (gn:datasetOfInbredSet rdfs:range gn:inbredSet)
+   (gn:datasetOfTissue rdfs:domain gn:dataset)
+   (gn:datasetOfTissue rdfs:range gn:tissue)
+   (gn:normalization rdfs:domain gn:dataset)
+   (gn:normalization rdfs:range gn:avgMethod)
+   (gn:datasetOfPlatform rdfs:domain gn:dataset)
+   (gn:datasetOfPlatform rdfs:range gn:geneChip)
+   (gn:accessionId rdfs:range rdfs:Literal)
+   (gn:datasetStatusName rdfs:range rdfs:Literal)
+   (gn:summary rdfs:range rdfs:Literal)
+   (gn:aboutTissue rdfs:range rdfs:Literal)
+   (gn:geoSeries rdfs:range rdfs:Literal)
+   (gn:name rdfs:range rdfs:Literal)
+   (gn:title rdfs:range rdfs:Literal)
+   (gn:specifics rdfs:range rdfs:Literal)
+   (gn:datasetGroup rdfs:range rdfs:Literal)
+   (gn:aboutCases rdfs:range rdfs:Literal)
+   (gn:aboutPlatform rdfs:range rdfs:Literal)
+   (gn:aboutDataProcessing rdfs:range rdfs:Literal)
+   (gn:notes rdfs:range rdfs:Literal)
+   (gn:experimentDesign rdfs:range rdfs:Literal)
+   (gn:contributors rdfs:range rdfs:Literal)
+   (gn:citation rdfs:range rdfs:Literal)
+   (gn:acknowledgment rdfs:range rdfs:Literal))
+  (triples (string->identifier "dataset"
+                               (field InfoFiles InfoPageName))
+    ;; Add GeneChipName and GeoPlatform:
+    ;; GeneChip.GeneChipName AS gene_chip_name
+    ;; GeneChip.GeoPlatform AS geo_platform
+    (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:name (field InfoFiles InfoPageName))
+    (set dct:created
+         (field ("IFNULL(GenoFreeze.CreateTime, IFNULL(PublishFreeze.CreateTime, IFNULL(ProbeSetFreeze.CreateTime, '')))"
+                 createTimeGenoFreeze)))
+    (set gn:datasetOfInvestigator
+         (investigator-attributes->id (field Investigators FirstName)
+                                      (field Investigators LastName)
+                                      (field Investigators Email)))
+    (set gn:accessionId (string-append "GN" (number->string
+                                             (field InfoFiles GN_AccesionId))))
+    (set gn:datasetStatusName (string-downcase
+                               (field DatasetStatus DatasetStatusName)))
+    (set gn:datasetOfSpecies (string->identifier "species"
+                              (field Species FullName BinomialName)))
+    (set gn:datasetOfTissue (string->identifier "tissue"
+                                                (field Tissue Short_Name)))
+    (set gn: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:datasetOfPlatform
+         (string->identifier "platform"
+                             (field GeneChip Name GeneChip)))
+    (set gn:summary
+         (sanitize-rdf-string (field Datasets Summary)))
+    (set gn:aboutTissue
+         (sanitize-rdf-string (field Datasets AboutTissue)))
+    (set gn:geoSeries
+         (and (not (string-prefix-ci? "no geo series"
+                                      (field Datasets GeoSeries)))
+              (field Datasets GeoSeries)))
+    (set gn:title (field InfoFiles Title))
+    (set gn:specifics (sanitize-rdf-string (field InfoFiles Specifics)))
+    (set gn:datasetGroup (field Datasets DatasetName DatasetGroup))
+    (set gn:aboutCases (sanitize-rdf-string (field Datasets AboutCases)))
+    (set gn:aboutPlatform (sanitize-rdf-string (field Datasets AboutPlatform)))
+    (set gn:aboutDataProcessing (sanitize-rdf-string
+                                 (field Datasets AboutDataProcessing)))
+    (set gn:notes (sanitize-rdf-string (field Datasets Notes)))
+    (set gn:experimentDesign (sanitize-rdf-string
+                              (field Datasets ExperimentDesign)))
+    (set gn:contributors (sanitize-rdf-string (field Datasets Contributors)))
+    (set gn:citation (sanitize-rdf-string (field Datasets Citation)))
+    (set gn:acknowledgment (sanitize-rdf-string
+                            (field Datasets Acknowledgment)))))
+
+
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-info-pages.ttl")
+     (lambda ()
+       (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+       (prefix "dct:" "<http://purl.org/dc/terms/>")
+       (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
+       (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "gn:" "<http://genenetwork.org/>")
+       (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
+       (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
+       (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
+       (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
+       (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
+       (prefix "omim:" "<https://www.omim.org/entry/>")
+       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
+       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
+       (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+       (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
+       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
+       (prefix "up:" "<http://purl.uniprot.org/core/>")
+       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+       (newline)
+       (dump-info-files db)
+       (dump-investigators db))
+     #:encoding "utf8")))
diff --git a/examples/dump-generif.scm b/examples/dump-generif.scm
new file mode 100755
index 0000000..415cb67
--- /dev/null
+++ b/examples/dump-generif.scm
@@ -0,0 +1,159 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 match)
+             (ice-9 regex)
+             (dump strings)
+             (dump sql)
+             (dump triples)
+             (dump special-forms))
+
+
+
+(define %connection-settings
+  (call-with-input-file (list-ref (command-line) 1)
+    read))
+
+(define %dump-directory
+  (list-ref (command-line) 2))
+
+
+
+(define-dump dump-genewiki-symbols
+  (tables (GeneRIF_BASIC
+           (left-join Species "USING (SpeciesId)"))
+          "GROUP BY GeneId ORDER BY BINARY symbol")
+  (schema-triples
+   (gn:symbol rdfs:domain gn:geneWikiEntry)
+   (gn:wikiEntryOfSpecies rdfs:range gn:species)
+   (gn:taxid rdfs:domain gn:geneWikiEntry))
+  (triples (ontology 'generif: (field GeneRIF_BASIC GeneId))
+    (multiset gn:symbol (string-split (field ("GROUP_CONCAT(DISTINCT symbol)" symbol))
+                                      #\,))
+    (multiset gn:wikiEntryOfSpecies
+              (string-split
+               (field ("GROUP_CONCAT(DISTINCT Species.SpeciesName)" species))
+               #\,))
+    (multiset gn:taxId (map (cut ontology 'taxon: <>)
+                            (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId))
+                                          #\,)))))
+
+(define-dump dump-gn-genewiki-entries
+  (tables (GeneRIF
+           (left-join GeneRIF_BASIC "USING (symbol)")
+           (left-join Species "ON Species.SpeciesId = GeneRIF.SpeciesId")
+           (left-join GeneRIFXRef "ON GeneRIFXRef.GeneRIFId = GeneRIF.Id")
+           (left-join GeneCategory "ON GeneRIFXRef.GeneCategoryId = GeneCategory.Id"))
+          "WHERE GeneRIF.display > 0 AND GeneRIF.VersionId = 0 GROUP BY GeneRIF.symbol")
+  (schema-triples
+   (gn:geneWikiEntry a rdfs:Class)
+   (gn:geneWikiEntry a owl:Class)
+   (gn:geneWikiEntry rdfs:comment "Represents GeneRIF Entries")
+   (gn:geneCategory rdfs:domain gn:geneWikiEntry)
+   (gn:geneWikiEntryOfGn rdfs:domain gn:geneWikiEntry)
+   (gn:geneWikiEntry rdfs:domain gn:geneWikiEntry))
+  (triples
+      (let ([geneid (field GeneRIF_BASIC GeneId)])
+        (if (eq? geneid 0)
+            (ontology 'gn:anonSymbol_
+                      (field GeneRIF symbol))
+            (ontology 'generif:
+                      geneid)))
+    (set rdf:type
+         (if (string-null? (field ("IFNULL(GeneRIF_BASIC.GeneId, '')" geneWikiEntryP)))
+             ""
+             'gn:geneWikiEntry))
+    (set gn:wikiEntryOfSpecies
+         (field Species SpeciesName))
+    ;; This only dumps symbols not present in the GeneRIF_BASIC table
+    (set gn:symbol (let ([geneid (field GeneRIF_BASIC GeneId)])
+                     (if (eq? geneid 0)
+                         (field GeneRIF symbol)
+                         "")))
+    (multiset gn:geneWikiEntryOfGn
+              (let* ([entries
+                      (field
+                       ("GROUP_CONCAT(DISTINCT CONCAT_WS('::::', IFNULL(GeneCategory.Name, ''), IFNULL(GeneRIF.PubMed_ID, ''), GeneRIF.email, CAST(CONVERT(BINARY CONVERT(GeneRIF.comment USING latin1) USING utf8) AS VARCHAR(15000)), GeneRIF.createtime, IFNULL(weburl, '')) SEPARATOR';;;;;')"
+                        wikientry))]
+                     [comments (string-split-substring entries ";;;;;")])
+                (map
+                 (match-lambda
+                   ((genecategory pmid email text createtime weburl)
+                    (blank-node
+                     (set gn:geneCategory genecategory)
+                     (multiset dct:source
+                               (map (lambda (el) (if (string-null? el)
+                                                     ""
+                                                     (ontology 'pubmed: el)))
+                                    (string-split pmid #\space)))
+                     (set dct:creator (regexp-substitute/global #f "@.*$"
+                                                                email
+                                                                'pre
+                                                                ""
+                                                                'post))
+                     (set gn:geneWikiEntry
+                          (annotate-field text '^^xsd:string))
+                     (set dct:created (annotate-field
+                                       createtime
+                                       '^^xsd:datetime))
+                     (set foaf:homepage weburl))))
+                 (map
+                  (cut string-split-substring <> "::::")
+                  comments))))))
+
+(define-dump dump-ncbi-genewiki-entries
+  (tables (GeneRIF_BASIC)
+          "GROUP BY GeneId, comment, createtime")
+  (schema-triples
+   (gn:geneWikiEntryofNCBI rdfs:domain gn:geneWikiEntry))
+  (triples (ontology 'generif:
+                     (field GeneRIF_BASIC GeneId))
+    (set gn:geneWikiEntryOfNCBI
+         (blank-node
+          (set gn:geneWikiEntry
+               (annotate-field (field GeneRIF_BASIC comment)
+                               '^^xsd:string))
+          (multiset dct:source (map (lambda (el) (if (string-null? el)
+                                                     ""
+                                                     (ontology 'pubmed: el)))
+                                    (string-split (field ("GROUP_CONCAT(PubMed_ID)" pmids))
+                                                  #\,)))
+          (set dct:created (annotate-field (time-unix->string
+                                            (field GeneRIF_BASIC createtime) "~5")
+                                           '^^xsd:datetime))))))
+
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-generif.ttl")
+     (lambda ()
+       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+       (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
+       (prefix "gn:" "<http://genenetwork.org/>")
+       (prefix "dct:" "<http://purl.org/dc/terms/>")
+       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+       (prefix "up:" "<http://purl.uniprot.org/core/>")
+       (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
+       (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
+       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
+       (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
+       (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
+       (prefix "omim:" "<https://www.omim.org/entry/>")
+       (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
+       (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
+       (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
+       (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+       (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
+       (newline)
+       (dump-genewiki-symbols db)
+       (dump-gn-genewiki-entries db)
+       (dump-ncbi-genewiki-entries db))
+     #:encoding "utf8")))
diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm
new file mode 100755
index 0000000..842e7e8
--- /dev/null
+++ b/examples/dump-phenotype.scm
@@ -0,0 +1,131 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (rnrs programs)
+             (rnrs io ports)
+             (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 match)
+             (ice-9 regex)
+             (dump strings)
+             (dump sql)
+             (dump triples)
+             (dump special-forms))
+
+
+
+(define %connection-settings
+  (call-with-input-file (list-ref (command-line) 1)
+    read))
+
+(define %dump-directory
+  (list-ref (command-line) 2))
+
+
+
+;; Only dump publish freeze entries that were not dumped from the InfoFiles page
+(define-dump dump-publishfreeze
+  (tables (PublishFreeze
+           (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")
+           (left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId"))
+          "WHERE PublishFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL")
+  (schema-triples
+   (gn:datasetOfInbredSet rdfs:range gn:inbredSet)
+   (gn:name rdfs:range rdfs:Literal)
+   (gn:fullName rdfs:range rdfs:Literal)
+   (gn:shortName rdfs:range rdfs:Literal)
+   (gn:createTime rdfs:range rdfs:Literal))
+  (triples (string->identifier "dataset" (field PublishFreeze Name))
+    (set rdf:type 'gn:phenotypeDataset)
+    (set gn:name (field PublishFreeze Name))
+    (set gn:fullName (field PublishFreeze FullName))
+    (set gn:shortName (field PublishFreeze ShortName))
+    (set gn:createTime (field PublishFreeze CreateTime))
+    (set gn:datasetOfInbredSet
+         (string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
+
+(define-dump dump-phenotypes
+  (tables (Phenotype
+           (left-join PublishXRef "ON Phenotype.Id = PublishXRef.PhenotypeId")
+           (left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
+           (left-join PublishFreeze "ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId")
+           (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")))
+  (schema-triples
+   (gn:phenotypeDataset rdfs:subPropertyOf gn:dataset))
+  (triples (ontology 'phenotype:
+                     (regexp-substitute/global #f "[^A-Za-z0-9:]"
+                                               (field ("CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, ':')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation))" abbrev))
+                                               'pre "_" 'post))
+    (set rdf:type 'gn:phenotype)
+    (set gn:name (sanitize-rdf-string
+                  (field
+                   ("CAST(CONVERT(BINARY CONVERT(CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '-')), 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(10000))"
+                    abbrev))))
+    ;; There is no row with an empty post-publication description so
+    ;; use this field as the main publication description
+    (set gn:publicationDescription
+         (sanitize-rdf-string
+          (field ("CAST(CONVERT(BINARY CONVERT(Phenotype.Post_publication_description USING latin1) USING utf8) AS CHAR(10000))"
+                  postPubDescr))))
+    (set gn:originalDescription (sanitize-rdf-string
+                                 (delete-substrings
+                                  (field Phenotype Original_description)
+                                  "Original post publication description: ")))
+    (set gn:prePublicationDescription
+         (sanitize-rdf-string
+          (field
+           ("CAST(CONVERT(BINARY CONVERT(Phenotype.Pre_publication_description USING latin1) USING utf8) AS VARCHAR(15000))"
+            prePubDesc))))
+    (set gn:prePublicationAbbreviation (sanitize-rdf-string (field Phenotype Pre_publication_abbreviation)))
+    (set gn:postPublicationAbbreviation (sanitize-rdf-string (field Phenotype Post_publication_abbreviation)))
+    (set gn:labCode (field Phenotype Lab_code))
+    (set gn:submitter (sanitize-rdf-string (field Phenotype Submitter)))
+    (set gn:owner (sanitize-rdf-string (field Phenotype Owner)))
+    (set gn:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
+                                 '^^xsd:double))
+    (set gn:locus (field PublishXRef Locus))
+    (set gn:LRS (annotate-field (field ("IFNULL(PublishXRef.LRS, '')" lrs)) '^^xsd:float))
+    (set gn:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:decimal))
+    (set gn:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:int))
+    (set gn:phenotypeOfDataset (string->identifier "dataset" (field PublishFreeze Name)))
+    (set gn:phenotypeOfPublication
+         (let ((pmid (field
+                      ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
+                       pmid)))
+               (publication-id (field Publication Id)))
+           (if (string-null? pmid)
+               (string->identifier "publication"
+                                   (number->string publication-id))
+               (ontology 'pubmed: pmid))))))
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-phenotype.ttl")
+     (lambda ()
+       (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+       (prefix "dct:" "<http://purl.org/dc/terms/>")
+       (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
+       (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "gn:" "<http://genenetwork.org/>")
+       (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
+       (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
+       (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
+       (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
+       (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
+       (prefix "omim:" "<https://www.omim.org/entry/>")
+       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
+       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
+       (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+       (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
+       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
+       (prefix "up:" "<http://purl.uniprot.org/core/>")
+       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+       (newline)
+       (dump-publishfreeze db)
+       (dump-phenotypes db))
+     #:encoding "utf8")))
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm
new file mode 100755
index 0000000..d1ea2ae
--- /dev/null
+++ b/examples/dump-probeset.scm
@@ -0,0 +1,213 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 match)
+             (ice-9 regex)
+             (dump strings)
+             (dump sql)
+             (dump triples)
+             (dump special-forms))
+
+
+
+(define %connection-settings
+  (call-with-input-file (list-ref (command-line) 1)
+    read))
+
+(define %dump-directory
+  (list-ref (command-line) 2))
+
+
+(define-dump dump-gene-chip
+  (tables (GeneChip))
+  (schema-triples
+   (gn:name rdfs:range rdfs:Literal))
+  (triples (string->identifier "platform" (field GeneChip Name))
+    (set rdf:type 'gn:platform)
+    (set gn:name (field GeneChip GeneChipName))))
+
+(define-dump dump-probeset
+  (tables (ProbeSet
+           (left-join ProbeSetXRef "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
+           (left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id")
+           (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")))
+  (schema-triples
+   (gn:name rdfs:range rdfs:Literal))
+  (triples (ontology 'gn:probeset_ (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
+                                           name)))
+    (set gn:probesetOfDataset
+         (string->identifier
+          "dataset"
+          (field ProbeSetFreeze Name)))
+    (set gn:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
+                                 '^^xsd:double))
+    (set gn:se (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" se))
+                               '^^xsd:double))
+    (set gn:LRS (annotate-field (field ("IFNULL(ProbeSetXRef.LRS, '')" LRS))
+                                '^^xsd:double))
+    (set gn:pValue (annotate-field (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
+                                   '^^xsd:double))
+    (set gn:additive (annotate-field (field ("IFNULL(ProbeSetXRef.additive, '')" additive))
+                                     '^^xsd:double))
+    (set gn:h2 (annotate-field (field ("IFNULL(ProbeSetXRef.h2, '')" h2))
+                               '^^xsd:float))
+    (set gn:locus (field ProbeSetXRef Locus))
+    (set gn:chipOf (string->identifier "platform" (field GeneChip Name)))
+    (set gn:name (field ProbeSet Name))
+    (set gn:symbol (field ProbeSet Symbol))
+    (set gn:description (field ProbeSet description))
+    (set gn:chr (field ProbeSet Chr))
+    (set gn:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
+    (set gn:chr_2016 (field ProbeSet Chr_2016))
+    (set gn:mb_2016 (annotate-field (field ("IFNULL(ProbeSet.Mb_2016, '')" Mb_2016)) '^^xsd:double))
+    (set gn:alias (string-trim-both (field ProbeSet alias)))
+    (set gn:generif (ontology 'generif: (field ProbeSet GeneId)))
+    (set gn:genbank (ontology 'nuccore: (field ProbeSet GenbankId)))
+    (set gn:snp (field ("IFNULL(ProbeSet.SNP, '')" SNP)))
+    (set gn:blatSeq (string-trim-both (field ProbeSet BlatSeq)))
+    (set gn:targetSeq (field ProbeSet TargetSeq))
+    (set gn:unigene (field ProbeSet UniGeneId))
+    (set gn:strandProbe (field ProbeSet Strand_Probe))
+    (set gn:strandGene (field ProbeSet Strand_Gene))
+    (set gn:omim (ontology 'omim: (field ProbeSet OMIM)))
+    (set gn:comments (sanitize-rdf-string (field ProbeSet comments)))
+    (set gn:targetRegion (field ProbeSet Probe_set_target_region))
+    (set gn:specificity (annotate-field
+                         (field ("IFNULL(ProbeSet.Probe_set_specificity, '')" Probe_set_specificity))
+                         '^^xsd:double))
+    (set gn:blatScore (annotate-field
+                       (field ("IFNULL(ProbeSet.Probe_set_BLAT_score, '')" Probe_set_BLAT_score))
+                       '^^xsd:double))
+    (set gn:blatMbStart (annotate-field
+                         (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '')" Probe_set_Blat_Mb_start))
+                         '^^xsd:double))
+    (set gn:blatMbend (annotate-field
+                       (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '')" Probe_set_Blat_Mb_end))
+                       '^^xsd:double))
+    (set gn:blatMbStart2016
+         (annotate-field
+          (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '')" Probe_set_Blat_Mb_start_2016)) '^^xsd:double))
+    (set gn:blatMbend2016
+         (annotate-field
+          (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end_2016, '')" Probe_set_Blat_Mb_end_2016)) '^^xsd:double))
+    (set gn:strand (field ProbeSet Probe_set_strand))
+    (set gn:noteByRW (field ProbeSet Probe_set_Note_by_RW))
+    (set gn:flag (field ProbeSet flag))
+    (set gn:symbolH (field ProbeSet Symbol_H))
+    (set gn:descriptionH (field ProbeSet Description_H))
+    (set gn:chromosomeH (field ProbeSet chromosome_H))
+    (set gn:mbH (annotate-field (field ProbeSet MB_H) '^^xsd:double))
+    (set gn:aliasH (field ProbeSet alias_H))
+    (set gn:geneIdH (field ProbeSet GeneId_H))
+    (set gn:chrNum (field ("IFNULL(ProbeSet.chr_num, '')" chr_num)))
+    (set gn:nameNum (field ("IFNULL(ProbeSet.name_num, '')" name_num)))
+    (set gn:probeTargetDescription (field ProbeSet Probe_Target_Description))
+    (set gn:RefSeq_TranscriptId (ontology 'nuccore: (field ProbeSet RefSeq_TranscriptId)))
+    (set gn:ENSEMBLGeneId (string-trim-both
+                           (field ProbeSet ENSEMBLGeneId)))
+    (set gn:Chr_mm8 (field ("IFNULL(ProbeSet.Chr_mm8, '')" Chr_mm8)))
+    (set gn:Mb_mm8 (field ("IFNULL(ProbeSet.Mb_mm8, '')" Mb_mm8)))
+    (set gn:probeSetBlatMbStart_mm8
+         (annotate-field
+          (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_mm8, '')" Probe_set_Blat_Mb_start_mm8))
+          '^^xsd:double))
+    (set gn:probeSetBlatMbEnd_mm8
+         (annotate-field 
+          (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end_mm8, '')" Probe_set_Blat_Mb_end_mm8))
+          '^^xsd:double))
+    (set gn:homoloGeneID (ontology
+                          'homologene:
+                          (field ProbeSet HomoloGeneID)))
+    (set gn:biotype_ENS (field ProbeSet Biotype_ENS))
+    (set gn:proteinName (field ProbeSet ProteinName))
+    (set gn:uniProtReference (ontology 'uniprot:
+                                       (field ProbeSet UniProtID)))
+    (set gn:flybase_Id (field ProbeSet Flybase_Id))
+    (set gn:RGD_ID (field ("IFNULL(ProbeSet.RGD_ID, '')" RGD_ID)))
+    (set gn:hgnc (ontology
+                  'hgnc: (field ProbeSet HGNC_ID)))
+    (set gn:HMDB_ID (field ProbeSet HMDB_ID))
+    (set gn:confidence (field ("IFNULL(ProbeSet.Confidence, '')" Confidence)))
+    (set gn:chebi_ID (ontology
+                      'chebi:
+                      (field
+                       ("IFNULL(ProbeSet.ChEBI_ID, '')"
+                        ChEBI_ID))))
+    (set gn:CASNumber (field ProbeSet CAS_number))
+    (set gn:PubChemID (ontology
+                       'pubchem:
+                       (field
+                        ("IFNULL(ProbeSet.PubChem_ID, '')"
+                         PubChem_ID))))
+    (set gn:chemSpiderID (field ("IFNULL(ProbeSet.ChemSpider_ID, '')" ChemSpider_ID)))
+    (set gn:uniiID (field ProbeSet UNII_ID))
+    (set gn:ECNumber (field ProbeSet EC_number))
+    (set gn:keggID (ontology 'kegg:
+                             (field ProbeSet KEGG_ID)))
+    (set gn:molecularWeight (annotate-field (field ProbeSet Molecular_Weight) '^^xsd:double))
+    (set gn:nugowikiID (field ("IFNULL(ProbeSet.Nugowiki_ID, '')" Nugowiki_ID)))
+    (set gn:type (field ProbeSet Type))
+    (set gn:tissue (field ProbeSet Tissue))
+    (set gn:primaryName (field ProbeSet PrimaryName))
+    (set gn:secondaryNames (field ProbeSet SecondaryNames))
+    (set gn:peptideSequence (field ProbeSet PeptideSequence))))
+
+;; Molecular Traits are also referred to as ProbeSets
+(define-dump dump-probesetfreeze
+  (tables (ProbeSetFreeze
+           (left-join ProbeFreeze "USING (ProbeFreezeId)")
+           (left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
+           (left-join InbredSet "ON ProbeFreeze.InbredSetId=InbredSet.Id")
+           (left-join Tissue "USING (TissueId)"))
+          "WHERE ProbeSetFreeze.public > 0 GROUP BY ProbeFreeze.Id")
+  (schema-triples
+   (gn:molecularTrait rdfs:range rdfs:Literal))
+  (triples
+      (string->identifier "dataset" (field ProbeSetFreeze Name))
+    (set rdf:type 'gn:dataset)
+    (set gn:avgMethod (string->identifier "avgmethod" (field AvgMethod Name)))
+    (set gn:fullName (field ProbeSetFreeze FullName))
+    (set gn:shortName (field ProbeSetFreeze ShortName))
+    (set dct:created (annotate-field
+                      (field ProbeSetFreeze CreateTime)
+                      '^^xsd:datetime))
+    (set gn:dataScale (field ProbeSetFreeze DataScale))
+    (set gn:tissueName (string->identifier "tissue" (field Tissue Short_Name)))
+    (set gn:datasetOfInbredSet
+         (string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
+
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-probeset.ttl")
+     (lambda ()
+       (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+       (prefix "dct:" "<http://purl.org/dc/terms/>")
+       (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
+       (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "gn:" "<http://genenetwork.org/>")
+       (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
+       (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
+       (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
+       (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
+       (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
+       (prefix "omim:" "<https://www.omim.org/entry/>")
+       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
+       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
+       (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+       (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
+       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
+       (prefix "up:" "<http://purl.uniprot.org/core/>")
+       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+       (newline)
+       (dump-gene-chip db)
+       (dump-probeset db)
+       (dump-probesetfreeze db))
+     #:encoding "utf8")))
diff --git a/examples/dump-publication.scm b/examples/dump-publication.scm
new file mode 100755
index 0000000..bed957a
--- /dev/null
+++ b/examples/dump-publication.scm
@@ -0,0 +1,90 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 match)
+             (ice-9 regex)
+             (dump strings)
+             (dump sql)
+             (dump triples)
+             (dump special-forms))
+
+
+
+(define %connection-settings
+  (call-with-input-file (list-ref (command-line) 1)
+    read))
+
+(define %dump-directory
+  (list-ref (command-line) 2))
+
+
+
+(define-dump dump-publication
+  (tables (Publication))
+  (schema-triples
+   (gn:pubMedId rdfs:range rdfs:Literal)
+   (gn:title rdfs:range rdfs:Literal)
+   (gn:journal rdfs:range rdfs:Literal)
+   (gn:volume rdfs:range rdfs:Literal)
+   (gn:pages rdfs:range rdfs:Literal)
+   (gn:month rdfs:range rdfs:Literal)
+   (gn:year rdfs:range rdfs:Literal)
+   (gn:author rdfs:range rdfs:Literal)
+   (gn:abstract rdfs:range rdfs:Literal))
+  (triples
+      (let ((pmid (field
+                   ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
+                    pmid)))
+            (publication-id (field Publication Id)))
+        (if (string-null? pmid)
+            (string->identifier "publication"
+                                (number->string publication-id))
+            (ontology 'pubmed: pmid)))
+    (set rdf:type 'gn:publication)
+    (set gn:pubMedId (field ("IFNULL(PubMed_ID, '')" pubmedId)))
+    (set gn:title (field Publication Title))
+    (set gn:journal (field Publication Journal))
+    (set gn:volume (field Publication Volume))
+    (set gn:pages (field Publication Pages))
+    (set gn:month (field Publication Month))
+    (set gn:year (field Publication Year))
+    (multiset gn:author
+              ;; The authors field is a comma
+              ;; separated list. Split it.
+              (map string-trim (string-split (sanitize-rdf-string (field Publication Authors)) #\,)))
+    (set gn:abstract
+         (sanitize-rdf-string (field Publication Abstract)))))
+
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-publication.ttl")
+     (lambda ()
+       (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+       (prefix "dct:" "<http://purl.org/dc/terms/>")
+       (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
+       (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "gn:" "<http://genenetwork.org/>")
+       (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
+       (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
+       (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
+       (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
+       (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
+       (prefix "omim:" "<https://www.omim.org/entry/>")
+       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
+       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
+       (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+       (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
+       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
+       (prefix "up:" "<http://purl.uniprot.org/core/>")
+       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+       (newline)
+       (dump-publication db))
+     #:encoding "utf8")))
diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm
new file mode 100755
index 0000000..ed4113c
--- /dev/null
+++ b/examples/dump-species-metadata.scm
@@ -0,0 +1,141 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 match)
+             (ice-9 regex)
+             (dump strings)
+             (dump sql)
+             (dump triples)
+             (dump special-forms))
+
+
+
+(define %connection-settings
+  (call-with-input-file (list-ref (command-line) 1)
+    read))
+
+(define %dump-directory
+  (list-ref (command-line) 2))
+
+
+
+(define-dump dump-species
+  (tables (Species))
+  (schema-triples
+   (gn:name rdfs:range rdfs:Literal)
+   (gn:displayName rdfs:range rdfs:Literal)
+   (gn:binomialName rdfs:range rdfs:Literal)
+   (gn:family rdfs:range rdfs:Literal))
+  (triples (string->identifier "species" (field Species FullName))
+    (set rdf:type 'gn:species)
+    (set gn:name (field Species SpeciesName))
+    (set gn:displayName (field Species MenuName))
+    (set gn:binomialName (field Species FullName))
+    (set gn:family (field Species Family))
+    (set up:organism (ontology 'taxon: (field Species TaxonomyId)))))
+
+(define-dump dump-strain
+  (tables (Strain
+           (join Species "ON Strain.SpeciesId = Species.SpeciesId")))
+  (schema-triples
+   (gn:strainOfSpecies rdfs:domain gn:strain)
+   (gn:strainOfSpecies rdfs:range gn:species)
+   (gn:name rdfs:range rdfs:Literal)
+   (gn:alias rdfs:range rdfs:Literal)
+   (gn:symbol rdfs:range rdfs:Literal))
+  (triples (string->identifier
+            "strain"
+            (regexp-substitute/global
+             #f "[^A-Za-z0-9:]"
+             (field ("CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARCHAR(15000))" StrainName))
+             'pre "_" 'post))
+    (set rdf:type 'gn:strain)
+    (set gn:strainOfSpecies
+         (string->identifier "species" (field Species FullName)))
+    ;; Name, and maybe a second name
+    (set gn:name (sanitize-rdf-string (field Strain Name)))
+    (set gn:name (sanitize-rdf-string (field Strain Name2)))
+    (set gn:alias (sanitize-rdf-string (field Strain Alias)))
+    (set gn:symbol (field Strain Symbol))))
+
+(define-dump dump-mapping-method
+  (tables (MappingMethod))
+  (triples (string->identifier "mappingMethod" (field MappingMethod Name))
+    (set rdf:type 'gn:mappingMethod)))
+
+(define-dump dump-inbred-set
+  (tables (InbredSet
+           (left-join Species "ON InbredSet.SpeciesId=Species.Id")
+           (left-join MappingMethod
+                       "ON InbredSet.MappingMethodId=MappingMethod.Id")))
+  (schema-triples
+   (gn:fullName rdfs:range rdfs:Literal)
+   (gn:geneticType rdfs:range rdfs:Literal)
+   (gn:inbredSetCode rdfs:range rdfs:Literal)
+   (gn:inbredFamily rdfs:range rdfs:Literal)
+   (gn:inbredSetOfSpecies rdfs:range gn:species)
+   (gn:inbredSetType rdfs:range rdfs:Literal)
+   (gn:phenotype rdfs:range gn:inbredSetType)
+   (gn:genotype rdfs:range gn:inbredSetType)
+   (gn:inbredSetOfMappingMethod rdfs:range gn:mappingMethod))
+  (triples (string->identifier "inbredSet" (field InbredSet Name))
+    (set rdf:type 'gn:inbredSet)
+    (set gn:binomialName (field InbredSet FullName))
+    (set gn:geneticType (field InbredSet GeneticType))
+    (set gn:inbredFamily (field InbredSet Family))
+    (set gn:inbredSetOfMappingMethod (field MappingMethod Name))
+    (set gn:inbredSetCode (field InbredSet InbredSetCode))
+    (set gn:inbredSetOfSpecies
+         (string->identifier "species" (field Species FullName BinomialName)))
+    (set gn:genotype
+         (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP)))
+    (set gn:phenotype
+         (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP)))))
+
+(define-dump dump-avg-method
+  ;; The Name and Normalization fields seem to be the same. Dump only
+  ;; the Name field.
+  (tables (AvgMethod))
+  (schema-triples
+   (gn:name rdfs:range rdfs:Literal))
+  (triples (string->identifier "avgmethod" (field AvgMethod Name))
+    (set rdf:type 'gn:avgMethod)
+    (set gn:name (field AvgMethod Name))))
+
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-species-metadata.ttl")
+     (lambda ()
+       (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+       (prefix "dct:" "<http://purl.org/dc/terms/>")
+       (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
+       (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "gn:" "<http://genenetwork.org/>")
+       (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
+       (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
+       (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
+       (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
+       (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
+       (prefix "omim:" "<https://www.omim.org/entry/>")
+       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
+       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
+       (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+       (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
+       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
+       (prefix "up:" "<http://purl.uniprot.org/core/>")
+       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+       (newline)
+       (dump-species db)
+       (dump-strain db)
+       (dump-mapping-method db)
+       (dump-inbred-set db)
+       (dump-avg-method db))
+     #:encoding "utf8")))
diff --git a/examples/dump-tissue.scm b/examples/dump-tissue.scm
new file mode 100755
index 0000000..3d55383
--- /dev/null
+++ b/examples/dump-tissue.scm
@@ -0,0 +1,66 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 match)
+             (ice-9 regex)
+             (dump strings)
+             (dump sql)
+             (dump triples)
+             (dump special-forms))
+
+
+
+(define %connection-settings
+  (call-with-input-file (list-ref (command-line) 1)
+    read))
+
+(define %dump-directory
+  (list-ref (command-line) 2))
+
+
+
+(define-dump dump-tissue
+  ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
+  ;; and BIRN_lex_Name are mostly NULL.
+  (tables (Tissue))
+  (schema-triples
+   (gn: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:name (field Tissue Name))))
+
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-tissue.ttl")
+     (lambda ()
+       (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+       (prefix "dct:" "<http://purl.org/dc/terms/>")
+       (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
+       (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "gn:" "<http://genenetwork.org/>")
+       (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
+       (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
+       (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
+       (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
+       (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
+       (prefix "omim:" "<https://www.omim.org/entry/>")
+       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
+       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
+       (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+       (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
+       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
+       (prefix "up:" "<http://purl.uniprot.org/core/>")
+       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+       (newline)
+       (dump-tissue db))
+     #:encoding "utf8")))