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-rwxr-xr-xexamples/dataset-metadata.scm (renamed from examples/dump-dataset-metadata.scm)30
-rwxr-xr-xexamples/generif.scm (renamed from examples/dump-generif.scm)18
-rwxr-xr-xexamples/genotype.scm (renamed from examples/dump-genotype.scm)10
-rwxr-xr-xexamples/phenotype.scm (renamed from examples/dump-phenotype.scm)10
-rwxr-xr-xexamples/probeset-data.scm (renamed from examples/dump-probeset-data.scm)20
-rwxr-xr-xexamples/probeset.scm (renamed from examples/dump-probeset.scm)10
-rwxr-xr-xexamples/publication.scm (renamed from examples/dump-publication.scm)10
-rwxr-xr-xexamples/species-metadata.scm (renamed from examples/dump-species-metadata.scm)28
-rwxr-xr-xexamples/tissue.scm (renamed from examples/dump-tissue.scm)10
9 files changed, 69 insertions, 77 deletions
diff --git a/examples/dump-dataset-metadata.scm b/examples/dataset-metadata.scm
index 6173201..5680a2b 100755
--- a/examples/dump-dataset-metadata.scm
+++ b/examples/dataset-metadata.scm
@@ -34,7 +34,7 @@
(list first-name last-name (fix-email-id email))
"_")))
-(define-transformer dump-investigators
+(define-transformer investigators
;; There are a few duplicate entries. We group by email to
;; deduplicate.
(tables (Investigators)
@@ -56,7 +56,7 @@
(set v:postal-code (field Investigators ZipCode))
(set v:country-name (field Investigators Country))))
-(define-transformer dump-gene-chip
+(define-transformer gene-chip
(tables (GeneChip
(left-join Species "USING (SpeciesId)")))
(schema-triples
@@ -87,7 +87,7 @@
(ontology 'geoSeries:
(string-trim-both (field GeneChip GeoPlatform))))))
-(define-transformer dump-info-files
+(define-transformer info-files
(tables (InfoFiles
(left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name")
(left-join GenoFreeze "ON InfoFiles.InfoPageName = GenoFreeze.Name")
@@ -251,7 +251,7 @@
(field Datasets Acknowledgment)))))
;; These are phenotype datasets that don't have Infofile metadata
-(define-transformer dump-publishfreeze
+(define-transformer publishfreeze
(tables (PublishFreeze
(left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")
(left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId"))
@@ -277,7 +277,7 @@
#:separator ""
#:proc string-capitalize-first))))
-(define-transformer dump-genofreeze
+(define-transformer genofreeze
(tables (GenoFreeze
(left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")
(left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId"))
@@ -308,7 +308,7 @@
#:proc string-capitalize-first))))
;; Molecular Traits are also referred to as ProbeSets
-(define-transformer dump-probesetfreeze
+(define-transformer probesetfreeze
(tables (ProbeSetFreeze
(left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
(left-join ProbeFreeze "USING (ProbeFreezeId)")
@@ -356,7 +356,7 @@
-(dump-with-documentation
+(with-documentation
(name "Info files / Investigators Metadata")
(connection %connection-settings)
(table-metadata? #f)
@@ -375,13 +375,13 @@
("taxon:" "<http://purl.uniprot.org/taxonomy/>")
("dct:" "<http://purl.org/dc/terms/>")))
(inputs
- (list dump-info-files
- dump-publishfreeze
- dump-genofreeze
- dump-probesetfreeze
- dump-investigators
- dump-gene-chip))
+ (list info-files
+ publishfreeze
+ genofreeze
+ probesetfreeze
+ investigators
+ gene-chip))
(outputs
- '(#:documentation "./docs/dump-info-pages.md"
- #:rdf "/export/data/genenetwork-virtuoso/dump-info-pages.ttl")))
+ '(#:documentation "./docs/info-pages.md"
+ #:rdf "/export/data/genenetwork-virtuoso/info-pages.ttl")))
diff --git a/examples/dump-generif.scm b/examples/generif.scm
index f754274..0b3c8e4 100755
--- a/examples/dump-generif.scm
+++ b/examples/generif.scm
@@ -18,7 +18,7 @@
-(define-transformer dump-genewiki-symbols
+(define-transformer genewiki-symbols
(tables (GeneRIF_BASIC
(left-join Species "USING (SpeciesId)"))
"GROUP BY GeneId ORDER BY BINARY symbol")
@@ -37,7 +37,7 @@
(string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId))
#\,)))))
-(define-transformer dump-gn-genewiki-entries
+(define-transformer gn-genewiki-entries
(tables (GeneRIF
(left-join GeneRIF_BASIC "USING (symbol)")
(left-join Species "ON Species.SpeciesId = GeneRIF.SpeciesId")
@@ -101,7 +101,7 @@
(cut string-split-substring <> "::::")
comments))))))
-(define-transformer dump-ncbi-genewiki-entries
+(define-transformer ncbi-genewiki-entries
(tables (GeneRIF_BASIC)
"GROUP BY GeneId, comment, createtime")
(schema-triples
@@ -124,7 +124,7 @@
-(dump-with-documentation
+(with-documentation
(name "GeneRIF Metadata")
(connection %connection-settings)
(table-metadata? #f)
@@ -141,10 +141,10 @@
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
("owl:" "<http://www.w3.org/2002/07/owl#>")))
(inputs
- (list ;; dump-genewiki-symbols
- dump-gn-genewiki-entries
- ;; dump-ncbi-genewiki-entries
+ (list ;; genewiki-symbols
+ gn-genewiki-entries
+ ;; ncbi-genewiki-entries
))
(outputs
- '(#:documentation "./docs/dump-generif.md"
- #:rdf "./verified-data/dump-generif.ttl")))
+ '(#:documentation "./docs/generif.md"
+ #:rdf "./verified-data/generif.ttl")))
diff --git a/examples/dump-genotype.scm b/examples/genotype.scm
index a055039..63b85a7 100755
--- a/examples/dump-genotype.scm
+++ b/examples/genotype.scm
@@ -30,7 +30,7 @@
["Bat (Glossophaga soricina)" "Glossophaga soricina"]
[str str]))
-(define-transformer dump-genotypes
+(define-transformer genotypes
(tables (Geno
(left-join Species "USING (SpeciesId)")))
(schema-triples
@@ -103,7 +103,7 @@
-(dump-with-documentation
+(with-documentation
(name "Genotype Metadata")
(connection %connection-settings)
(table-metadata? #f)
@@ -118,7 +118,7 @@
("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
(inputs
- (list dump-genotypes))
+ (list genotypes))
(outputs
- '(#:documentation "./docs/dump-genotype.md"
- #:rdf "/export/data/genenetwork-virtuoso/dump-genotype.ttl")))
+ '(#:documentation "./docs/genotype.md"
+ #:rdf "/export/data/genenetwork-virtuoso/genotype.ttl")))
diff --git a/examples/dump-phenotype.scm b/examples/phenotype.scm
index b7ae003..1c68159 100755
--- a/examples/dump-phenotype.scm
+++ b/examples/phenotype.scm
@@ -19,7 +19,7 @@
read))
-(define-transformer dump-phenotypes
+(define-transformer phenotypes
(tables (PublishXRef
(left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
(left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
@@ -102,7 +102,7 @@
-(dump-with-documentation
+(with-documentation
(name "Phenotypes Metadata")
(connection %connection-settings)
(table-metadata? #f)
@@ -119,7 +119,7 @@
("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
(inputs
(list
- dump-phenotypes))
+ phenotypes))
(outputs
- '(#:documentation "./docs/dump-phenotype.md"
- #:rdf "/export/data/genenetwork-virtuoso/dump-phenotype.ttl")))
+ '(#:documentation "./docs/phenotype.md"
+ #:rdf "/export/data/genenetwork-virtuoso/phenotype.ttl")))
diff --git a/examples/dump-probeset-data.scm b/examples/probeset-data.scm
index 55f3f4b..d46bcda 100755
--- a/examples/dump-probeset-data.scm
+++ b/examples/probeset-data.scm
@@ -18,7 +18,7 @@
-(define-transformer dump-probeset-data
+(define-transformer probeset-data
(tables (ProbeSetXRef
(left-join ProbeSet "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
(left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id"))
@@ -74,19 +74,11 @@
(set gnt:pValue (annotate-field (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
'^^xsd:double))
(set gnt:h2 (annotate-field (field ("IFNULL(ProbeSetXRef.h2, '')" h2))
- '^^xsd:double))
- (set gnt:belongsToDataset
- (string->identifier
- ""
- (regexp-substitute/global #f "[^A-Za-z0-9:]"
- (field ProbeSetFreeze Name)
- 'pre "_" 'post)
- #:separator ""
- #:proc string-capitalize-first))))
+ '^^xsd:double))))
-(dump-with-documentation
+(with-documentation
(name "Probeset Summary Statistics")
(connection %connection-settings)
(table-metadata? #f)
@@ -100,7 +92,7 @@
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
(inputs
- (list dump-probeset-data))
+ (list probeset-data))
(outputs
- '(#:documentation "./docs/dump-probeset-summary-stats.md"
- #:rdf "./verified-data/dump-probeset-summary-stats.ttl")))
+ '(#:documentation "./docs/probeset-summary-stats.md"
+ #:rdf "./verified-data/probeset-summary-stats.ttl")))
diff --git a/examples/dump-probeset.scm b/examples/probeset.scm
index 3a55506..68ddb59 100755
--- a/examples/dump-probeset.scm
+++ b/examples/probeset.scm
@@ -17,7 +17,7 @@
read))
-(define-transformer dump-probeset
+(define-transformer probeset
(tables (ProbeSet
(left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")))
(schema-triples
@@ -156,7 +156,7 @@
-(dump-with-documentation
+(with-documentation
(name "ProbeSet Metadata")
(connection %connection-settings)
(table-metadata? #f)
@@ -178,7 +178,7 @@
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")))
(inputs
- (list dump-probeset))
+ (list probeset))
(outputs
- '(#:documentation "./docs/dump-probeset.md"
- #:rdf "./verified-data/dump-probeset.ttl")))
+ '(#:documentation "./docs/probeset.md"
+ #:rdf "./verified-data/probeset.ttl")))
diff --git a/examples/dump-publication.scm b/examples/publication.scm
index 1881872..313ee96 100755
--- a/examples/dump-publication.scm
+++ b/examples/publication.scm
@@ -18,7 +18,7 @@
-(define-transformer dump-publication
+(define-transformer publication
(tables (Publication))
(triples
(let ((pmid (field
@@ -59,7 +59,7 @@
-(dump-with-documentation
+(with-documentation
(name "Publications Metadata")
(connection %connection-settings)
(table-metadata? #f)
@@ -75,7 +75,7 @@
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")))
(inputs
- (list dump-publication))
+ (list publication))
(outputs
- '(#:documentation "./docs/dump-publication.md"
- #:rdf "./verified-data/dump-publication.ttl")))
+ '(#:documentation "./docs/publication.md"
+ #:rdf "./verified-data/publication.ttl")))
diff --git a/examples/dump-species-metadata.scm b/examples/species-metadata.scm
index b0ac6f8..f3794b8 100755
--- a/examples/dump-species-metadata.scm
+++ b/examples/species-metadata.scm
@@ -28,7 +28,7 @@
["Bat (Glossophaga soricina)" "Glossophaga soricina"]
[str str]))
-(define-transformer dump-species
+(define-transformer species
(tables (Species))
(schema-triples
(gnc:species a skos:Concept)
@@ -97,7 +97,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
!#
-(define-transformer dump-strain
+(define-transformer strain
(tables (Strain
(left-join Species "ON Strain.SpeciesId = Species.SpeciesId")))
(schema-triples
@@ -129,7 +129,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
(set gnt:alias (sanitize-rdf-string (field ("IF ((Strain.Alias != Strain.Name), Strain.Alias, '')" Alias))))
(set gnt:symbol (field ("IF ((Strain.Symbol != Strain.Name), Strain.Symbol, '')" Symbol)))))
-(define-transformer dump-mapping-method
+(define-transformer mapping-method
(tables (MappingMethod))
(schema-triples
(gnc:mappingMethod a skos:Concept)
@@ -140,7 +140,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
(set rdfs:label (field MappingMethod Name))))
-(define-transformer dump-inbred-set
+(define-transformer inbred-set
(tables (InbredSet
(left-join Species "ON InbredSet.SpeciesId=Species.Id")
(left-join MappingMethod
@@ -152,7 +152,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
(gnt:geneticType rdfs:domain gnc:set)
(gnt:code a owl:ObjectProperty)
(gnt:code rdfs:domain gnc:set)
- ;; Already defined as an owl prop in dump-species
+ ;; Already defined as an owl prop in species
(gnt:family rdfs:domain gnc:set)
(gnt:phenotype a owl:ObjectProperty)
(gnt:phenotype rdfs:domain gnc:set)
@@ -189,7 +189,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
molecularTrait))
"||")))))
-(define-transformer dump-avg-method
+(define-transformer avg-method
;; The Name and Normalization fields seem to be the same. Dump only
;; the Name field.
(tables (AvgMethod))
@@ -201,7 +201,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
-(dump-with-documentation
+(with-documentation
(name "Species Metadata")
(connection %connection-settings)
(table-metadata? #f)
@@ -216,11 +216,11 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
(inputs
(list
- dump-inbred-set
- dump-species
- dump-strain
- dump-mapping-method
- dump-avg-method))
+ inbred-set
+ species
+ strain
+ mapping-method
+ avg-method))
(outputs
- '(#:documentation "./docs/dump-species-metadata.md"
- #:rdf "/export/data/genenetwork-virtuoso/dump-species-metadata.ttl")))
+ '(#:documentation "./docs/species-metadata.md"
+ #:rdf "/export/data/genenetwork-virtuoso/species-metadata.ttl")))
diff --git a/examples/dump-tissue.scm b/examples/tissue.scm
index 3658a26..8ce96c8 100755
--- a/examples/dump-tissue.scm
+++ b/examples/tissue.scm
@@ -18,7 +18,7 @@
-(define-transformer dump-tissue
+(define-transformer tissue
;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
;; and BIRN_lex_Name are mostly NULL.
(tables (Tissue))
@@ -32,7 +32,7 @@
-(dump-with-documentation
+(with-documentation
(name "Tissue Metadata")
(connection %connection-settings)
(table-metadata? #f)
@@ -44,7 +44,7 @@
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
(inputs
- (list dump-tissue))
+ (list tissue))
(outputs
- '(#:documentation "./docs/dump-tissue.md"
- #:rdf "./verified-data/dump-tissue.ttl")))
+ '(#:documentation "./docs/tissue.md"
+ #:rdf "./verified-data/tissue.ttl")))
generated by cgit v1.2.3 (git 2.25.4) at 2024-07-07 14:46:01 +0000