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authorMunyoki Kilyungi2023-05-26 08:35:54 +0300
committerBonfaceKilz2023-05-26 08:40:22 +0300
commit53c519c6d07992a0249e8f365f8b1a1af7a13886 (patch)
treefb44f29010e72d8832b38a8d485ca7017c144d6f
parent976831a5be7984f1a1a23e1c04693dbf5241ca07 (diff)
downloadgn-transform-databases-53c519c6d07992a0249e8f365f8b1a1af7a13886.tar.gz
Create a new probesetfreeze dump
This way, the probeset dump will become smaller. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
-rwxr-xr-xexamples/dump-probeset.scm39
-rwxr-xr-xexamples/dump-probesetfreeze.scm92
2 files changed, 92 insertions, 39 deletions
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm
index a71f708..8e809a5 100755
--- a/examples/dump-probeset.scm
+++ b/examples/dump-probeset.scm
@@ -20,14 +20,6 @@
(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")
@@ -144,35 +136,6 @@
(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 InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
- (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 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
- (schema-triples
- (gn:avgMethod rdfs:range rdfs:Literal)
- (gn:dataScale rdfs:range rdfs:Literal))
- (triples
- (ontology 'probeset:
- (regexp-substitute/global #f "[^A-Za-z0-9:]"
- (field ProbeSetFreeze Name)
- 'pre "_" 'post))
- (set rdf:type 'gn:probesetDataset)
- (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
@@ -203,7 +166,5 @@
(prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
(prefix "probeset:" "<http://genenetwork.org/probeset/>")
(newline)
- (dump-gene-chip db)
- (dump-probesetfreeze db)
(dump-probeset db))
#:encoding "utf8")))
diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm
new file mode 100755
index 0000000..b238851
--- /dev/null
+++ b/examples/dump-probesetfreeze.scm
@@ -0,0 +1,92 @@
+#! /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))))
+
+;; Molecular Traits are also referred to as ProbeSets
+(define-dump dump-probesetfreeze
+ (tables (ProbeSetFreeze
+ (left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
+ (left-join ProbeFreeze "USING (ProbeFreezeId)")
+ (left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
+ (left-join InbredSet "ON ProbeFreeze.InbredSetId = InbredSet.Id")
+ (left-join Tissue "ON ProbeFreeze.TissueId = Tissue.TissueId"))
+ "WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
+ (schema-triples
+ (gn:avgMethod rdfs:range rdfs:Literal)
+ (gn:dataScale rdfs:range rdfs:Literal))
+ (triples
+ (ontology 'probeset:
+ (regexp-substitute/global #f "[^A-Za-z0-9:]"
+ (field ProbeSetFreeze Name)
+ 'pre "_" 'post))
+ (set rdf:type 'gn:probesetDataset)
+ (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-probesetfreeze.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#>")
+ (prefix "probeset:" "<http://genenetwork.org/probeset/>")
+ (newline)
+ (dump-gene-chip db)
+ (dump-probesetfreeze db))
+ #:encoding "utf8")))