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-rwxr-xr-xexamples/dump-probeset.scm171
1 files changed, 149 insertions, 22 deletions
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm
index 4d5f9a5..a9b6c7c 100755
--- a/examples/dump-probeset.scm
+++ b/examples/dump-probeset.scm
@@ -21,29 +21,144 @@
(tables (ProbeSet
(left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")))
(schema-triples
- (gnt:name rdfs:range rdfs:Literal)
- (gnt:probeset rdfs:range rdfs:Literal))
- (triples (ontology
- 'probeset:
- (string-trim-both
+ (gnc:probeset a skos:Concept)
+ (gnc:probeset
+ skos:description
+ "This is a set of controlled terms that are used to describe a given probeset")
+ (gnt:hasChip a owl:ObjectProperty)
+ (gnt:hasChip rdfs:domain gnc:probeset)
+ (gnt:hasTargetId a owl:ObjectProperty)
+ (gnt:hasTargetId rdfs:domain gnc:probeset)
+ (gnt:symbol rdfs:domain gnc:probeset)
+ (gnt:targetsRegion a owl:ObjectProperty)
+ (gnt:targetsRegion rdfs:domain gnc:probeset)
+ (gnt:chr rdfs:domain gnc:probeset)
+ (gnt:mb rdfs:domain gnc:probeset)
+ (gnt:mbMm8 rdfs:domain gnc:probeset)
+ (gnt:mb2016 rdfs:domain gnc:probeset)
+ (gnt:hasSpecificity a owl:ObjectProperty)
+ (gnt:hasSpecificity rdfs:domain gnc:probeset)
+ (gnt:hasBlatScore a owl:ObjectProperty)
+ (gnt:hasBlatScore rdfs:domain gnc:probeset)
+ (gnt:hasBlatMbStart a owl:ObjectProperty)
+ (gnt:hasBlatMbStart rdfs:domain gnc:probeset)
+ (gnt:hasBlatMbStart2016 a owl:ObjectProperty)
+ (gnt:hasBlatMbStart2016 rdfs:domain gnc:probeset)
+ (gnt:hasBlatMbEnd a owl:ObjectProperty)
+ (gnt:hasBlatMbEnd rdfs:domain gnc:probeset)
+ (gnt:hasBlatMbEnd2016 a owl:ObjectProperty)
+ (gnt:hasBlatMbEnd2016 rdfs:domain gnc:probeset)
+ (gnt:hasBlatSeq a owl:ObjectProperty)
+ (gnt:hasBlatSeq rdfs:domain gnc:probeset)
+ (gnt:hasTargetSeq a owl:ObjectProperty)
+ (gnt:hasTargetSeq rdfs:domain gnc:probeset)
+ (gnt:hasHomologeneId a owl:ObjectProperty)
+ (gnt:hasHomologeneId rdfs:domain gnc:probeset)
+ (gnt:hasPubChemId a owl:ObjectProperty)
+ (gnt:hasPubChemId rdfs:domain gnc:probeset)
+ (gnt:hasKeggId a owl:ObjectProperty)
+ (gnt:hasKeggId rdfs:domain gnc:probeset)
+ (gnt:hasOmimId a owl:ObjectProperty)
+ (gnt:hasOmimId rdfs:domain gnc:probeset)
+ (gnt:hasChebiId a owl:ObjectProperty)
+ (gnt:hasChebiId rdfs:domain gnc:probeset))
+ (triples
+ (let ((id (field ("IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name))"
+ ProbeSetIdName)))
+ (probeset-id (field ProbeSet Id)))
+ (if (string-null? id)
+ (string->identifier
+ "probeset"
+ (number->string
+ probeset-id))
+ (string->identifier
+ ""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
- (field ("IFNULL(NULLIF(TRIM(ProbeSet.Name), ''), ProbeSet.Id)"
- name))
- 'pre "_" 'post)))
- (set rdf:type 'gn-id:probeset)
- (set gnt:chipOf (string->identifier "platform" (field GeneChip Name)))
- (set gnt:name (field ProbeSet Name))
- (set gnt:symbol (delete-substrings (field ProbeSet Symbol) "\""))
- (set gnt:description (sanitize-rdf-string
- (field ProbeSet description)))
+ id
+ 'pre "_" 'post)
+ #:separator ""
+ #:proc string-capitalize-first)))
+ (set rdf:type 'gnc:probeset)
+ (set rdfs:label (field ProbeSet Name))
+ (set skos:altLabel
+ (replace-substrings
+ (field ProbeSet alias)
+ '(("\r\n" . "; "))))
+ (set gnt:hasChip
+ (string->identifier
+ "platform"
+ (field ("IFNULL(GeneChip.Name, '')" GeneChipName))))
+ (set gnt:hasTargetId
+ (field ("NULLIF(TRIM(ProbeSet.TargetId), '')"
+ TargetId)))
+ (set gnt:symbol (field ProbeSet Symbol))
+ (set dct:description (sanitize-rdf-string (field ProbeSet description)))
+ (set gnt:targetsRegion
+ (sanitize-rdf-string
+ (field ("NULLIF(TRIM(ProbeSet.Probe_set_target_region), '')"
+ Probe_set_target_region))))
(set gnt:chr (field ProbeSet Chr))
(set gnt:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
- (set gnt:blatSeq (sanitize-rdf-string
- (string-trim-both (field ProbeSet BlatSeq))))
- (set gnt:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq)))
- (set gnt:uniProtReference (ontology 'uniprot:
- (field ProbeSet UniProtID)))))
+ (set gnt:mbMm8 (annotate-field (field ("IFNULL(ProbeSet.Mb_mm8, '')" Mb_mm8))
+ '^^xsd:double))
+ (set gnt:mb2016
+ (annotate-field (field ("IFNULL(ProbeSet.Mb_2016, '')" Mb_2016))
+ '^^xsd:double))
+ (set gnt:hasSpecificity
+ (annotate-field (field ("IFNULL(ProbeSet.Probe_set_specificity, '')"
+ Probe_set_specificity))
+ '^^xsd:double))
+ (set gnt:hasBlatScore
+ (annotate-field (field ("IFNULL(ProbeSet.Probe_set_BLAT_score, '')"
+ Probe_set_BLAT_score))
+ '^^xsd:double))
+ (set gnt:hasBlatMbStart
+ (annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '')"
+ Probe_set_Blat_Mb_start))
+ '^^xsd:double))
+ (set gnt:hasBlatMbStart2016
+ (annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '')"
+ Probe_set_Blat_Mb_start_2016))
+ '^^xsd:double))
+ (set gnt:hasBlatMbEnd
+ (annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '')"
+ Probe_set_Blat_Mb_end))
+ '^^xsd:double))
+ (set gnt:hasBlatMbEnd2016
+ (annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '')"
+ Probe_set_Blat_Mb_start_2016))
+ '^^xsd:double))
+ (set gnt:hasBlatSeq (sanitize-rdf-string (field ProbeSet BlatSeq)))
+ (set gnt:hasTargetSeq (sanitize-rdf-string (field ProbeSet TargetSeq)))
+ (set gnt:hasHomologeneId (ontology 'homologene:
+ (field ("IFNULL(ProbeSet.HomoloGeneID, '')"
+ HomoloGeneID))))
+ (set gnt:hasUniprotId (ontology 'uniprot:
+ (field ("IFNULL(ProbeSet.UniProtID, '')"
+ UniProtID))))
+ (set gnt:hasPubChemId (ontology
+ 'pubchem:
+ (field ("IFNULL(ProbeSet.PubChem_ID, '')"
+ PubChem_ID))))
+ (set gnt:hasKeggId (ontology
+ 'kegg:
+ (field ("IFNULL(ProbeSet.KEGG_ID, '')"
+ KEGG_ID))))
+ (set gnt:hasOmimId (ontology
+ 'omim:
+ (let ((omim (field ("IFNULL(ProbeSet.OMIM, '')"
+ OMIM))))
+ (if (number? omim)
+ omim
+ (regexp-substitute/global
+ #f "[^0-9]"
+ omim
+ 'pre "" 'post)))))
+ (set gnt:hasChebiId (ontology
+ 'chebi:
+ (field ("IFNULL(ProbeSet.ChEBI_ID, '')"
+ ChEBI_ID))))))
@@ -53,10 +168,22 @@
(connection %connection-settings)
(table-metadata? #f)
(prefixes
- '(("probeset:" "<http://genenetwork.org/probeset/>")
+ '(("gn:" "<http://genenetwork.org/id/>")
+ ("probeset:" "<http://genenetwork.org/probeset/>")
+ ("gnc:" "<http://genenetwork.org/category/>")
+ ("gnt:" "<http://genenetwork.org/term/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
- ("rdfs:" "<http://www.w3.org/2000/01/rdf-r")
- ("uniprot:" "<http://purl.uniprot.org/uniprot/>")))
+ ("kegg:" "<http://bio2rdf.org/ns/kegg#>")
+ ("pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+ ("omim:" "<https://www.omim.org/entry/>")
+ ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+ ("uniprot:" "<http://purl.uniprot.org/uniprot/>")
+ ("chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+ ("dct:" "<http://purl.org/dc/terms/>")
+ ("owl:" "<http://www.w3.org/2002/07/owl#>")
+ ("homologene:" "<https://bio2rdf.org/homologene:>")
+ ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+ ("skos:" "<http://www.w3.org/2004/02/skos/core#>")))
(inputs
(list dump-probeset))
(outputs