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#! /usr/bin/env guile
!#
(use-modules (srfi srfi-1)
(srfi srfi-26)
(ice-9 getopt-long)
(ice-9 match)
(ice-9 regex)
(transform strings)
(transform sql)
(transform triples)
(transform special-forms))
(define-transformer gn:platform->metadata
(tables (GeneChip
(left-join Species "USING (SpeciesId)")))
(schema-triples
(gnc:gene_chip a skos:ConceptScheme)
(gnc:gene_chip skos:prefLabel "Gene Chip Vocabulary")
(gnc:gene_chip skos:definition "A controlled vocabulary used to describe gene chip and microarray platforms.")
(gnt:has_geo_series_id rdf:type owl:ObjectProperty)
(gnt:has_geo_series_id rdf:label "has GEO Series ID")
(gnt:has_geo_series_id rdfs:domain skos:Concept)
(gnt:has_go_tree_value a owl:ObjectProperty)
(gnt:has_go_tree_value rdfs:label "has GO tree value")
(gnt:has_go_tree_value
rdfs:comment
"Associates a gene chip concept with a Gene Ontology term used for categorization.")
(gnt:has_go_tree_value rdfs:domain skos:Concept)
(gnt:has_go_tree_value rdfs:range xsd:string))
(triples (string->identifier "platform" (field GeneChip Name) #:separator "_")
(set rdf:type 'skos:Concept)
(set skos:inScheme (field GeneChip GeneChipName))
(set skos:prefLabel (field GeneChip Name))
(set skos:altLabel (field ("IF(GeneChip.GeneChipName != GeneChip.Title, Title, NULL)"
Title)))
(set gnt:has_go_tree_value (field GeneChip Go_tree_value))
(set gnt:has_species
(string->identifier "" (remap-species-identifiers (field Species Fullname))))
(set gnt:has_geo_series_id
(ontology 'geoSeries:
(string-trim-both (field GeneChip GeoPlatform))))))
(let* ((option-spec
'((settings (single-char #\s) (value #t))
(output (single-char #\o) (value #t))
(documentation (single-char #\d) (value #t))))
(options (getopt-long (command-line) option-spec))
(settings (option-ref options 'settings #f))
(output (option-ref options 'output #f))
(documentation (option-ref options 'documentation #f))
(%connection-settings
(call-with-input-file settings
read)))
(with-documentation
(name "GeneChip Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
("gn:" "<http://rdf.genenetwork.org/v1/id/>")
("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
(inputs
(list gene-chip))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
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