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-rwxr-xr-xexamples/genbank.scm80
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+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+ (srfi srfi-26)
+ (rnrs bytevectors)
+ (ice-9 getopt-long)
+ (ice-9 match)
+ (ice-9 regex)
+ (transform strings)
+ (transform sql)
+ (transform triples)
+ (transform special-forms)
+ (transform uuid))
+
+
+
+(define (remap-species-identifiers str)
+ "This procedure remaps identifiers to standard binominal. Obviously this should
+ be sorted by correcting the database!"
+ (match str
+ ["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"]
+ ["Oryzias latipes (Japanese medaka)" "Oryzias latipes"]
+ ["Macaca mulatta" "Macaca nemestrina"]
+ ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
+ [str str]))
+
+(define-transformer genbank
+ (tables (Genbank
+ (left-join Species "USING (SpeciesId)")))
+ (schema-triples
+ (gnc:nucleotide a skos:Concept)
+ (gnt:hasSequence rdfs:domain gnc:nucleotide))
+ (triples (ontology
+ 'genbank:
+ (field Genbank Id))
+ (set gnt:hasSequence (field Genbank Sequence))
+ (set xkos:classifiedUnder
+ (string->identifier "" (remap-species-identifiers (field Species Fullname))))))
+
+
+
+(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 "Genebank Metadata")
+ (connection %connection-settings)
+ (table-metadata? #f)
+ (prefixes
+ '(("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+ ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+ ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+ ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
+ ("gn:" "<http://genenetwork.org/id/>")
+ ("gnc:" "<http://genenetwork.org/category/>")
+ ("gnt:" "<http://genenetwork.org/term/>")
+ ("dct:" "<http://purl.org/dc/terms/>")
+ ("foaf:" "<http://xmlns.com/foaf/0.1/>")
+ ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+ ("ncbiTaxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>")
+ ("generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+ ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+ ("genbank:" "<https://bioregistry.io/reference/genbank:>")
+ ("owl:" "<http://www.w3.org/2002/07/owl#>")))
+ (inputs
+ (list
+ genbank))
+ (outputs
+ `(#:documentation ,documentation
+ #:rdf ,output))))