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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))
(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 gnt:belongsToSpecies
(string->identifier "" (remap-species-identifiers (field Species Fullname))
#:separator ""
#:proc string-capitalize-first))))
(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))))
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