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#! /usr/bin/env guile
!#
(use-modules (srfi srfi-1)
(srfi srfi-26)
(ice-9 match)
(ice-9 regex)
(transform strings)
(transform sql)
(transform triples)
(transform special-forms))
(define %connection-settings
(call-with-input-file (list-ref (command-line) 1)
read))
(define-transformer tissue
;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
;; and BIRN_lex_Name are mostly NULL.
(tables (Tissue))
(schema-triples
(gnc:tissue a skos:Concept))
;; Hopefully the Short_Name field is distinct and can be used as an
;; identifier.
(triples (string->identifier "tissue" (field Tissue Short_Name))
(set rdf:type 'gnc:tissue)
(set rdfs:label (field Tissue Name))))
(with-documentation
(name "Tissue Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("gn:" "<http://genenetwork.org/id/>")
("gnt:" "<http://genenetwork.org/terms/>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("gnc:" "<http://genenetwork.org/category/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
(inputs
(list tissue))
(outputs
'(#:documentation "./docs/tissue.md"
#:rdf "./verified-data/tissue.ttl")))
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