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#! /usr/bin/env guile
!#
;; This script imports GeneRIF data downloaded from
;; https://ftp.ncbi.nih.gov/gene/GeneRIF/generifs_basic.gz into RDF.
(use-modules (rnrs io ports)
(srfi srfi-26)
(srfi srfi-171)
(ice-9 match)
(ice-9 regex)
(dump triples)
(dump utils)
(zlib))
(define decode-html-entities
(cut regexp-substitute/global
#f
;; We tolerate the absence of the trailing semicolon.
"&#([[:digit:]]+);{0,1}"
<>
'pre
(compose string integer->char string->number (cut match:substring <> 1))
'post))
(define (main generif-data-file dump-directory)
(with-output-to-file (string-append dump-directory "/generif.ttl")
(lambda ()
(prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
(prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
(prefix "gn:" "<http://genenetwork.org/>")
(newline)
;; TODO: Link to gene objects, not merely literal Gene IDs.
(triple 'gn:geneId 'rdfs:domain 'gn:geneRIF)
(triple 'gn:geneId 'rdfs:range 'rdfs:Literal)
;; TODO: Link to gn:publication objects, not merely literal
;; PubMed IDs.
(triple 'gn:geneRIFEvidencedByPubMedId 'rdfs:domain 'gn:geneRIF)
(triple 'gn:geneRIFEvidencedByPubMedId 'rdfs:range 'rdfs:Literal)
(triple 'gn:geneRIFText 'rdfs:domain 'gn:geneRIF)
(triple 'gn:geneRIFText 'rdfs:range 'rdfs:Literal)
(call-with-gzip-input-port (open-input-file generif-data-file)
(lambda (port)
;; Read and discard header.
(get-line port)
;; Dump other lines.
(port-transduce
(compose (tenumerate)
(tmap (match-lambda
;; Is there a better way to identify
;; GeneRIF entries instead of merely
;; enumerating them?
((i . line)
(match (string-split line #\tab)
((_ gene-id pubmed-id _ text)
(scm->triples
`((rdf:type . gn:geneRIF)
(gn:geneId . ,(string->number gene-id))
(gn:pubMedId . ,(string->number pubmed-id))
;; Some text has HTML
;; entities. Decode them.
(gn:geneRIFText . ,(decode-html-entities text)))
(string->identifier "geneRIF" (number->string i)))))))))
(const #t)
get-line
port))))))
(match (command-line)
((arg0 generif-data-file dump-directory)
(main generif-data-file dump-directory))
((arg0 _ ...)
(format (current-error-port) "Usage: ~a GENERIF-DATA-FILE DUMP-DIRECTORY~%" arg0)
(exit #f)))
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