1 files changed, 0 insertions, 74 deletions
diff --git a/import-generif.scm b/import-generif.scm
deleted file mode 100755
index 69a5f78..0000000
--- a/import-generif.scm
+++ /dev/null
@@ -1,74 +0,0 @@
-#! /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)))