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