diff options
| -rwxr-xr-x | dump.scm | 54 |
1 files changed, 1 insertions, 53 deletions
diff --git a/dump.scm b/dump.scm index 3a827d8..412df2f 100755 --- a/dump.scm +++ b/dump.scm @@ -939,57 +939,6 @@ is a <table> object." )) -;; Import GeneRIF - -;; Download GeneRIF data from -;; https://ftp.ncbi.nih.gov/gene/GeneRIF/generifs_basic.gz -(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 (import-generif generif-data-file) - ;; 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)))) - - ;; Main function (call-with-genenetwork-database @@ -1020,6 +969,5 @@ is a <table> object." (dump-info-files db) (dump-schema db) (dump-groups db) - (dump-published-phenotypes db) - (import-generif (assq-ref %connection-settings 'generif-data-file)))))) + (dump-published-phenotypes db))))) |