diff options
Diffstat (limited to 'examples/genelist.scm')
| -rwxr-xr-x | examples/genelist.scm | 36 |
1 files changed, 14 insertions, 22 deletions
diff --git a/examples/genelist.scm b/examples/genelist.scm index 18fd30b..dbca921 100755 --- a/examples/genelist.scm +++ b/examples/genelist.scm @@ -77,12 +77,9 @@ (gnt:has_target_seq rdfs:domain gnc:probeset)) (triples (string->identifier - "gene" (regexp-substitute/global - #f "[^A-Za-z0-9:]" - (string-trim-both - (field ("CONCAT_WS('_', GeneSymbol, GeneID, AlignID)" GENE_UID))) - 'pre "_" 'post) - #:proc (lambda (x) x)) + "gene" (normalize-string-field (string-trim-both + (field ("CONCAT_WS('_', GeneSymbol, GeneID, AlignID)" GENE_UID)))) + #:separator "_") (set rdf:type 'gnc:gene) (set gnt:gene_symbol (field GeneList GeneSymbol)) (set dct:description (sanitize-rdf-string (field GeneList GeneDescription))) @@ -225,20 +222,14 @@ ""))) (set gnt:chromosome (field GeneList Chromosome)) (set gnt:tx_start (annotate-field - (field GeneList tx_start) + (field GeneList TxStart) '^^xsd:double)) (set gnt:tx_end (annotate-field - (field GeneList tx_end) + (field GeneList TxEnd) '^^xsd:double)) (set gnt:strand (string-trim-both (field GeneList Strand))) (set - gnt:belongs_to_species - (string->identifier - "" - (remap-species-identifiers - (string-trim-both (field Species Name))) - #:separator "" - #:proc string-capitalize-first)) + gnt:belongs_to_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))) (set gnt:transcript (ontology 'transcript: @@ -259,10 +250,11 @@ (if (number? gene-uid) (number->string gene-uid) - gene-uid))) + gene-uid) + #:separator "_")) (set rdf:type 'gnc:gene) (set gnt:belongs_to_species 'gn:Rattus_norvegicus) - (set gnt:gene_symbol (string-trim-both (field GeneList_rn33 gene_symbol))) + (set gnt:gene_symbol (string-trim-both (field GeneList_rn33 geneSymbol))) (set gnt:chromosome (field GeneList_rn33 chromosome)) (set gnt:tx_start (annotate-field (field GeneList_rn33 txStart) @@ -280,7 +272,7 @@ gnc:has_kg_id (string-trim-both (field GeneList_rn33 kgID))) (set dct:references - (let ((symbol (field GeneList_rn33 gene_symbol))) + (let ((symbol (field GeneList_rn33 geneSymbol))) (if (not (string-blank? symbol)) (string->symbol (format #f @@ -290,7 +282,7 @@ "a gnc:PantherLink")) ""))) (set dct:references - (let ((symbol (string-trim-both (field GeneList_rn33 gene_symbol)))) + (let ((symbol (string-trim-both (field GeneList_rn33 geneSymbol)))) (if (not (string-blank? symbol)) (string->symbol (format #f @@ -300,7 +292,7 @@ "a gnc:ebi_gwas_link")) ""))) (set dct:references - (let ((symbol (string-trim-both (field GeneList_rn33 gene_symbol)))) + (let ((symbol (string-trim-both (field GeneList_rn33 geneSymbol)))) (if (not (string-blank? symbol)) (string->symbol (format #f @@ -311,7 +303,7 @@ "a gnc:panther_link")) ""))) (set dct:references - (let ((symbol (string-trim-both (field GeneList_rn33 gene_symbol)))) + (let ((symbol (string-trim-both (field GeneList_rn33 geneSymbol)))) (if (not (string-blank? symbol)) (string->symbol (format #f @@ -322,7 +314,7 @@ "a gnc:gtex_link")) ""))) (set dct:references - (let ((symbol (string-trim-both (field GeneList_rn33 gene_symbol)))) + (let ((symbol (string-trim-both (field GeneList_rn33 geneSymbol)))) (if (not (string-blank? symbol)) (string->symbol (format #f |