diff options
Diffstat (limited to 'transform/triples.scm')
| -rw-r--r-- | transform/triples.scm | 24 |
1 files changed, 18 insertions, 6 deletions
diff --git a/transform/triples.scm b/transform/triples.scm index 9775d36..13758e5 100644 --- a/transform/triples.scm +++ b/transform/triples.scm @@ -8,8 +8,19 @@ triple scm->triples annotate-field + remap-species-identifiers string->binomial-name)) +(define (remap-species-identifiers str) + "This procedure remaps identifiers to standard binominal. Obviously this should + be sorted by correcting the database!" + (match str + ["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"] + ["Oryzias latipes (Japanese medaka)" "Oryzias latipes"] + ["Macaca mulatta" "Macaca nemestrina"] + ["Bat (Glossophaga soricina)" "Glossophaga soricina"] + [str str])) + (define (annotate-field field schema) (let ([schema (cond ((symbol? schema) (symbol->string schema)) @@ -28,7 +39,7 @@ #:optional #:key (ontology "gn:") (separator "") - (proc string-capitalize-first)) + (proc (lambda (x) x))) "Convert STR to a turtle identifier after replacing illegal characters with an underscore and prefixing with gn:PREFIX." (if (or (and (string? str) (string-null? str)) @@ -40,11 +51,12 @@ characters with an underscore and prefixing with gn:PREFIX." (lambda (c) (eq? c #\))) (string-map (lambda (c) - (case c - ((#\/ #\< #\> #\+ #\( #\space #\@) #\_) - (else c))) - (proc - (string-trim-right str #\.)))))))) + (if (or (char-alphabetic? c) + (char-numeric? c) + (char=? c #\_)) + c + #\_)) + (proc str))))))) (define* (prefix prefix iri #:optional (ttl? #t)) |