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| -rwxr-xr-x | examples/genbank.scm | 80 |
1 files changed, 80 insertions, 0 deletions
diff --git a/examples/genbank.scm b/examples/genbank.scm new file mode 100755 index 0000000..65eed0c --- /dev/null +++ b/examples/genbank.scm @@ -0,0 +1,80 @@ +#! /usr/bin/env guile +!# + +(use-modules (srfi srfi-1) + (srfi srfi-26) + (rnrs bytevectors) + (ice-9 getopt-long) + (ice-9 match) + (ice-9 regex) + (transform strings) + (transform sql) + (transform triples) + (transform special-forms) + (transform uuid)) + + + +(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-transformer genbank + (tables (Genbank + (left-join Species "USING (SpeciesId)"))) + (schema-triples + (gnc:nucleotide a skos:Concept) + (gnt:hasSequence rdfs:domain gnc:nucleotide)) + (triples (ontology + 'genbank: + (field Genbank Id)) + (set gnt:hasSequence (field Genbank Sequence)) + (set xkos:classifiedUnder + (string->identifier "" (remap-species-identifiers (field Species Fullname)))))) + + + +(let* ((option-spec + '((settings (single-char #\s) (value #t)) + (output (single-char #\o) (value #t)) + (documentation (single-char #\d) (value #t)))) + (options (getopt-long (command-line) option-spec)) + (settings (option-ref options 'settings #f)) + (output (option-ref options 'output #f)) + (documentation (option-ref options 'documentation #f)) + (%connection-settings + (call-with-input-file settings + read))) + + (with-documentation + (name "Genebank Metadata") + (connection %connection-settings) + (table-metadata? #f) + (prefixes + '(("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + ("skos:" "<http://www.w3.org/2004/02/skos/core#>") + ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>") + ("gn:" "<http://genenetwork.org/id/>") + ("gnc:" "<http://genenetwork.org/category/>") + ("gnt:" "<http://genenetwork.org/term/>") + ("dct:" "<http://purl.org/dc/terms/>") + ("foaf:" "<http://xmlns.com/foaf/0.1/>") + ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") + ("ncbiTaxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>") + ("generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") + ("xsd:" "<http://www.w3.org/2001/XMLSchema#>") + ("genbank:" "<https://bioregistry.io/reference/genbank:>") + ("owl:" "<http://www.w3.org/2002/07/owl#>"))) + (inputs + (list + genbank)) + (outputs + `(#:documentation ,documentation + #:rdf ,output)))) |