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Diffstat (limited to 'examples/publication.scm')
-rwxr-xr-x | examples/publication.scm | 81 |
1 files changed, 81 insertions, 0 deletions
diff --git a/examples/publication.scm b/examples/publication.scm new file mode 100755 index 0000000..313ee96 --- /dev/null +++ b/examples/publication.scm @@ -0,0 +1,81 @@ +#! /usr/bin/env guile +!# + +(use-modules (srfi srfi-1) + (srfi srfi-26) + (ice-9 match) + (ice-9 regex) + (dump strings) + (dump sql) + (dump triples) + (dump special-forms)) + + + +(define %connection-settings + (call-with-input-file (list-ref (command-line) 1) + read)) + + + +(define-transformer publication + (tables (Publication)) + (triples + (let ((pmid (field + ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))" + pmid))) + (publication-id (field Publication Id))) + (if (string-null? pmid) + (string->identifier "unpublished" + (number->string publication-id)) + (ontology 'pubmed: pmid))) + (set rdf:type 'fabio:ResearchPaper) + (set fabio:hasPubMedId + (ontology 'pubmed: (field ("IFNULL(PubMed_ID, '')" pubmedId)))) + (set dct:title (delete-substrings (field Publication Title) + "Unknown")) + (set fabio:Journal (delete-substrings (field Publication Journal) + "Unknown")) + (set prism:volume (delete-substrings (field Publication Volume) + "Unknown")) + (set fabio:page (delete-substrings (field Publication Pages) + "Unknown")) + (set prism:publicationDate (annotate-field + (delete-substrings (field Publication Month) + "Unknown") + '^^xsd:gMonth)) + (set fabio:hasPublicationYear + (annotate-field + (field + ("IF(Publication.Year = 0, NULL, Publication.Year)" Year)) + '^^xsd:gYear)) + (multiset dct:creator + ;; The authors field is a comma + ;; separated list. Split it. + (map string-trim (string-split (sanitize-rdf-string (field Publication Authors)) #\,))) + (set dct:abstract + (sanitize-rdf-string + (field Publication Abstract))))) + + + +(with-documentation + (name "Publications Metadata") + (connection %connection-settings) + (table-metadata? #f) + (prefixes + '(("gnt:" "<http://genenetwork.org/terms/>") + ("fabio:" "<http://purl.org/spar/fabio/>") + ("dct:" "<http://purl.org/dc/terms/>") + ("prism:" "<http://prismstandard.org/namespaces/basic/2.0/>") + ("gn:" "<http://genenetwork.org/id/>") + ("gnc:" "<http://genenetwork.org/category/>") + ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") + ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + ("xsd:" "<http://www.w3.org/2001/XMLSchema#>") + ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>"))) + (inputs + (list publication)) + (outputs + '(#:documentation "./docs/publication.md" + #:rdf "./verified-data/publication.ttl"))) |