aboutsummaryrefslogtreecommitdiff
path: root/examples/publication.scm
diff options
context:
space:
mode:
Diffstat (limited to 'examples/publication.scm')
-rwxr-xr-xexamples/publication.scm81
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identifier "unpublished"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")))