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#! /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 %dump-directory
(list-ref (command-line) 2))
(define-dump dump-publication
(tables (Publication))
(schema-triples
(gn:pubMedId rdfs:range rdfs:Literal)
(gn:title rdfs:range rdfs:Literal)
(gn:journal rdfs:range rdfs:Literal)
(gn:volume rdfs:range rdfs:Literal)
(gn:pages rdfs:range rdfs:Literal)
(gn:month rdfs:range rdfs:Literal)
(gn:year rdfs:range rdfs:Literal)
(gn:author rdfs:range rdfs:Literal)
(gn:abstract rdfs:range rdfs:Literal))
(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identifier "unpublished"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 'publication: pmid)))
(set rdf:type 'gn:publication)
(set gn:pubMedId (ontology 'pubmed: (field ("IFNULL(PubMed_ID, '')" pubmedId))))
(set gn:title (delete-substrings (field Publication Title)
"Unknown"))
(set gn:journal (delete-substrings (field Publication Journal)
"Unknown"))
(set gn:volume (delete-substrings (field Publication Volume)
"Unknown"))
(set gn:pages (delete-substrings (field Publication Pages)
"Unknown"))
(set gn:month (delete-substrings (field Publication Month)
"Unknown"))
(set gn:year (field Publication Year))
(multiset gn:author
;; The authors field is a comma
;; separated list. Split it.
(map string-trim (string-split (sanitize-rdf-string (field Publication Authors)) #\,)))
(set gn:abstract
(sanitize-rdf-string
(field ("CAST(CONVERT(BINARY CONVERT(Publication.Abstract USING latin1) USING utf8) AS VARCHAR(100))" Abstract))))))
(call-with-target-database
%connection-settings
(lambda (db)
(with-output-to-file (string-append %dump-directory "dump-publication.ttl")
(lambda ()
(prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
(prefix "dct:" "<http://purl.org/dc/terms/>")
(prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
(prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
(prefix "gn:" "<http://genenetwork.org/>")
(prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
(prefix "homologene:" "<https://bio2rdf.org/homologene:>")
(prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
(prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
(prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
(prefix "omim:" "<https://www.omim.org/entry/>")
(prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
(prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
(prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
(prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
(prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
(prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
(prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
(prefix "up:" "<http://purl.uniprot.org/core/>")
(prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
(prefix "publication:" "<http://genenetwork.org/publication/>")
(newline)
(dump-publication db))
#:encoding "utf8")))
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