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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-genewiki-symbols
(tables (GeneRIF_BASIC
(left-join Species "USING (SpeciesId)"))
"GROUP BY GeneId ORDER BY BINARY symbol")
(schema-triples
(gn:symbol rdfs:domain gn:geneWikiEntry)
(gn:wikiEntryOfSpecies rdfs:range gn:species)
(gn:taxid rdfs:domain gn:geneWikiEntry))
(triples (ontology 'generif: (field GeneRIF_BASIC GeneId))
(multiset gn:symbol (string-split (field ("GROUP_CONCAT(DISTINCT symbol)" symbol))
#\,))
(multiset gn:wikiEntryOfSpecies
(string-split
(field ("GROUP_CONCAT(DISTINCT Species.SpeciesName)" species))
#\,))
(multiset gn:taxId (map (cut ontology 'ncbiTaxon: <>)
(string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId))
#\,)))))
(define-dump dump-gn-genewiki-entries
(tables (GeneRIF
(left-join GeneRIF_BASIC "USING (symbol)")
(left-join Species "ON Species.SpeciesId = GeneRIF.SpeciesId")
(left-join GeneRIFXRef "ON GeneRIFXRef.GeneRIFId = GeneRIF.Id")
(left-join GeneCategory "ON GeneRIFXRef.GeneCategoryId = GeneCategory.Id"))
"WHERE GeneRIF.display > 0 AND GeneRIF.VersionId = 0 GROUP BY GeneRIF.symbol")
(schema-triples
(gn:geneWikiEntry a rdfs:Class)
(gn:geneWikiEntry a owl:Class)
(gn:geneWikiEntry rdfs:comment "Represents GeneRIF Entries")
(gn:geneCategory rdfs:domain gn:geneWikiEntry)
(gn:geneWikiEntryOfGn rdfs:domain gn:geneWikiEntry)
(gn:geneWikiEntry rdfs:domain gn:geneWikiEntry))
(triples
(let ([geneid (field GeneRIF_BASIC GeneId)])
(if (eq? geneid 0)
(ontology 'gn:anonSymbol_
(field GeneRIF symbol))
(ontology 'generif:
geneid)))
(set rdf:type
(if (string-null? (field ("IFNULL(GeneRIF_BASIC.GeneId, '')" geneWikiEntryP)))
""
'gn:geneWikiEntry))
(set gn:wikiEntryOfSpecies
(field Species SpeciesName))
;; This only dumps symbols not present in the GeneRIF_BASIC table
(set gn:symbol (let ([geneid (field GeneRIF_BASIC GeneId)])
(if (eq? geneid 0)
(field GeneRIF symbol)
"")))
(multiset gn:geneWikiEntryOfGn
(let* ([entries
(sanitize-rdf-string
(field
("GROUP_CONCAT(DISTINCT CONCAT_WS('::::', IFNULL(GeneCategory.Name, ''), IFNULL(GeneRIF.PubMed_ID, ''), GeneRIF.email, CAST(CONVERT(BINARY CONVERT(GeneRIF.comment USING latin1) USING utf8) AS VARCHAR(15000)), GeneRIF.createtime, IFNULL(weburl, '')) SEPARATOR';;;;;')"
wikientry)))]
[comments (string-split-substring entries ";;;;;")])
(map
(match-lambda
((genecategory pmid email text createtime weburl)
(blank-node
(set gn:geneCategory genecategory)
(multiset dct:source
(map (lambda (el) (if (string-null? el)
""
(ontology 'pubmed: el)))
(string-split pmid #\space)))
(set dct:creator (regexp-substitute/global #f "@.*$"
email
'pre
""
'post))
(set gn:geneWikiEntry
(annotate-field text '^^xsd:string))
(set dct:created (annotate-field
createtime
'^^xsd:datetime))
(set foaf:homepage weburl))))
(map
(cut string-split-substring <> "::::")
comments))))))
(define-dump dump-ncbi-genewiki-entries
(tables (GeneRIF_BASIC)
"GROUP BY GeneId, comment, createtime")
(schema-triples
(gn:geneWikiEntryofNCBI rdfs:domain gn:geneWikiEntry))
(triples (ontology 'generif:
(field GeneRIF_BASIC GeneId))
(set gn:geneWikiEntryOfNCBI
(blank-node
(set gn:geneWikiEntry
(annotate-field (field GeneRIF_BASIC comment)
'^^xsd:string))
(multiset dct:source (map (lambda (el) (if (string-null? el)
""
(ontology 'pubmed: el)))
(string-split (field ("GROUP_CONCAT(PubMed_ID)" pmids))
#\,)))
(set dct:created (annotate-field (time-unix->string
(field GeneRIF_BASIC createtime) "~5")
'^^xsd:datetime))))))
(call-with-target-database
%connection-settings
(lambda (db)
(with-output-to-file (string-append %dump-directory "dump-generif.ttl")
(lambda ()
(prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
(prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
(prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
(prefix "gn:" "<http://genenetwork.org/>")
(prefix "dct:" "<http://purl.org/dc/terms/>")
(prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
(prefix "up:" "<http://purl.uniprot.org/core/>")
(prefix "ncbiTaxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>")
(prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
(prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
(prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
(prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
(prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
(prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
(prefix "omim:" "<https://www.omim.org/entry/>")
(prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
(prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
(prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
(prefix "homologene:" "<https://bio2rdf.org/homologene:>")
(prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
(prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
(newline)
(dump-genewiki-symbols db)
(dump-gn-genewiki-entries db)
(dump-ncbi-genewiki-entries db))
#:encoding "utf8")))
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