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#! /usr/bin/env guile
!#
(use-modules (srfi srfi-1)
(srfi srfi-26)
(rnrs bytevectors)
(ice-9 format)
(ice-9 getopt-long)
(ice-9 match)
(ice-9 regex)
(transform strings)
(transform sql)
(transform triples)
(transform special-forms)
(transform uuid))
(define-transformer genewiki-symbols
(tables (GeneRIF_BASIC)
"GROUP BY BINARY symbol")
(triples
(string->identifier
"symbol"
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field GeneRIF_BASIC symbol)
'pre "_" 'post)
#:proc (lambda (x) x))
(set rdfs:label
(field GeneRIF_BASIC symbol))))
;; Some symbols exist in the RIF table that don't exist in the GeneRIF
;; table.
(define-transformer generif-symbols
(tables (GeneRIF)
"WHERE symbol NOT IN (SELECT symbol from GeneRIF_BASIC) GROUP BY BINARY symbol")
(triples
(string->identifier
"symbol"
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field GeneRIF symbol)
'pre "_" 'post)
#:proc (lambda (x) x))
(set rdfs:label
(field GeneRIF symbol))))
(define-transformer gn-genewiki-entries
(tables (GeneRIF
(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.comment IS NOT NULL
GROUP BY GeneRIF.Id, GeneRIF.versionId, GeneRIF.symbol")
(schema-triples
(gnc:GeneWikiEntry a rdfs:Class)
(gnc:GNWikiEntry rdfs:subClassOf gnc:GeneWikiEntry)
(gnt:initial a owl:ObjectProperty)
(gnt:initial rdfs:domain gnc:GeneWikiEntry)
(gnt:initial skos:definition "Optional user or project code or your initials")
(gnt:reason a owl:ObjectProperty)
(gnt:reason rdfs:domain gnc:GeneWikiEntry)
(gnt:reason skos:definition "The reason why this resource was modified")
(gnc:GNWikiEntry rdfs:comment "Represents GeneRIF Entries entered from GeneNetwork")
(gnt:geneSymbol rdfs:domain gnc:GNWikiEntry))
;; We want to avoid manually generating a unique identifier for each
;; comment. As such we use a blank node (that has the comment) as
;; the subject of the triples produced by matching the
;; predicateObjectList production:
;; <https://www.w3.org/TR/turtle/#grammar-production-predicateObjectList>
(triples
(format #f "[ rdfs:label '''~a'''@en] "
(field GeneRIF comment))
(set rdf:type
(let* ((create-time (field
("CAST(createtime AS CHAR)" EntryCreateTime)))
(pmid (field GeneRIF PubMed_ID PMID))
(web-url (field GeneRIF weburl))
(species (string->identifier
""
(remap-species-identifiers (field Species Fullname))
#:separator ""
#:proc string-capitalize-first))
(version-id (field GeneRIF versionId))
(identifier (field GeneRIF Id))
(initial (sanitize-rdf-string (field GeneRIF initial)))
(reason (field GeneRIF reason))
(email (sanitize-rdf-string (field GeneRIF email)))
(category
(field ("GROUP_CONCAT(DISTINCT GeneCategory.Name SEPARATOR ';')"
GeneCategory))))
(string->symbol
(string-append
(format #f "gnc:GNWikiEntry ;\n")
(if (string? species)
""
(format #f "\tgnt:belongsToSpecies ~a ;\n"
species))
(format #f "\tdct:created ~s^^xsd:datetime ;\n"
create-time)
(if (and (string? pmid) (not (string-null? pmid)))
(format #f
"\tdct:references ( ~{pubmed:~a ~}) ;\n"
(string-split pmid #\space))
"\tdct:references rdf:nil ;\n")
(if (string-blank? email)
""
(format #f "\tfoaf:mbox <~a> ;\n" email))
(format #f "\tdct:identifier \"~s\"^^xsd:integer ;\n" identifier)
(if (and (string? web-url) (not (string-null? web-url)))
(format #f "\tfoaf:homepage <~a> ;\n"
web-url)
"")
(format #f "\tdct:hasVersion \"~s\"^^xsd:integer ;\n" version-id)
(if (or (null? initial)
(string-blank? initial))
"" (format #f "\tgnt:initial ~s ;\n" initial))
(if (string-blank? reason)
""
(format #f "\tgnt:reason ~s ;\n" reason))
(if (string-blank? category)
"\tgnt:belongsToCategory rdf:nil ;\n"
(format #f
"\tgnt:belongsToCategory ( ~{~s ~}) ;\n"
(string-split category #\;)))
;; We have this symbol at the very end of this transform
;; because we have a strong guarantee that it will be a
;; non-null value hence always terminating this triple
;; properly with a "."
(format
#f "\tgnt:symbol ~a"
(string->identifier
"symbol"
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field GeneRIF symbol)
'pre "_" 'post)
#:proc (lambda (x) x)))))))))
(define-transformer ncbi-genewiki-entries
(tables (GeneRIF_BASIC
(left-join Species "USING (SpeciesId)"))
"WHERE GeneRIF_BASIC.comment IS NOT NULL AND TRIM(GeneRIF_BASIC.comment) != '' AND TRIM(GeneRIF_BASIC.symbol) != '' GROUP BY GeneRIF_BASIC.comment, GeneRIF_BASIC.createtime, GeneRIF_BASIC.VersionId, GeneRIF_BASIC.SpeciesId, GeneRIF_BASIC.TaxID")
(schema-triples
(gnc:NCBIWikiEntry rdfs:subClassOf gnc:GeneWikiEntry)
(gnc:NCBIWikiEntry rdfs:comment "Represents GeneRIF Entries obtained from NCBI")
(gnt:hasVersionId a owl:ObjectProperty)
(gnt:hasVersionId rdfs:domain gnc:NCBIWikiEntry)
(gnt:hasVersionId skos:definition "The VersionId of this this resource"))
(triples
(string->identifier
"symbol"
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field GeneRIF_BASIC symbol GeneRIFSymbol)
'pre "_" 'post)
#:proc (lambda (x) x))
(set rdfs:comment
(let ([ncbi-comment (sanitize-rdf-string (field GeneRIF_BASIC comment))]
[species-name
(string->identifier
""
(remap-species-identifiers (field Species Fullname SpeciesFullName))
#:separator ""
#:proc string-capitalize-first)]
[taxonomic-id (field GeneRIF_BASIC TaxID TaxonomicId)]
[create-time (field GeneRIF_BASIC createtime EntryCreateTime)]
[pmid (field GeneRIF_BASIC PubMed_ID PMID)]
[gene-id (field GeneRIF_BASIC GeneId)]
[version-id (field GeneRIF_BASIC VersionId)])
(string->symbol
(string-append
"[ "
(format #f "rdf:type gnc:NCBIWikiEntry ; ")
(format #f "rdfs:comment ~s^^xsd:string ; "
ncbi-comment)
(format #f "gnt:belongsToSpecies ~a ; "
species-name)
(if (eq? #f taxonomic-id)
""
(format #f "skos:notation taxon:~a ; "
taxonomic-id))
(format #f "gnt:hasGeneId generif:~a ; "
gene-id)
(format #f "dct:hasVersion '~a'^^xsd:int ; "
version-id)
(if (and (string? pmid) (not (string-null? pmid)))
(format #f
"~{dct:references pubmed:~a ; ~}"
(string-split pmid #\space))
"")
(if (string? create-time)
""
(format #f "dct:created ~s^^xsd:datetime ; "
(time-unix->string
create-time "~5")))
" ]"))))))
(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 "GeneRIF 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/>")
("taxon:" "<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#>")
("owl:" "<http://www.w3.org/2002/07/owl#>")))
(inputs
(list
genewiki-symbols
generif-symbols
gn-genewiki-entries
ncbi-genewiki-entries))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
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