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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 (remap-species-identifiers str)
"This procedure remaps identifiers to standard binominal. Obviously this should
be sorted by correcting the database!"
(match str
["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"]
["Oryzias latipes (Japanese medaka)" "Oryzias latipes"]
["Macaca mulatta" "Macaca nemestrina"]
["Bat (Glossophaga soricina)" "Glossophaga soricina"]
[str str]))
(define (fix-email-id email)
(string-delete #\space email))
(define (investigator-attributes->id first-name last-name email)
;; There is just one record corresponding to "Evan Williams" which
;; does not have an email ID. To accommodate that record, we
;; construct the investigator ID from not just the email ID, but
;; also the first and the last names. It would be preferable to just
;; find Evan Williams' email ID and insert it into the database.
(string->identifier "investigator"
(string-join
(list first-name last-name (fix-email-id email))
"_")))
(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))))
(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")
(left-join Investigators "ON Investigators.Email = GeneRIF.email"))
"WHERE GeneRIF.display > 0 AND GeneRIF.VersionId = 0 AND GeneRIF.comment IS NOT NULL GROUP BY GeneRIF.comment, BINARY GeneRIF.symbol")
(schema-triples
(gnc:GeneWikiEntry a rdfs:Class)
(gnc:GNWikiEntry rdfs:subClassOf gnc:GeneWikiEntry)
(gnc:GNWikiEntry rdfs:comment "Represents GeneRIF Entries entered from GeneNetwork")
(gnt:symbol rdfs:domain gnc:GNWikiEntry))
(triples
(string->identifier
"symbol"
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field GeneRIF symbol)
'pre "_" 'post)
#:proc (lambda (x) x))
(set rdfs:comment
(let* ([generif-comment (sanitize-rdf-string (field GeneRIF comment))]
[create-time (field GeneRIF createtime 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)]
[categories
(remove (lambda (x)
(or (eq? x #f)
(and (string? x)
(string-null? x))))
(remove-duplicates
(string-split-substring
(field ("GROUP_CONCAT(DISTINCT GeneCategory.Name SEPARATOR '$$')"
GeneCategory))
"$$")))])
(string->symbol
(string-append
"[ "
(format #f "rdf:type gnc:GNWikiEntry ; ")
(if (string? species)
""
(format #f "gnt:belongsToSpecies ~a ; "
species))
(format #f "rdfs:comment ~s^^xsd:string ; "
generif-comment)
(if (string? create-time)
""
(format #f "dct:created ~s^^xsd:datetime ; "
(time-unix->string
create-time "~5")))
(if (and (string? pmid) (not (string-null? pmid)))
(format #f
"~{dct:references pubmed:~a ; ~}"
(string-split pmid #\space))
"")
(if (and (not (string-null?
(string-trim-both (field GeneRIF email))))
(not (string-null? (field Investigators Email))))
(format #f "dct:creator ~a ; "
(investigator-attributes->id
(field Investigators FirstName)
(field Investigators LastName)
(field Investigators Email)))
"")
(if (not (null? categories))
(format #f
"~{gnt:belongsToCategory ~s ; ~}"
categories)
"")
(if (and (string? web-url) (not (string-null? web-url)))
(format #f "foaf:homepage ~s ; "
web-url)
"")
" ] "))))))
(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:hasGeneId a owl:ObjectProperty)
(gnt:hasGeneId rdfs:domain gnc:NCBIWikiEntry)
(gnt:hasGeneId skos:definition "The GeneId of this this resource")
(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 "gnt:hasVersionId '~a'^^xsd:integer ; "
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
gn-genewiki-entries
ncbi-genewiki-entries))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
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