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#! /usr/bin/env guile
!#
(use-modules (srfi srfi-1)
(srfi srfi-26)
(rnrs bytevectors)
(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
(left-join Species "USING (SpeciesId)"))
"GROUP BY GeneId ORDER BY BINARY symbol")
(schema-triples
(gnt:belongsToSpecies rdfs:domain gnc:strain)
(gnt:belongsToSpecies rdfs:domain gnc:NCBIWikiEntry)
(gnt:symbol rdfs:domain gnc:NCBIWikiEntry))
(triples (ontology 'generif: (field GeneRIF_BASIC GeneId))
(multiset gnt:symbol (string-split (field ("GROUP_CONCAT(DISTINCT symbol)" symbol))
#\,))
(multiset gnt:belongsToSpecies
(string-split
(field ("GROUP_CONCAT(DISTINCT Species.SpeciesName)" species))
#\,))
(multiset dct:relation
(map
(cut ontology 'ncbiTaxon: <>)
(string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId))
#\,)))))
(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, GeneRIF.createtime")
(schema-triples
(gnc:GeneWikiEntry a rdfs:Class)
(gnc:GNWikiEntry rdfs:subClassOf gnc:GeneWikiEntry)
(gnc:GNWikiEntry rdfs:comment "Represents GeneRIF Entries entered from GeneNetwork")
(gnt:belongsToCategory rdfs:domain gnc:GNWikiEntry)
(gnt:belongsToSpecies rdfs:domain gnc:GNWikiEntry)
(gnt:symbol rdfs:domain gnc:GNWikiEntry))
(triples
(string->identifier
"generif"
(make-version-3-uuid
(u8-list->bytevector
;; URL namespace UUID is 6ba7b811-9dad-11d1-80b4-00c04fd430c8
'(107 167 184 17 157 173 17 209 128 180
0 192 79 212 48 200))
(format #f "~a~a~a~a"
(field Species FullName)
(field GeneRIF comment)
(field GeneRIF symbol)
(field GeneRIF createtime))
""))
(set rdf:type 'gnc:GNWikiEntry)
(set rdfs:label (sanitize-rdf-string (field GeneRIF comment)))
(set gnt:symbol (field GeneRIF symbol))
(multiset gnt:belongsToCategory
(remove-duplicates
(string-split-substring
(field ("GROUP_CONCAT(DISTINCT GeneCategory.Name SEPARATOR '$$')"
GeneCategory))
"$$")))
(set gnt:belongsToSpecies
(string->identifier
""
(remap-species-identifiers (field Species Fullname))
#:separator ""
#:proc string-capitalize-first))
(multiset dct:references
(map (lambda (x)
(ontology 'pubmed: x))
(string-split
(let ((pmid (field
("IFNULL(GeneRIF.PubMed_ID, '')"
PubMed_ID))))
(if (number? pmid)
(number->string pmid)
pmid))
#\space)))
(set dct:created
(let ((createtime (field GeneRIF createtime)))
(if (string? createtime)
""
(annotate-field
(time-unix->string
createtime "~5")
'^^xsd:datetime))))
(set dct:creator
(if (and (not (string-null?
(string-trim-both (field GeneRIF email))))
(not (string-null? (field Investigators Email))))
(investigator-attributes->id
(field Investigators FirstName)
(field Investigators LastName)
(field Investigators Email))
""))
(set foaf:homepage (field GeneRIF weburl))))
(define-transformer ncbi-genewiki-entries
(tables (GeneRIF_BASIC)
"GROUP BY GeneId, comment, createtime")
(schema-triples
(gnc:NCBIWikiEntry rdfs:subClassOf gnc:GeneWikiEntry)
(gnc:NCBIWikiEntry rdfs:comment "Represents GeneRIF Entries obtained from NCBI"))
(triples
(string->identifier
"generif"
(make-version-3-uuid
(u8-list->bytevector
;; URL namespace UUID is 6ba7b811-9dad-11d1-80b4-00c04fd430c8
'(107 167 184 17 157 173 17 209 128 180
0 192 79 212 48 200))
(format #f "~a~a~a~a~a"
(field GeneRIF_BASIC GeneId)
(field GeneRIF_BASIC VersionId)
(field GeneRIF_BASIC comment)
(field GeneRIF_BASIC symbol)
(field GeneRIF_BASIC createtime))
""))
(set rdf:type 'gnc:NCBIWikiEntry)
(set rdfs:label
(annotate-field (field GeneRIF_BASIC comment)
'^^xsd:string))
(set gnt:symbol (field GeneRIF_BASIC symbol))
(multiset dct:references
(map
(lambda (el)
(if (string-null? el)
""
(ontology 'pubmed: el)))
(string-split (field ("GROUP_CONCAT(PubMed_ID)" pmids))
#\,)))
(set gnt:hasVersion
(format #f "~a" (field GeneRIF_BASIC VersionId)))
(set dct:created
(let ((createtime (field GeneRIF_BASIC createtime)))
(if (string? createtime)
""
(annotate-field
(time-unix->string
createtime "~5")
'^^xsd:datetime))))))
(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#>")
("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/>")
("ncbiTaxon:" "<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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