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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 (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-dump dump-gene-chip
(tables (GeneChip
(left-join Species "USING (SpeciesId)")))
(schema-triples
(gnc:geneChip a skos:Concept)
(gnc:geneChip
skos:description
"This is a set of controlled terms that are used to describe a given gene chip/platform")
(gnt:hasGeoSeriesId rdfs:domain gnc:platform)
(gnt:belongsToSpecies a owl:ObjectProperty)
(gnt:belongsToSpecies skos:definition "This resource belongs to this given species")
(gnt:belongsToSpecies rdfs:domain gnc:geneChip)
(gnt:hasGeoSeriesId rdfs:domain gnc:geneChip)
(gnt:hasGOTreeValue a owl:ObjectProperty)
(gnt:hasGOTreeValue skos:definition "This resource the following GO tree value")
(gnt:hasGOTreeValue rdfs:domain gnc:geneChip))
(triples (string->identifier "platform" (field GeneChip Name))
(set rdf:type 'gnc:geneChip)
(set rdfs:label (field GeneChip GeneChipName))
(set skos:prefLabel (field GeneChip Name))
(set skos:altLabel (field ("IF(GeneChip.GeneChipName != GeneChip.Title, Title, NULL)"
Title)))
(set gnt:hasGOTreeValue (field GeneChip Go_tree_value))
(set gnt:belongsToSpecies
(string->identifier "" (remap-species-identifiers (field Species Fullname))
#:separator ""
#:proc string-capitalize-first))
(set gnt:hasGeoSeriesId
(ontology 'geoSeries:
(string-trim-both (field GeneChip GeoPlatform))))))
;; Molecular Traits are also referred to as ProbeSets
(define-dump dump-probesetfreeze
(tables (ProbeSetFreeze
(left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
(left-join ProbeFreeze "USING (ProbeFreezeId)")
(left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
(left-join InbredSet "ON ProbeFreeze.InbredSetId = InbredSet.Id")
(left-join Tissue "ON ProbeFreeze.TissueId = Tissue.TissueId"))
"WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
(schema-triples
(gnc:probeset rdfs:subClassOf gnc:dataset)
(gnt:usesNormalization rdfs:domain gnc:probeset)
(gnt:usesDataScale rdfs:domain gnc:probeset)
(gnt:usesDataScale a owl:ObjectProperty)
(gnt:usesDataScale skos:definition "Thi data scale this resource uses"))
(triples
(string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ProbeSetFreeze Name)
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gnc:probeset)
(set gnt:usesNormalization
(string->identifier "avgmethod"
;; If AvgMethodName is NULL, assume N/A.
(if (string-blank? (field AvgMethod Name AvgMethodName))
"N/A" (field AvgMethod Name AvgMethodName))))
(set dct:title (field ProbeSetFreeze FullName))
(set rdfs:label (field ProbeSetFreeze Name))
(set skos:altLabel (field ProbeSetFreeze Name2))
(set skos:prefLabel (field ProbeSetFreeze ShortName))
(set dct:created (annotate-field
(field ProbeSetFreeze CreateTime)
'^^xsd:datetime))
(set gnt:usesDataScale (field ProbeSetFreeze DataScale))
(set gnt:hasTissue
(string->identifier
"tissue"
(field Tissue Short_Name)))
(set gnt:belongsToInbredSet
(string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
(dump-with-documentation
(name "Probeset freeze metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
("gn:" "<http://genenetwork.org/id/>")
("gnc:" "<http://genenetwork.org/category/>")
("dct:" "<http://purl.org/dc/terms/>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("gnt:" "<http://genenetwork.org/term/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
(inputs
(list dump-gene-chip
dump-probesetfreeze))
(outputs
'(#:documentation "./docs/dump-gene-chip.md"
#:rdf "./verified-data/dump-probesetfreeze.ttl")))
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