diff options
Diffstat (limited to 'examples/genotype-datasets.scm')
| -rwxr-xr-x | examples/genotype-datasets.scm | 53 |
1 files changed, 33 insertions, 20 deletions
diff --git a/examples/genotype-datasets.scm b/examples/genotype-datasets.scm index f140600..38d524b 100755 --- a/examples/genotype-datasets.scm +++ b/examples/genotype-datasets.scm @@ -15,29 +15,39 @@ (define-transformer gn:set->gn:dataset - (tables (Datasets - (inner-join InfoFiles "ON InfoFiles.DatasetId = Datasets.DatasetId") - (inner-join InbredSet "ON InbredSet.Id = InfoFiles.InbredSetId") + (tables (Species + (inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id") (inner-join GenoFreeze "ON GenoFreeze.InbredSetId = InbredSet.Id")) - "WHERE GenoFreeze.public > 0 GROUP BY Datasets.DatasetId") - (schema-triples - (gnt:has_genotype_data rdf:type owl:ObjectProperty) - (gnt:has_genotype_data rdfs:label "this resources has genotype data.") - (gnt:has_genotype_data rdfs:comment "Associates a resource with its genotype data.") - (gnt:has_genotype_data rdfs:domain gnc:set) - (gnt:has_genotype_data rdfs:range dcat:Dataset) - (gnt:has_genotype_data rdfs:subPropertyOf dct:relation)) + "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND Species.Name != 'monkey' GROUP BY Species.Name, GenoFreeze.ShortName") (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") - (set gnt:has_genotype_data (string->identifier "dataset" (field GenoFreeze Name) #:separator "_")))) + (multiset gnt:has_genotype_data + (map (cut string->identifier "dataset" <> #:separator "_") + (string-split + (field ("GROUP_CONCAT(GenoFreeze.Name SEPARATOR ',')" + dataset_name)) + #\,))))) -(define-transformer gn:dataset->gn:set - (tables (Datasets - (inner-join InfoFiles "ON InfoFiles.DatasetId = Datasets.DatasetId") - (inner-join InbredSet "ON InbredSet.Id = InfoFiles.InbredSetId") - (inner-join GenoFreeze "ON GenoFreeze.InbredSetId = InbredSet.Id")) - "WHERE GenoFreeze.public > 0 GROUP BY Datasets.DatasetId") +(define-transformer gn:dataset->metadata + (tables (GenoFreeze + (inner-join InbredSet "ON InbredSet.Id = GenoFreeze.InbredSetId") + (inner-join Species "ON InbredSet.SpeciesId = Species.Id")) + "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND Species.Name != 'monkey'") + (triples (string->identifier "dataset" (field GenoFreeze Name) #:separator "_") + (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")) + (set dct:created (annotate-field (field GenoFreeze CreateTime) '^^xsd:datetime)))) + +(define-transformer gn:dataset->marker/snp-count + (tables (GenoFreeze + (inner-join InbredSet "ON InbredSet.Id = GenoFreeze.InbredSetId") + (inner-join Species "ON InbredSet.SpeciesId = Species.Id") + (inner-join Geno "ON Geno.SpeciesId = Species.Id")) + "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND Species.Name != 'monkey' GROUP BY GenoFreeze.Name") (triples (string->identifier "dataset" (field GenoFreeze Name) #:separator "_") - (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) + (set gnt:has_marker_count + (string->symbol + (format #f "'~s'^^xsd:integer" + (field + ("COUNT(DISTINCT Geno.Marker_Name)" MarkerCount))))))) (let* ((option-spec @@ -68,7 +78,10 @@ ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>") ("xsd:" "<http://www.w3.org/2001/XMLSchema#>"))) (inputs - (list gn:set->gn:dataset gn:dataset->gn:set)) + (list + gn:set->gn:dataset + gn:dataset->metadata + gn:dataset->marker/snp-count)) (outputs `(#:documentation ,documentation #:rdf ,output)))) |