diff options
| -rwxr-xr-x | examples/dump-species-metadata.scm | 29 |
1 files changed, 21 insertions, 8 deletions
diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm index ebfc1a2..f991505 100755 --- a/examples/dump-species-metadata.scm +++ b/examples/dump-species-metadata.scm @@ -99,11 +99,12 @@ (set rdf:type 'gnc:mappingMethod) (set rdfs:label (field MappingMethod Name)))) + (define-dump dump-inbred-set (tables (InbredSet (left-join Species "ON InbredSet.SpeciesId=Species.Id") (left-join MappingMethod - "ON InbredSet.MappingMethodId=MappingMethod.Id"))) + "ON InbredSet.MappingMethodId=MappingMethod.Id"))) (schema-triples (gnc:inbredSet skos:broader gnc:species) (gnc:inbredSet skos:definition "A set of terms used to describe an inbred set") @@ -131,12 +132,21 @@ (set gnt:code (field InbredSet InbredSetCode)) (set gnt:species (string->identifier "" (remap-species-identifiers (field Species Fullname)) - #:separator "" - #:proc string-capitalize-first)) + #:separator "" + #:proc string-capitalize-first)) (set gnt:genotype (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP))) (set gnt:phenotype - (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP))))) + (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP))) + (multiset gnt:molecularTrait + (map + (lambda (x) + (string->identifier "tissue" + x)) + (string-split-substring + (field ("(SELECT GROUP_CONCAT(DISTINCT Tissue.Short_Name SEPARATOR'||') AS MolecularTraits FROM ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species WHERE ProbeFreeze.TissueId = Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id ORDER BY Tissue.Name)" + molecularTrait)) + "||"))))) (define-dump dump-avg-method ;; The Name and Normalization fields seem to be the same. Dump only @@ -159,14 +169,17 @@ ("gnc:" "<http://genenetwork.org/category/>") ("owl:" "<http://www.w3.org/2002/07/owl#>") ("gnt:" "<http://genenetwork.org/term/>") + ("skos:" "<http://www.w3.org/2004/02/skos/core#>") ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") ("taxon:" "<http://purl.uniprot.org/taxonomy/>"))) (inputs - (list dump-species - dump-strain - dump-mapping-method - dump-avg-method)) + (list + dump-inbred-set + dump-species + dump-strain + dump-mapping-method + dump-avg-method)) (outputs '(#:documentation "./docs/dump-species-metadata.md" #:rdf "./verified-data/dump-species-metadata.ttl"))) |