diff options
Diffstat (limited to 'examples/species-metadata.scm')
| -rwxr-xr-x | examples/species-metadata.scm | 77 |
1 files changed, 0 insertions, 77 deletions
diff --git a/examples/species-metadata.scm b/examples/species-metadata.scm index b330b12..89f2e27 100755 --- a/examples/species-metadata.scm +++ b/examples/species-metadata.scm @@ -21,33 +21,6 @@ ["Bat (Glossophaga soricina)" "Glossophaga soricina"] [str str])) -(define-transformer species - (tables (Species)) - (schema-triples - (gnc:species a skos:Concept) - (gnc:species skos:description "This is a set of controlled terms that are used to describe a given species") - (gnc:species skos:broader gnc:family) - (gnt:binomialName a owl:ObjectProperty) - (gnt:binomialName rdfs:domain gnc:species) - (gnt:family a owl:ObjectProperty) - (gnt:family rdfs:domain gnc:species) - (gnt:family skos:definition "This resource belongs to this family") - (gnt:organism a owl:ObjectProperty) - (gnt:organism rdfs:domain gnc:species) - (gnt:shortName a owl:ObjectProperty) - (gnt:shortName rdfs:domain gnc:species)) - (triples - (string->identifier "" (remap-species-identifiers (field Species Fullname)) - #:separator "" - #:proc string-capitalize-first) - (set rdf:type 'gnc:species) - (set skos:label (field Species SpeciesName)) - (set skos:altLabel (field Species Name)) - (set rdfs:label (field Species MenuName)) - (set gnt:binomialName (field Species FullName)) - (set gnt:family (field Species Family)) - (set gnt:organism (ontology 'taxon: (field Species TaxonomyId))))) - #! The ProbeData table contains StrainID. @@ -132,56 +105,6 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used. (set rdf:type 'gnc:mappingMethod) (set rdfs:label (field MappingMethod Name)))) - -(define-transformer inbred-set - (tables (InbredSet - (left-join Species "ON InbredSet.SpeciesId=Species.Id") - (left-join MappingMethod - "ON InbredSet.MappingMethodId=MappingMethod.Id"))) - (schema-triples - (gnc:set skos:broader gnc:species) - (gnc:set skos:definition "A set of terms used to describe an set, which can be inbredSet, outbredSet etc etc.") - (gnt:geneticType a owl:ObjectProperty) - (gnt:geneticType rdfs:domain gnc:set) - (gnt:code a owl:ObjectProperty) - (gnt:code rdfs:domain gnc:set) - ;; Already defined as an owl prop in species - (gnt:family rdfs:domain gnc:set) - (gnt:phenotype a owl:ObjectProperty) - (gnt:phenotype rdfs:domain gnc:set) - (gnt:genotype a owl:ObjectProperty) - (gnt:genotype rdfs:domain gnt:inbredSet) - (gnt:mappingMethod a owl:ObjectProperty) - (gnt:mappingMethod rdfs:domain gnc:set)) - (triples (string->identifier - "set" (field InbredSet Name) - #:separator "" - #:proc string-capitalize-first) - (set rdf:type 'gnc:set) - (set rdfs:label (field InbredSet FullName)) - (set skos:altLabel (field InbredSet Name)) - (set gnt:geneticType (field InbredSet GeneticType)) - (set gnt:family (field InbredSet Family)) - (set gnt:mappingMethod (field MappingMethod Name)) - (set gnt:code (field InbredSet InbredSetCode)) - (set gnt:belongsToSpecies - (string->identifier "" (remap-species-identifiers (field Species Fullname)) - #: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))) - (multiset gnt:hasTissue - (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-transformer avg-method ;; The Name and Normalization fields seem to be the same. Dump only ;; the Name field. |