diff options
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/molecular-traits.scm | 42 |
1 files changed, 19 insertions, 23 deletions
diff --git a/examples/molecular-traits.scm b/examples/molecular-traits.scm index 6ece7b5..47efb98 100755 --- a/examples/molecular-traits.scm +++ b/examples/molecular-traits.scm @@ -11,15 +11,15 @@ (transform triples) (transform special-forms)) -(define-transformer tissue +(define-transformer molecular-entities (tables (Tissue)) (schema-triples - (gnc:tissue a owl:Class) - (gnc:tissue a skos:Concept) - (gnc:tissue rdfs:subClassOf obo:UBERON_0000479) - (gnc:tissue rdfs:label "Tissue (GN)")) + (gnc:molecular_trait a owl:Class) + (gnc:molecular_trait a skos:Concept) + (gnc:molecular_trait rdfs:subClassOf obo:UBERON_0000479) + (gnc:molecular_trait rdfs:label "Molecular Trait. This describes a melecular trait of a given species. We combine the species name and the tissue name in order to differentiate the traits across different inbredset groups.")) (triples (string->identifier "tissue" (field Tissue Short_Name) #:separator "_") - (set rdf:type 'gnc:tissue) + (set rdf:type 'gnc:molecular_trait) (set skos:prefLabel (field Tissue Name)) (set skos:altLabel (field Tissue Short_Name)))) @@ -31,30 +31,26 @@ (inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id")) "WHERE ProbeSetFreeze.public > 0 GROUP BY Species.Name, Tissue.Short_Name") (schema-triples - (gnc:molecular_trait a owl:Class) - (gnc:molecular_trait a skos:Concept) - (gnc:molecular_trait rdfs:subClassOf obo:UBERON_0000479) - (gnc:molecular_trait rdfs:label "Molecular Trait. This describe a melecular trait of a given species. We combine the species name and the tissue name in order to differentiate the traits across different inbredset groups.") - (gnt:has_tissue rdf:type owl:ObjectProperty) - (gnt:has_tissue rdfs:domain gnc:molecular_traits) - (gnt:has_tissue rdfs:range gnc:tissue) - (gnt:has_tissue rdfs:label "has tissue")) + (gnt:has_molecular_trait rdf:type owl:ObjectProperty) + (gnt:has_molecular_trait rdfs:domain gnc:set) + (gnt:has_molecular_trait rdfs:range gnc:molecular_traits) + (gnt:has_molecular_trait rdfs:label "has molecular trait")) (triples (string->identifier (format #f "trait_~a" (field Species Name)) (field Tissue Short_Name) #:separator "_") - (set rdf:type 'gnc:molecular_trait) + (set rdf:type 'gnc:molecular_entity) (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")) (set gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))) - (multiset gnt:has_dataset + (multiset gnt:has_probeset_data (map (cut string->identifier "dataset" <> #:separator "_") (string-split (field ("GROUP_CONCAT(ProbeSetFreeze.Name SEPARATOR ',')" dataset_name)) #\,))) - (set gnt:has_tissue + (set gnt:has_molecular_trait (string->identifier "tissue" (field Tissue Short_Name) #:separator "_")))) @@ -67,12 +63,12 @@ (inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id")) "WHERE ProbeSetFreeze.public > 0 GROUP BY Species.Name, Tissue.Short_Name") (schema-triples - (gnt:has_molecular_trait rdf:type owl:ObjectProperty) - (gnt:has_molecular_trait rdfs:domain gnc:set) - (gnt:has_molecular_trait rdfs:range gnc:molecular_traits) - (gnt:has_molecular_trait rdfs:label "has molecular trait")) + (gnc:molecular_entity a owl:Class) + (gnc:molecular_entity a skos:Concept) + (gnc:molecular_entity rdfs:subClassOf obo:UBERON_0000479) + (gnc:molecular_entity rdfs:label "This points this to resource which has molecular trait.")) (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") - (set gnt:has_molecular_trait + (set gnt:has_molecular_entity (string->identifier (format #f "trait_~a" (field Species Name)) (field Tissue Short_Name) #:separator "_")))) @@ -106,7 +102,7 @@ ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>"))) (inputs (list - tissue + molecular-entities molecular-traits list-molecular-traits)) (outputs |