diff options
| -rwxr-xr-x | dump.scm | 71 |
1 files changed, 69 insertions, 2 deletions
diff --git a/dump.scm b/dump.scm index 7c5c11f..eac2442 100755 --- a/dump.scm +++ b/dump.scm @@ -244,6 +244,10 @@ ALIST field-name) forms." (define-dump dump-species (tables (Species)) + (schema-triples + (gn:name rdfs:range rdfs:Literal) + (gn:menuname rdfs:range rdfs:Literal) + (gn:binomialName rdfs:range rdfs:Literal)) (triples (binomial-name->species-id (field Species FullName)) (set rdf:type 'gn:species) (set gn:name (field Species SpeciesName)) @@ -255,7 +259,10 @@ ALIST field-name) forms." (join Species "ON Strain.SpeciesId = Species.SpeciesId"))) (schema-triples (gn:strainOfSpecies rdfs:domain gn:strain) - (gn:strainOfSpecies rdfs:range gn:species)) + (gn:strainOfSpecies rdfs:range gn:species) + (gn:name rdfs:range rdfs:Literal) + (gn:alias rdfs:range rdfs:Literal) + (gn:symbol rdfs:range rdfs:Literal)) (triples (string->identifier "strain" (field Strain Name)) (set rdf:type 'gn:strain) (set gn:strainOfSpecies @@ -282,6 +289,10 @@ ALIST field-name) forms." (define-dump dump-inbred-set (tables (InbredSet (inner-join Species "USING (SpeciesId)"))) + (schema-triples + (gn:fullName rdfs:range rdfs:Literal) + (gn:geneticType rdfs:range rdfs:Literal) + (gn:family rdfs:range rdfs:Literal)) (triples (inbred-set-name->id (field InbredSet Name)) (set rdf:type 'gn:inbredSet) (set gn:fullName (field InbredSet FullName)) @@ -295,6 +306,15 @@ ALIST field-name) forms." (define-dump dump-phenotype (tables (Phenotype)) + (schema-triples + (gn:prePublicationDescription rdfs:range rdfs:Literal) + (gn:postPublicationDescription rdfs:range rdfs:Literal) + (gn:originalDescription rdfs:range rdfs:Literal) + (gn:labCode rdfs:range rdfs:Literal) + (gn:submitter rdfs:range rdfs:Literal) + (gn:owner rdfs:range rdfs:Literal) + (gn:authorizedUsers rdfs:range rdfs:Literal) + (gn:units rdfs:range rdfs:Literal)) (triples (phenotype-id->id (field Phenotype Id)) (set rdf:type 'gn:phenotype) (set gn:prePublicationDescription (field Phenotype Pre_publication_description)) @@ -309,6 +329,16 @@ ALIST field-name) forms." (define-dump dump-publication (tables (Publication)) + (schema-triples + (gn:pubMedId rdfs:range rdfs:Literal) + (gn:title rdfs:range rdfs:Literal) + (gn:journal rdfs:range rdfs:Literal) + (gn:volume rdfs:range rdfs:Literal) + (gn:pages rdfs:range rdfs:Literal) + (gn:month rdfs:range rdfs:Literal) + (gn:year rdfs:range rdfs:Literal) + (gn:author rdfs:range rdfs:Literal) + (gn:abstract rdfs:range rdfs:Literal)) (triples (string->identifier "publication" (number->string (field Publication Id))) (set rdf:type 'gn:publication) @@ -344,6 +374,8 @@ ALIST field-name) forms." ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID ;; and BIRN_lex_Name are mostly NULL. (tables (Tissue)) + (schema-triples + (gn:name rdfs:range rdfs:Literal)) ;; Hopefully the Short_Name field is distinct and can be used as an ;; identifier. (triples (tissue-short-name->id (field Tissue Short_Name)) @@ -370,6 +402,20 @@ ALIST field-name) forms." ;; deduplicate. (tables (Investigators) "GROUP BY Email") + (schema-triples + ;; TODO: Are ranges required for FOAF predicates? Can they not be + ;; obtained from the FOAF spec? + (foaf:name rdfs:range rdfs:Literal) + (foaf:givenName rdfs:range rdfs:Literal) + (foaf:familyName rdfs:range rdfs:Literal) + (foaf:phone rdfs:range rdfs:Literal) + (foaf:mbox rdfs:range rdfs:Literal) + (foaf:homepage rdfs:range rdfs:Literal) + (gn:address rdfs:range rdfs:Literal) + (gn:city rdfs:range rdfs:Literal) + (gn:state rdfs:range rdfs:Literal) + (gn:zipCode rdfs:range rdfs:Literal) + (gn:country rdfs:range rdfs:Literal)) (triples (investigator-attributes->id (field Investigators FirstName) (field Investigators LastName) (field Investigators Email)) @@ -396,6 +442,8 @@ ALIST field-name) forms." ;; There are two records with Name as "N/A". Deduplicate. (tables (AvgMethod) "GROUP BY Name") + (schema-triples + (gn:name rdfs:range rdfs:Literal)) (triples (avg-method-name->id (field AvgMethod Name)) (set rdf:type 'gn:avgMethod) (set gn:name (field AvgMethod Name)))) @@ -405,6 +453,8 @@ ALIST field-name) forms." (define-dump dump-gene-chip (tables (GeneChip)) + (schema-triples + (gn:name rdfs:range rdfs:Literal)) (triples (gene-chip-name->id (field GeneChip Name)) (set rdf:type 'gn:platform) (set gn:name (field GeneChip GeneChipName)))) @@ -433,7 +483,24 @@ ALIST field-name) forms." (gn:normalization rdfs:domain gn:dataset) (gn:normalization rdfs:range gn:avgMethod) (gn:datasetOfPlatform rdfs:domain gn:dataset) - (gn:datasetOfPlatform rdfs:range gn:geneChip)) + (gn:datasetOfPlatform rdfs:range gn:geneChip) + (gn:accessionId rdfs:range rdfs:Literal) + (gn:datasetStatusName rdfs:range rdfs:Literal) + (gn:summary rdfs:range rdfs:Literal) + (gn:aboutTissue rdfs:range rdfs:Literal) + (gn:geoSeries rdfs:range rdfs:Literal) + (gn:name rdfs:range rdfs:Literal) + (gn:title rdfs:range rdfs:Literal) + (gn:specifics rdfs:range rdfs:Literal) + (gn:datasetGroup rdfs:range rdfs:Literal) + (gn:aboutCases rdfs:range rdfs:Literal) + (gn:aboutPlatform rdfs:range rdfs:Literal) + (gn:aboutDataProcessing rdfs:range rdfs:Literal) + (gn:notes rdfs:range rdfs:Literal) + (gn:experimentDesign rdfs:range rdfs:Literal) + (gn:contributors rdfs:range rdfs:Literal) + (gn:citation rdfs:range rdfs:Literal) + (gn:acknowledgment rdfs:range rdfs:Literal)) (triples (string->identifier "dataset" (number->string (field InfoFiles GN_AccesionId))) (set rdf:type 'gn:dataset) |