diff options
| -rwxr-xr-x | dump.scm | 86 |
1 files changed, 86 insertions, 0 deletions
@@ -385,7 +385,91 @@ must be remedied." (set gn:inbredSetOfSpecies (binomial-name->species-id (field Species FullName BinomialName))))) +;; Metadata for published datasets +(define-dump dump-publishfreeze + (tables (PublishFreeze + (left-join InbredSet "USING (InbredSetId)"))) (schema-triples + (gn:datasetOfInbredSet rdfs:range gn:inbredSet) + (gn:name rdfs:range rdfs:Literal) + (gn:fullName rdfs:range rdfs:Literal) + (gn:shortName rdfs:range rdfs:Literal) + (gn:createTime rdfs:range rdfs:Literal)) + (triples (string->identifier "dataset" (field PublishFreeze Name)) + (set rdf:type 'gn:dataset) + (set gn:name (field PublishFreeze Name)) + (set gn:fullName (field PublishFreeze FullName)) + (set gn:shortName (field PublishFreeze ShortName)) + (set gn:createTime (field PublishFreeze CreateTime)) + (set gn:datasetOfInbredSet + (inbred-set-name->id (field InbredSet Name InbredSetName))))) + +;; Phenotype metadata +(define-dump dump-published-phenotypes + (tables (PublishXRef + (inner-join + Phenotype + "ON PublishXRef.PhenotypeId = Phenotype.Id") + (inner-join + Publication + "ON PublishXRef.PublicationId = +Publication.Id") + (inner-join PublishFreeze "USING (InbredSetId)")) + "WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1") + (schema-triples + (gn:prePublicationDescription rdfs:range rdfs:Literal) + (gn:postPublicationDescription rdfs:range rdfs:Literal) + (gn:originalDescription rdfs:range rdfs:Literal) + (gn:units rdfs:range rdfs:Literal) + (gn:prePublicationAbbreviation rdfs:range rdfs:Literal) + (gn:postPublicationAbbreviation rdfs:range rdfs:Literal) + (gn:labCode rdfs:range rdfs:Literal) + (gn:submitter rdfs:range rdfs:Literal) + (gn:owner rdfs:range rdfs:Literal) + (gn:phenotypeOfDataset rdfs:range gn:dataset) + (gn:pubMedId rdfs:range rdfs:Literal) + (gn:publicationId rdfs:range gn:publication) + (gn:mean rdfs:range rdfs:Literal) + (gn:locus rdfs:range rdfs:Literal) + (gn:lrs rdfs:range rdfs:Literal) + (gn:additive rdfs:range rdfs:Literal) + (gn:sequence rdfs:range rdfs:Literal) + (gn:comments rdfs:range rdfs:Literal)) + ;; In GN, a given trait is identified by the id of the PublishXRef! + (triples (string->identifier "phenotype" + (number->string + (field PublishXRef Id))) + (set rdf:type 'gn:phenotype) + (set rdf:type 'gn:phenotype) + (set gn:prePublicationDescription (field Phenotype Pre_publication_description)) + (set gn:prePublicationDescription (field Phenotype Pre_publication_description)) + (set gn:postPublicationDescription (field Phenotype Post_publication_description)) + (set gn:originalDescription (field Phenotype Original_description)) + (set gn:units (field Phenotype Units)) + (set gn:prePublicationAbbreviation (field Phenotype Pre_publication_description)) + (set gn:postPublicationAbbreviation (field Phenotype Post_publication_abbreviation)) + (set gn:labCode (field Phenotype Lab_code)) + (multiset gn:submitter + (map string-trim (string-split + (field Phenotype Submitter) #\,))) + (multiset gn:owner + (map string-trim (string-split + (field Phenotype Owner) #\,))) + (set gn:pubMedId (field Publication PubMed_ID)) + (set gn:publicationId + (string->identifier + "publication" + (number->string (field Publication Id)))) + (set gn:mean (field PublishXRef mean)) + (set gn:locus (field PublishXRef Locus)) + (set gn:lrs (field PublishXRef LRS)) + (set gn:additive (field PublishXRef additive)) + (set gn:sequence (field PublishXRef Sequence)) + (set gn:comments (field PublishXRef comments)) + (set gn:phenotypeOfDataset + (string->identifier "dataset" + (field PublishFreeze Name))))) + (define-dump dump-publication (tables (Publication)) @@ -783,6 +867,7 @@ is a <table> object." (dump-strain db) (dump-mapping-method db) (dump-inbred-set db) + (dump-publishfreeze db) (dump-publication db) (dump-tissue db) (dump-investigators db) @@ -792,3 +877,4 @@ is a <table> object." (dump-schema db) (dump-groups db) (import-generif (assq-ref %connection-settings 'generif-data-file)))))) + (dump-published-phenotypes db) |