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diff --git a/rdf-documentation/dump-phenotype.md b/rdf-documentation/dump-phenotype.md deleted file mode 100644 index c9436a3..0000000 --- a/rdf-documentation/dump-phenotype.md +++ /dev/null @@ -1,121 +0,0 @@ -# Phenotypes Metadata -## 'dump-publishfreeze' - -## Generated Triples: - -The following SQL query was executed: - -```sql -SELECT PublishFreeze.Name, PublishFreeze.Name, PublishFreeze.FullName, PublishFreeze.ShortName, PublishFreeze.CreateTime, InbredSet.Name FROM PublishFreeze LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = PublishFreeze.Name LEFT JOIN InbredSet ON PublishFreeze.InbredSetId = InbredSet.InbredSetId WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoFileId IS NULL -``` - -The above query results to triples that have the form: - -```text -gn:Publishfreeze_name_ -> rdf:type -> gnc:phenotypeDataset -gn:Publishfreeze_name_ -> rdfs:label -> PublishFreeze(Name) -gn:Publishfreeze_name_ -> skos:prefLabel -> PublishFreeze(FullName) -gn:Publishfreeze_name_ -> skos:altLabel -> PublishFreeze(ShortName) -gn:Publishfreeze_name_ -> dct:created -> "PublishFreeze(CreateTime)"^^xsd:date -gn:Publishfreeze_name_ -> gnt:belongsToInbredSet -> gn:Inbredset_name -``` -Here's an example query: - -```sparql -PREFIX dct: <http://purl.org/dc/terms/> -PREFIX gn: <http://genenetwork.org/id/> -PREFIX owl: <http://www.w3.org/2002/07/owl#> -PREFIX gnc: <http://genenetwork.org/category/> -PREFIX gnt: <http://genenetwork.org/terms/> -PREFIX skos: <http://www.w3.org/2004/02/skos/core#> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/> - -SELECT * WHERE { - ?s rdf:type gnc:phenotypeDataset . - ?s rdfs:label "B6D2F2-PSUPublish" . - ?s skos:prefLabel "B6D2F2 PSU Phenotypes" . - ?s ?p ?o . -} -``` - -Expected Result: - -```rdf -gn:B6d2f2_psupublish rdf:type gnc:phenotypeDataset . -gn:B6d2f2_psupublish rdfs:label "B6D2F2-PSUPublish" . -gn:B6d2f2_psupublish skos:prefLabel "B6D2F2 PSU Phenotypes" . -gn:B6d2f2_psupublish skos:altLabel "B6D2F2 PSU Publish" . -gn:B6d2f2_psupublish dct:created "2015-03-18"^^xsd:date . -gn:B6d2f2_psupublish gnt:belongsToInbredSet gn:B6d2f2-psupublish . -``` - - -## 'dump-phenotypes' - -## Generated Triples: - -The following SQL query was executed: - -```sql -SELECT CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id) AS Phenotype, CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id) AS Phenotype, Phenotype.Post_publication_description, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, IFNULL(PublishXRef.mean, '') AS mean, PublishXRef.Locus, IFNULL(PublishXRef.LRS, '') AS lrs, IFNULL(PublishXRef.additive, '') AS additive, PublishXRef.Sequence, IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT)) AS pmid, Publication.Id FROM PublishXRef LEFT JOIN InbredSet ON InbredSet.InbredSetId = PublishXRef.InbredSetId LEFT JOIN Publication ON Publication.Id = PublishXRef.PublicationId LEFT JOIN Phenotype ON Phenotype.Id = PublishXRef.PhenotypeId WHERE PublishXRef.InbredSetId IN (SELECT PublishFreeze.InbredSetId FROM PublishFreeze) -``` - -The above query results to triples that have the form: - -```text -gn:trait_phenotype -> rdf:type -> gnc:phenotype -gn:trait_phenotype -> rdfs:label -> Phenotype -gn:trait_phenotype -> dct:description -> PhenotypePost_publication_description -gn:trait_phenotype -> gnt:abbreviation -> Phenotype(Post_publication_abbreviation) -gn:trait_phenotype -> gnt:labCode -> Phenotype(Lab_code) -gn:trait_phenotype -> gnt:submitter -> PhenotypeSubmitter -gn:trait_phenotype -> gnt:mean -> "mean"^^xsd:double -gn:trait_phenotype -> gnt:locus -> PublishXRef(Locus) -gn:trait_phenotype -> gnt:LRS -> "lrs"^^xsd:double -gn:trait_phenotype -> gnt:additive -> "additive"^^xsd:double -gn:trait_phenotype -> gnt:sequence -> "PublishXRef(Sequence)"^^xsd:integer -gn:trait_phenotype -> dct:isReferencedBy -> pubmed:pmid -gn:trait_phenotype -> dct:contributor -> PhenotypeOwner -``` -Here's an example query: - -```sparql -PREFIX dct: <http://purl.org/dc/terms/> -PREFIX gn: <http://genenetwork.org/id/> -PREFIX owl: <http://www.w3.org/2002/07/owl#> -PREFIX gnc: <http://genenetwork.org/category/> -PREFIX gnt: <http://genenetwork.org/terms/> -PREFIX skos: <http://www.w3.org/2004/02/skos/core#> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/> - -SELECT * WHERE { - ?s rdf:type gnc:phenotype . - ?s rdfs:label "BXD_10001" . - ?s dct:description "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" . - ?s gnt:abbreviation "CBLWT2" . - ?s ?p ?o . -} -``` - -Expected Result: - -```rdf -gn:trait_bxd_10001 rdf:type gnc:phenotype . -gn:trait_bxd_10001 rdfs:label "BXD_10001" . -gn:trait_bxd_10001 dct:description "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" . -gn:trait_bxd_10001 gnt:abbreviation "CBLWT2" . -gn:trait_bxd_10001 gnt:submitter "robwilliams" . -gn:trait_bxd_10001 gnt:mean "52.13529418496525"^^xsd:double . -gn:trait_bxd_10001 gnt:locus "rs48756159" . -gn:trait_bxd_10001 gnt:LRS "13.4974911471087"^^xsd:double . -gn:trait_bxd_10001 gnt:additive "2.39444435069444"^^xsd:double . -gn:trait_bxd_10001 gnt:sequence "1"^^xsd:integer . -gn:trait_bxd_10001 dct:isReferencedBy pubmed:11438585 . -``` - |