diff options
Diffstat (limited to 'rdf-documentation/phenotype-metadata.md')
-rw-r--r-- | rdf-documentation/phenotype-metadata.md | 64 |
1 files changed, 33 insertions, 31 deletions
diff --git a/rdf-documentation/phenotype-metadata.md b/rdf-documentation/phenotype-metadata.md index b673bb1..8a7e421 100644 --- a/rdf-documentation/phenotype-metadata.md +++ b/rdf-documentation/phenotype-metadata.md @@ -6,27 +6,27 @@ The following SQL query was executed: ```sql -SELECT CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id) AS Phenotype, InbredSet.Name, PublishXRef.Id, 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) +SELECT CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id) AS Phenotype, InbredSet.Name AS InbredSetName, PublishXRef.Id, 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 -> gnt:belongsToSet -> gn:setInbredset_name -gn:trait_phenotype -> rdfs:label -> PublishXRef(Id) -gn:trait_phenotype -> skos:altLabel -> 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 +gn:traitPhenotype -> rdf:type -> gnc:Phenotype +gn:traitPhenotype -> xkos:classifiedUnder -> gn:setInbredset_inbredsetname +gn:traitPhenotype -> rdfs:label -> PublishXRef(Id) +gn:traitPhenotype -> skos:altLabel -> Phenotype +gn:traitPhenotype -> dct:description -> PhenotypePost_publication_description +gn:traitPhenotype -> gnt:abbreviation -> Phenotype(Post_publication_abbreviation) +gn:traitPhenotype -> gnt:labCode -> Phenotype(Lab_code) +gn:traitPhenotype -> gnt:submitter -> PhenotypeSubmitter +gn:traitPhenotype -> gnt:mean -> "mean"^^xsd:double +gn:traitPhenotype -> gnt:locus -> PublishXRef(Locus) +gn:traitPhenotype -> gnt:LRS -> "lrs"^^xsd:double +gn:traitPhenotype -> gnt:additive -> "additive"^^xsd:double +gn:traitPhenotype -> gnt:sequence -> "PublishXRef(Sequence)"^^xsd:integer +gn:traitPhenotype -> dct:isReferencedBy -> pubmed:pmid +gn:traitPhenotype -> dct:contributor -> PhenotypeOwner ``` Here's an example query: @@ -36,15 +36,17 @@ 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 sdmx-measure: <http://purl.org/linked-data/sdmx/2009/measure#> 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 qb: <http://purl.org/linked-data/cube#> PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/> SELECT * WHERE { - ?s rdf:type gnc:phenotype . - ?s gnt:belongsToSet gn:setBxd . + ?s rdf:type gnc:Phenotype . + ?s xkos:classifiedUnder gn:setBxd . ?s rdfs:label "10001" . ?s skos:altLabel "BXD_10001" . ?s ?p ?o . @@ -54,18 +56,18 @@ SELECT * WHERE { Expected Result: ```rdf -gn:trait_bxd_10001 rdf:type gnc:phenotype . -gn:trait_bxd_10001 gnt:belongsToSet gn:setBxd . -gn:trait_bxd_10001 rdfs:label "10001" . -gn:trait_bxd_10001 skos:altLabel "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 . +gn:traitBxd_10001 rdf:type gnc:Phenotype . +gn:traitBxd_10001 xkos:classifiedUnder gn:setBxd . +gn:traitBxd_10001 rdfs:label "10001" . +gn:traitBxd_10001 skos:altLabel "BXD_10001" . +gn:traitBxd_10001 dct:description "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" . +gn:traitBxd_10001 gnt:abbreviation "CBLWT2" . +gn:traitBxd_10001 gnt:submitter "robwilliams" . +gn:traitBxd_10001 gnt:mean "52.13529418496525"^^xsd:double . +gn:traitBxd_10001 gnt:locus "rs48756159" . +gn:traitBxd_10001 gnt:LRS "13.4974911471087"^^xsd:double . +gn:traitBxd_10001 gnt:additive "2.39444435069444"^^xsd:double . +gn:traitBxd_10001 gnt:sequence "1"^^xsd:integer . +gn:traitBxd_10001 dct:isReferencedBy pubmed:11438585 . ``` |