diff options
Diffstat (limited to 'rdf-documentation/phenotype-metadata.md')
| -rw-r--r-- | rdf-documentation/phenotype-metadata.md | 19 |
1 files changed, 10 insertions, 9 deletions
diff --git a/rdf-documentation/phenotype-metadata.md b/rdf-documentation/phenotype-metadata.md index 8a7e421..d811d40 100644 --- a/rdf-documentation/phenotype-metadata.md +++ b/rdf-documentation/phenotype-metadata.md @@ -6,14 +6,14 @@ The following SQL query was executed: ```sql -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) +SELECT CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id) AS Phenotype, InbredSet.Name AS InbredSetName, PublishXRef.Id, CONCAT(IFNULL(InbredSet.InbredSetCode, 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/4.604), '') AS lrs, IFNULL(PublishXRef.additive, '') AS additive, PublishXRef.Sequence, IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT)) AS pmid, Publication.Id AS PublicationId 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 ``` The above query results to triples that have the form: ```text gn:traitPhenotype -> rdf:type -> gnc:Phenotype -gn:traitPhenotype -> xkos:classifiedUnder -> gn:setInbredset_inbredsetname +gn:traitPhenotype -> gnt:belongsToGroup -> gn:setInbredset_inbredsetname gn:traitPhenotype -> rdfs:label -> PublishXRef(Id) gn:traitPhenotype -> skos:altLabel -> Phenotype gn:traitPhenotype -> dct:description -> PhenotypePost_publication_description @@ -21,8 +21,8 @@ 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:locus -> gn:Publishxreflocus +gn:traitPhenotype -> gnt:lodScore -> "lrs"^^xsd:double gn:traitPhenotype -> gnt:additive -> "additive"^^xsd:double gn:traitPhenotype -> gnt:sequence -> "PublishXRef(Sequence)"^^xsd:integer gn:traitPhenotype -> dct:isReferencedBy -> pubmed:pmid @@ -35,18 +35,19 @@ 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 gnt: <http://genenetwork.org/term/> 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 xkos: <http://rdf-vocabulary.ddialliance.org/xkos#> PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/> SELECT * WHERE { ?s rdf:type gnc:Phenotype . - ?s xkos:classifiedUnder gn:setBxd . + ?s gnt:belongsToGroup gn:setBxd . ?s rdfs:label "10001" . ?s skos:altLabel "BXD_10001" . ?s ?p ?o . @@ -57,15 +58,15 @@ Expected Result: ```rdf gn:traitBxd_10001 rdf:type gnc:Phenotype . -gn:traitBxd_10001 xkos:classifiedUnder gn:setBxd . +gn:traitBxd_10001 gnt:belongsToGroup 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:locus gn:Rs48756159 . +gn:traitBxd_10001 gnt:lodScore "2.9316879120566246"^^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 . |