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diff --git a/rdf-documentation/phenotype-metadata.md b/rdf-documentation/phenotype-metadata.md new file mode 100644 index 0000000..b673bb1 --- /dev/null +++ b/rdf-documentation/phenotype-metadata.md @@ -0,0 +1,71 @@ +# Phenotypes Metadata +## 'phenotypes' + +## Generated Triples: + +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) +``` + +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 +``` +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 gnt:belongsToSet gn:setBxd . + ?s rdfs:label "10001" . + ?s skos:altLabel "BXD_10001" . + ?s ?p ?o . +} +``` + +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 . +``` + |