Update documentation.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

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 .