Update auto-generated docs

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

4 files changed, 184 insertions, 189 deletions

diff --git a/rdf-documentation/dump-genotype.md b/rdf-documentation/dump-genotype.md
index 07533f9..2f5edbc 100644
--- a/rdf-documentation/dump-genotype.md
+++ b/rdf-documentation/dump-genotype.md
@@ -59,25 +59,24 @@ gn:B6d2rigeno gnt:belongsToInbredSet gn:_b6d2ri .
 The following SQL query was executed:
 
 ```sql
-SELECT CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, '_')), Geno.Name) AS abbrev, Geno.Name, Geno.Chr, IFNULL(Geno.Mb, '') AS Mb, IFNULL(Geno.Mb_mm8, '') AS Mb_mm8, IFNULL(Geno.Mb_2016, '') AS Mb_2016, Geno.Sequence, Geno.Source, IF((Source2 = Source), NULL, Source2) AS Source2, IFNULL(GenoFreeze.Name, '') AS DatasetName, Geno.chr_num, Geno.Comments, GenoXRef.cM FROM Geno LEFT JOIN GenoXRef ON Geno.Id = GenoXRef.GenoId LEFT JOIN GenoFreeze ON GenoFreeze.Id = GenoXRef.GenoFreezeId LEFT JOIN InbredSet ON InbredSet.InbredSetId = GenoFreeze.InbredSetId LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = GenoFreeze.Name
+SELECT Geno.Name, Geno.Name, Geno.Chr, IFNULL(Geno.Mb, '') AS Mb, IFNULL(Geno.Mb_mm8, '') AS Mb_mm8, IFNULL(Geno.Mb_2016, '') AS Mb_2016, Geno.Sequence, Geno.Source, IF((Source2 = Source), NULL, Source2) AS Source2, Species.Fullname, Geno.chr_num, Geno.Comments FROM Geno LEFT JOIN Species USING (SpeciesId)
 ```
 
 The above query results to triples that have the form:
 
 ```text
-gn:Abbrev -> rdf:type -> gnc:genotype 
-gn:Abbrev -> skos:prefLabel -> GenoName 
-gn:Abbrev -> gnt:chr -> Geno(Chr) 
-gn:Abbrev -> gnt:mb -> "Mb"^^xsd:double 
-gn:Abbrev -> gnt:mbMm8 -> "Mb_mm8"^^xsd:double 
-gn:Abbrev -> gnt:mb2016 -> "Mb_2016"^^xsd:double 
-gn:Abbrev -> gnt:hasSequence -> Geno(Sequence) 
-gn:Abbrev -> gnt:hasSource -> Geno(Source) 
-gn:Abbrev -> gnt:hasAltSourceName -> Source2 
-gn:Abbrev -> gnt:belongsToDataset -> gn:Datasetname 
-gn:Abbrev -> gnt:chrNum -> "Geno(chr_num)"^^xsd:int 
-gn:Abbrev -> rdfs:comments -> Geno(Comments) 
-gn:Abbrev -> gnt:cM -> "GenoXRef(cM)"^^xsd:int 
+gn:Geno_name_ -> rdf:type -> gnc:genotype 
+gn:Geno_name_ -> skos:prefLabel -> GenoName 
+gn:Geno_name_ -> gnt:chr -> Geno(Chr) 
+gn:Geno_name_ -> gnt:mb -> "Mb"^^xsd:double 
+gn:Geno_name_ -> gnt:mbMm8 -> "Mb_mm8"^^xsd:double 
+gn:Geno_name_ -> gnt:mb2016 -> "Mb_2016"^^xsd:double 
+gn:Geno_name_ -> gnt:hasSequence -> Geno(Sequence) 
+gn:Geno_name_ -> gnt:hasSource -> Geno(Source) 
+gn:Geno_name_ -> gnt:hasAltSourceName -> Source2 
+gn:Geno_name_ -> gnt:belongsToSpecies -> gn:Species_fullname 
+gn:Geno_name_ -> gnt:chrNum -> "Geno(chr_num)"^^xsd:int 
+gn:Geno_name_ -> rdfs:comments -> Geno(Comments) 
 ```
 Here's an example query:
 
@@ -94,9 +93,9 @@ PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 
 SELECT * WHERE { 
     ?s rdf:type gnc:genotype .
-    ?s skos:prefLabel "D1Mit118" .
+    ?s skos:prefLabel "D1Mit296" .
     ?s gnt:chr "1" .
-    ?s gnt:mb #{"3.968933"^^xsd:double}# .
+    ?s gnt:mb #{"9.749729"^^xsd:double}# .
     ?s ?p ?o .
 }
 ```
@@ -104,16 +103,15 @@ SELECT * WHERE {
 Expected Result:
 
 ```rdf
-gn:B6d2f2geno_d1mit118 rdf:type gnc:genotype .
-gn:B6d2f2geno_d1mit118 skos:prefLabel "D1Mit118" .
-gn:B6d2f2geno_d1mit118 gnt:chr "1" .
-gn:B6d2f2geno_d1mit118 gnt:mb "3.968933"^^xsd:double .
-gn:B6d2f2geno_d1mit118 gnt:mbMm8 "3.959096"^^xsd:double .
-gn:B6d2f2geno_d1mit118 gnt:mb2016 "3.959014"^^xsd:double .
-gn:B6d2f2geno_d1mit118 gnt:hasSequence "TAATACGACTCNCTATAGGGCGAATTGAGGCCCTCTAGATGCATGCTCGANCGGCCGCCAGTGTGCTGGAAAGCCAGCCTGGNCTACAGAGCTCAAGAGACCACATGTGATACTTGCCTTTCTGAGTCTAACATATATAGAATGATCTAATGGTCTCTAATCACACACTTTTTTTTGTGAATGAAACTTATTAAGAGTTTTATATTTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGTGTCTCTGTGTGTGTGT" .
-gn:B6d2f2geno_d1mit118 gnt:hasSource "Mit" .
-gn:B6d2f2geno_d1mit118 gnt:belongsToDataset gn:B6d2f2geno .
-gn:B6d2f2geno_d1mit118 gnt:chrNum "1"^^xsd:int .
-gn:B6d2f2geno_d1mit118 gnt:cM "0.0"^^xsd:int .
+gn:D1mit296 rdf:type gnc:genotype .
+gn:D1mit296 skos:prefLabel "D1Mit296" .
+gn:D1mit296 gnt:chr "1" .
+gn:D1mit296 gnt:mb "9.749729"^^xsd:double .
+gn:D1mit296 gnt:mbMm8 "9.734943"^^xsd:double .
+gn:D1mit296 gnt:mb2016 "9.73981"^^xsd:double .
+gn:D1mit296 gnt:hasSequence "CTTGCATGCCTGCGGNTNCGNACTCTAGAGGATCTCCCTATTATTNTNACATNACTTTNAATTAAAATAATAATCAGATAACTTCAACNNNNTGNNCACTTCTGTCAAGTGGACAGAAATAAACATAGAGCCTAATTATCCTGAATTTNAGAGAAAAGAGTGTGTTTANCACAANAGAACAGTTATAGATCTACACACACACACACACACACACACACACACACATACAGTTTGAAAAATGCATCAGTTGAGACC" .
+gn:D1mit296 gnt:hasSource "Mit" .
+gn:D1mit296 gnt:belongsToSpecies gn:Mus_musculus .
+gn:D1mit296 gnt:chrNum "1"^^xsd:int .
 ```
 
diff --git a/rdf-documentation/dump-phenotype.md b/rdf-documentation/dump-phenotype.md
index dc9b6dd..c9436a3 100644
--- a/rdf-documentation/dump-phenotype.md
+++ b/rdf-documentation/dump-phenotype.md
@@ -60,28 +60,25 @@ gn:B6d2f2_psupublish gnt:belongsToInbredSet gn:B6d2f2-psupublish .
 The following SQL query was executed:
 
 ```sql
-SELECT CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '_')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation)) AS abbrev, IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation) AS PhenotypeName, CONCAT(InbredSet.Name, '_', PublishXRef.Id) AS phenotypeAltName, Phenotype.Post_publication_description, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Owner, IFNULL(PublishXRef.mean, '') AS mean, PublishXRef.Locus, IFNULL(PublishXRef.LRS, '') AS lrs, IFNULL(PublishXRef.additive, '') AS additive, PublishXRef.Sequence, InfoFiles.InfoPageName, IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT)) AS pmid, Publication.Id FROM Phenotype LEFT JOIN PublishXRef ON Phenotype.Id = PublishXRef.PhenotypeId LEFT JOIN Publication ON Publication.Id = PublishXRef.PublicationId LEFT JOIN InbredSet ON InbredSet.InbredSetId = PublishXRef.InbredSetId LEFT JOIN PublishFreeze ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = PublishFreeze.Name WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND PublishFreeze.Id IS NOT NULL
+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:Abbrev -> rdf:type -> gnc:phenotype 
-gn:Abbrev -> skos:prefLabel -> PhenotypeName 
-gn:Abbrev -> skos:altLabel -> phenotypeAltName 
-gn:Abbrev -> dct:description -> PhenotypePost_publication_description 
-gn:Abbrev -> gnt:abbreviation -> Phenotype(Post_publication_abbreviation) 
-gn:Abbrev -> gnt:labCode -> Phenotype(Lab_code) 
-gn:Abbrev -> gnt:submitter -> PhenotypeSubmitter 
-gn:Abbrev -> dct:contributor -> PhenotypeOwner 
-gn:Abbrev -> gnt:mean -> "mean"^^xsd:double 
-gn:Abbrev -> gnt:locus -> PublishXRef(Locus) 
-gn:Abbrev -> gnt:LRS -> "lrs"^^xsd:double 
-gn:Abbrev -> gnt:additive -> "additive"^^xsd:double 
-gn:Abbrev -> gnt:sequence -> "PublishXRef(Sequence)"^^xsd:integer 
-gn:Abbrev -> gnt:belongsToDataset -> gn:Infofiles_infopagename_ 
-gn:Abbrev -> dct:isReferencedBy -> pubmed:pmid 
-gn:Abbrev -> dct:contributor -> PhenotypeOwner 
+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:
 
@@ -99,9 +96,9 @@ PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
 
 SELECT * WHERE { 
     ?s rdf:type gnc:phenotype .
-    ?s skos:prefLabel "CBLWT2" .
-    ?s skos:altLabel "BXD_10001" .
+    ?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 .
 }
 ```
@@ -109,18 +106,16 @@ SELECT * WHERE {
 Expected Result:
 
 ```rdf
-gn:Bxdpublish_cblwt2 rdf:type gnc:phenotype .
-gn:Bxdpublish_cblwt2 skos:prefLabel "CBLWT2" .
-gn:Bxdpublish_cblwt2 skos:altLabel "BXD_10001" .
-gn:Bxdpublish_cblwt2 dct:description "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" .
-gn:Bxdpublish_cblwt2 gnt:abbreviation "CBLWT2" .
-gn:Bxdpublish_cblwt2 gnt:submitter "robwilliams" .
-gn:Bxdpublish_cblwt2 gnt:mean "52.13529418496525"^^xsd:double .
-gn:Bxdpublish_cblwt2 gnt:locus "rs48756159" .
-gn:Bxdpublish_cblwt2 gnt:LRS "13.4974911471087"^^xsd:double .
-gn:Bxdpublish_cblwt2 gnt:additive "2.39444435069444"^^xsd:double .
-gn:Bxdpublish_cblwt2 gnt:sequence "1"^^xsd:integer .
-gn:Bxdpublish_cblwt2 gnt:belongsToDataset gn:Bxdpublish .
-gn:Bxdpublish_cblwt2 dct:isReferencedBy pubmed:11438585 .
+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 .
 ```
 
diff --git a/rdf-documentation/dump-probeset-summary-stats.md b/rdf-documentation/dump-probeset-summary-stats.md
index 55771ab..422513b 100644
--- a/rdf-documentation/dump-probeset-summary-stats.md
+++ b/rdf-documentation/dump-probeset-summary-stats.md
@@ -29,6 +29,8 @@ Here's an example query:
 PREFIX gn: <http://genenetwork.org/id/> 
 PREFIX gnc: <http://genenetwork.org/category/> 
 PREFIX gnt: <http://genenetwork.org/id/> 
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#> 
+PREFIX owl: <http://www.w3.org/2002/07/owl#> 
 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#> 
diff --git a/rdf-documentation/dump-species-metadata.md b/rdf-documentation/dump-species-metadata.md
index 495905a..160cf44 100644
--- a/rdf-documentation/dump-species-metadata.md
+++ b/rdf-documentation/dump-species-metadata.md
@@ -18,10 +18,10 @@ gn:Inbredset_name -> gnt:geneticType -> InbredSet(GeneticType)
 gn:Inbredset_name -> gnt:family -> InbredSet(Family) 
 gn:Inbredset_name -> gnt:mappingMethod -> MappingMethod(Name) 
 gn:Inbredset_name -> gnt:code -> InbredSet(InbredSetCode) 
-gn:Inbredset_name -> gnt:species -> gn:Species_fullname 
+gn:Inbredset_name -> gnt:belongsToSpecies -> gn:Species_fullname 
 gn:Inbredset_name -> gnt:genotype -> genotypeP 
 gn:Inbredset_name -> gnt:phenotype -> phenotypeP 
-gn:Inbredset_name -> gnt:molecularTrait -> gn:tissue_moleculartrait 
+gn:Inbredset_name -> gnt:hasTissue -> gn:tissue_moleculartrait 
 ```
 Here's an example query:
 
@@ -53,133 +53,133 @@ gn:Bxd gnt:geneticType "riset" .
 gn:Bxd gnt:family "Reference Populations (replicate average, SE, N)" .
 gn:Bxd gnt:mappingMethod "BXD" .
 gn:Bxd gnt:code "BXD" .
-gn:Bxd gnt:species gn:Mus_musculus .
+gn:Bxd gnt:belongsToSpecies gn:Mus_musculus .
 gn:Bxd gnt:genotype "Traits and Cofactors" .
 gn:Bxd gnt:phenotype "DNA Markers and SNPs" .
-gn:Bxd gnt:molecularTrait gn:tissue_a1c .
-gn:Bxd gnt:molecularTrait gn:tissue_acc .
-gn:Bxd gnt:molecularTrait gn:tissue_adr .
-gn:Bxd gnt:molecularTrait gn:tissue_amg .
-gn:Bxd gnt:molecularTrait gn:tissue_bebv .
-gn:Bxd gnt:molecularTrait gn:tissue_bla .
-gn:Bxd gnt:molecularTrait gn:tissue_brmet .
-gn:Bxd gnt:molecularTrait gn:tissue_brmicrorna .
-gn:Bxd gnt:molecularTrait gn:tissue_brn .
-gn:Bxd gnt:molecularTrait gn:tissue_cart .
-gn:Bxd gnt:molecularTrait gn:tissue_cb .
-gn:Bxd gnt:molecularTrait gn:tissue_cbc .
-gn:Bxd gnt:molecularTrait gn:tissue_ctx .
-gn:Bxd gnt:molecularTrait gn:tissue_dfc .
-gn:Bxd gnt:molecularTrait gn:tissue_drg .
-gn:Bxd gnt:molecularTrait gn:tissue_ec .
-gn:Bxd gnt:molecularTrait gn:tissue_emb .
-gn:Bxd gnt:molecularTrait gn:tissue_eye .
-gn:Bxd gnt:molecularTrait gn:tissue_fat .
-gn:Bxd gnt:molecularTrait gn:tissue_fecmet .
-gn:Bxd gnt:molecularTrait gn:tissue_femur .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_aor .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_atr .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_blo .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_bonm .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_bre .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_cau .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_cer .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_cerv .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_cml .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_col .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_colsig .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_cor .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_ebv .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_eso .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_esogas .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_fal .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_fro .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_muc .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_ner .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_pan .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_put .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_sintter .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_skinex .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_skisex .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_sn .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_sto .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_sub .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_tf .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_thy .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_tib .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_vag .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_ven .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_vis .
-gn:Bxd gnt:molecularTrait gn:tissue_gtex_who .
-gn:Bxd gnt:molecularTrait gn:tissue_gut .
-gn:Bxd gnt:molecularTrait gn:tissue_hea .
-gn:Bxd gnt:molecularTrait gn:tissue_hip .
-gn:Bxd gnt:molecularTrait gn:tissue_hippreccel .
-gn:Bxd gnt:molecularTrait gn:tissue_hipprot .
-gn:Bxd gnt:molecularTrait gn:tissue_hip_mirna .
-gn:Bxd gnt:molecularTrait gn:tissue_hsc .
-gn:Bxd gnt:molecularTrait gn:tissue_hyp .
-gn:Bxd gnt:molecularTrait gn:tissue_ifra_ctx .
-gn:Bxd gnt:molecularTrait gn:tissue_ipc .
-gn:Bxd gnt:molecularTrait gn:tissue_isl .
-gn:Bxd gnt:molecularTrait gn:tissue_itc .
-gn:Bxd gnt:molecularTrait gn:tissue_kid .
-gn:Bxd gnt:molecularTrait gn:tissue_lathab .
-gn:Bxd gnt:molecularTrait gn:tissue_lcm_brreg .
-gn:Bxd gnt:molecularTrait gn:tissue_leaf .
-gn:Bxd gnt:molecularTrait gn:tissue_liv .
-gn:Bxd gnt:molecularTrait gn:tissue_livdnam .
-gn:Bxd gnt:molecularTrait gn:tissue_livmet .
-gn:Bxd gnt:molecularTrait gn:tissue_livpro .
-gn:Bxd gnt:molecularTrait gn:tissue_lung .
-gn:Bxd gnt:molecularTrait gn:tissue_m1c .
-gn:Bxd gnt:molecularTrait gn:tissue_mam .
-gn:Bxd gnt:molecularTrait gn:tissue_mamtum .
-gn:Bxd gnt:molecularTrait gn:tissue_mbr .
-gn:Bxd gnt:molecularTrait gn:tissue_md .
-gn:Bxd gnt:molecularTrait gn:tissue_methyl .
-gn:Bxd gnt:molecularTrait gn:tissue_mfc .
-gn:Bxd gnt:molecularTrait gn:tissue_musmet .
-gn:Bxd gnt:molecularTrait gn:tissue_nac .
-gn:Bxd gnt:molecularTrait gn:tissue_nbcb .
-gn:Bxd gnt:molecularTrait gn:tissue_neutrophil .
-gn:Bxd gnt:molecularTrait gn:tissue_ocl .
-gn:Bxd gnt:molecularTrait gn:tissue_ofc .
-gn:Bxd gnt:molecularTrait gn:tissue_of_ctx .
-gn:Bxd gnt:molecularTrait gn:tissue_ova .
-gn:Bxd gnt:molecularTrait gn:tissue_pcg .
-gn:Bxd gnt:molecularTrait gn:tissue_pfc .
-gn:Bxd gnt:molecularTrait gn:tissue_pg .
-gn:Bxd gnt:molecularTrait gn:tissue_pln .
-gn:Bxd gnt:molecularTrait gn:tissue_pl_ctx .
-gn:Bxd gnt:molecularTrait gn:tissue_pons .
-gn:Bxd gnt:molecularTrait gn:tissue_pro .
-gn:Bxd gnt:molecularTrait gn:tissue_ret .
-gn:Bxd gnt:molecularTrait gn:tissue_ret_mirna .
-gn:Bxd gnt:molecularTrait gn:tissue_ret_sc-rna-s .
-gn:Bxd gnt:molecularTrait gn:tissue_s1c .
-gn:Bxd gnt:molecularTrait gn:tissue_sal .
-gn:Bxd gnt:molecularTrait gn:tissue_sg .
-gn:Bxd gnt:molecularTrait gn:tissue_skm .
-gn:Bxd gnt:molecularTrait gn:tissue_spi .
-gn:Bxd gnt:molecularTrait gn:tissue_spl .
-gn:Bxd gnt:molecularTrait gn:tissue_stc .
-gn:Bxd gnt:molecularTrait gn:tissue_str .
-gn:Bxd gnt:molecularTrait gn:tissue_tc .
-gn:Bxd gnt:molecularTrait gn:tissue_tes .
-gn:Bxd gnt:molecularTrait gn:tissue_tes_dna_met .
-gn:Bxd gnt:molecularTrait gn:tissue_thelp .
-gn:Bxd gnt:molecularTrait gn:tissue_thy .
-gn:Bxd gnt:molecularTrait gn:tissue_treg .
-gn:Bxd gnt:molecularTrait gn:tissue_ute .
-gn:Bxd gnt:molecularTrait gn:tissue_v1 .
-gn:Bxd gnt:molecularTrait gn:tissue_vfc .
-gn:Bxd gnt:molecularTrait gn:tissue_vta .
-gn:Bxd gnt:molecularTrait gn:tissue_wb .
-gn:Bxd gnt:molecularTrait gn:tissue_wbc .
-gn:Bxd gnt:molecularTrait gn:tissue_wbpr .
-gn:Bxd gnt:molecularTrait gn:tissue_wfat .
-gn:Bxd gnt:molecularTrait gn:tissue_wfat_pro .
+gn:Bxd gnt:hasTissue gn:tissue_a1c .
+gn:Bxd gnt:hasTissue gn:tissue_acc .
+gn:Bxd gnt:hasTissue gn:tissue_adr .
+gn:Bxd gnt:hasTissue gn:tissue_amg .
+gn:Bxd gnt:hasTissue gn:tissue_bebv .
+gn:Bxd gnt:hasTissue gn:tissue_bla .
+gn:Bxd gnt:hasTissue gn:tissue_brmet .
+gn:Bxd gnt:hasTissue gn:tissue_brmicrorna .
+gn:Bxd gnt:hasTissue gn:tissue_brn .
+gn:Bxd gnt:hasTissue gn:tissue_cart .
+gn:Bxd gnt:hasTissue gn:tissue_cb .
+gn:Bxd gnt:hasTissue gn:tissue_cbc .
+gn:Bxd gnt:hasTissue gn:tissue_ctx .
+gn:Bxd gnt:hasTissue gn:tissue_dfc .
+gn:Bxd gnt:hasTissue gn:tissue_drg .
+gn:Bxd gnt:hasTissue gn:tissue_ec .
+gn:Bxd gnt:hasTissue gn:tissue_emb .
+gn:Bxd gnt:hasTissue gn:tissue_eye .
+gn:Bxd gnt:hasTissue gn:tissue_fat .
+gn:Bxd gnt:hasTissue gn:tissue_fecmet .
+gn:Bxd gnt:hasTissue gn:tissue_femur .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_aor .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_atr .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_blo .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_bonm .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_bre .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_cau .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_cer .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_cerv .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_cml .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_col .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_colsig .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_cor .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_ebv .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_eso .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_esogas .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_fal .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_fro .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_muc .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_ner .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_pan .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_put .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_sintter .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_skinex .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_skisex .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_sn .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_sto .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_sub .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_tf .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_thy .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_tib .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_vag .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_ven .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_vis .
+gn:Bxd gnt:hasTissue gn:tissue_gtex_who .
+gn:Bxd gnt:hasTissue gn:tissue_gut .
+gn:Bxd gnt:hasTissue gn:tissue_hea .
+gn:Bxd gnt:hasTissue gn:tissue_hip .
+gn:Bxd gnt:hasTissue gn:tissue_hippreccel .
+gn:Bxd gnt:hasTissue gn:tissue_hipprot .
+gn:Bxd gnt:hasTissue gn:tissue_hip_mirna .
+gn:Bxd gnt:hasTissue gn:tissue_hsc .
+gn:Bxd gnt:hasTissue gn:tissue_hyp .
+gn:Bxd gnt:hasTissue gn:tissue_ifra_ctx .
+gn:Bxd gnt:hasTissue gn:tissue_ipc .
+gn:Bxd gnt:hasTissue gn:tissue_isl .
+gn:Bxd gnt:hasTissue gn:tissue_itc .
+gn:Bxd gnt:hasTissue gn:tissue_kid .
+gn:Bxd gnt:hasTissue gn:tissue_lathab .
+gn:Bxd gnt:hasTissue gn:tissue_lcm_brreg .
+gn:Bxd gnt:hasTissue gn:tissue_leaf .
+gn:Bxd gnt:hasTissue gn:tissue_liv .
+gn:Bxd gnt:hasTissue gn:tissue_livdnam .
+gn:Bxd gnt:hasTissue gn:tissue_livmet .
+gn:Bxd gnt:hasTissue gn:tissue_livpro .
+gn:Bxd gnt:hasTissue gn:tissue_lung .
+gn:Bxd gnt:hasTissue gn:tissue_m1c .
+gn:Bxd gnt:hasTissue gn:tissue_mam .
+gn:Bxd gnt:hasTissue gn:tissue_mamtum .
+gn:Bxd gnt:hasTissue gn:tissue_mbr .
+gn:Bxd gnt:hasTissue gn:tissue_md .
+gn:Bxd gnt:hasTissue gn:tissue_methyl .
+gn:Bxd gnt:hasTissue gn:tissue_mfc .
+gn:Bxd gnt:hasTissue gn:tissue_musmet .
+gn:Bxd gnt:hasTissue gn:tissue_nac .
+gn:Bxd gnt:hasTissue gn:tissue_nbcb .
+gn:Bxd gnt:hasTissue gn:tissue_neutrophil .
+gn:Bxd gnt:hasTissue gn:tissue_ocl .
+gn:Bxd gnt:hasTissue gn:tissue_ofc .
+gn:Bxd gnt:hasTissue gn:tissue_of_ctx .
+gn:Bxd gnt:hasTissue gn:tissue_ova .
+gn:Bxd gnt:hasTissue gn:tissue_pcg .
+gn:Bxd gnt:hasTissue gn:tissue_pfc .
+gn:Bxd gnt:hasTissue gn:tissue_pg .
+gn:Bxd gnt:hasTissue gn:tissue_pln .
+gn:Bxd gnt:hasTissue gn:tissue_pl_ctx .
+gn:Bxd gnt:hasTissue gn:tissue_pons .
+gn:Bxd gnt:hasTissue gn:tissue_pro .
+gn:Bxd gnt:hasTissue gn:tissue_ret .
+gn:Bxd gnt:hasTissue gn:tissue_ret_mirna .
+gn:Bxd gnt:hasTissue gn:tissue_ret_sc-rna-s .
+gn:Bxd gnt:hasTissue gn:tissue_s1c .
+gn:Bxd gnt:hasTissue gn:tissue_sal .
+gn:Bxd gnt:hasTissue gn:tissue_sg .
+gn:Bxd gnt:hasTissue gn:tissue_skm .
+gn:Bxd gnt:hasTissue gn:tissue_spi .
+gn:Bxd gnt:hasTissue gn:tissue_spl .
+gn:Bxd gnt:hasTissue gn:tissue_stc .
+gn:Bxd gnt:hasTissue gn:tissue_str .
+gn:Bxd gnt:hasTissue gn:tissue_tc .
+gn:Bxd gnt:hasTissue gn:tissue_tes .
+gn:Bxd gnt:hasTissue gn:tissue_tes_dna_met .
+gn:Bxd gnt:hasTissue gn:tissue_thelp .
+gn:Bxd gnt:hasTissue gn:tissue_thy .
+gn:Bxd gnt:hasTissue gn:tissue_treg .
+gn:Bxd gnt:hasTissue gn:tissue_ute .
+gn:Bxd gnt:hasTissue gn:tissue_v1 .
+gn:Bxd gnt:hasTissue gn:tissue_vfc .
+gn:Bxd gnt:hasTissue gn:tissue_vta .
+gn:Bxd gnt:hasTissue gn:tissue_wb .
+gn:Bxd gnt:hasTissue gn:tissue_wbc .
+gn:Bxd gnt:hasTissue gn:tissue_wbpr .
+gn:Bxd gnt:hasTissue gn:tissue_wfat .
+gn:Bxd gnt:hasTissue gn:tissue_wfat_pro .
 ```
 
 
@@ -251,7 +251,7 @@ The above query results to triples that have the form:
 
 ```text
 gn:Strain_name_ -> rdf:type -> gnc:strain 
-gn:Strain_name_ -> gnt:species -> gn:Species_fullname 
+gn:Strain_name_ -> gnt:belongsToSpecies -> gn:Species_fullname 
 gn:Strain_name_ -> rdfs:label -> StrainName 
 gn:Strain_name_ -> rdfs:label -> Name2 
 gn:Strain_name_ -> gnt:alias -> Alias 
@@ -271,7 +271,7 @@ PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
 
 SELECT * WHERE { 
     ?s rdf:type gnc:strain .
-    ?s gnt:species gn:Mus_musculus .
+    ?s gnt:belongsToSpecies gn:Mus_musculus .
     ?s rdfs:label "B6D2F1" .
     ?s ?p ?o .
 }
@@ -281,7 +281,7 @@ Expected Result:
 
 ```rdf
 gn:B6d2f1 rdf:type gnc:strain .
-gn:B6d2f1 gnt:species gn:Mus_musculus .
+gn:B6d2f1 gnt:belongsToSpecies gn:Mus_musculus .
 gn:B6d2f1 rdfs:label "B6D2F1" .
 ```