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authorMunyoki Kilyungi2023-08-19 14:39:51 +0300
committerMunyoki Kilyungi2023-08-19 14:39:51 +0300
commita390d7a79cc66cbd22618af16431a0d1e51fc0b2 (patch)
treef0d7947feb70bdb58906890fd85829420fa08333 /rdf-documentation
parentbe450b02198f08363986aecfd5227752d2e4ca72 (diff)
downloadgn-docs-a390d7a79cc66cbd22618af16431a0d1e51fc0b2.tar.gz
Update auto-generated docs
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'rdf-documentation')
-rw-r--r--rdf-documentation/dump-genotype.md52
-rw-r--r--rdf-documentation/dump-phenotype.md59
-rw-r--r--rdf-documentation/dump-probeset-summary-stats.md2
-rw-r--r--rdf-documentation/dump-species-metadata.md260
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" .
```