Update docs for dump-species-metadata

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

1 files changed, 200 insertions, 10 deletions

diff --git a/rdf-documentation/dump-species-metadata.md b/rdf-documentation/dump-species-metadata.md
index 4c0e123..6a3c485 100644
--- a/rdf-documentation/dump-species-metadata.md
+++ b/rdf-documentation/dump-species-metadata.md
@@ -1,19 +1,204 @@
-# Species Metadata## 'dump-species'
+# Species Metadata
+## 'dump-inbred-set'
 
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT InbredSet.Name, InbredSet.FullName, InbredSet.GeneticType, InbredSet.Family, MappingMethod.Name, InbredSet.InbredSetCode, Species.Fullname, IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '') AS genotypeP, IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '') AS phenotypeP, (SELECT GROUP_CONCAT(DISTINCT Tissue.Short_Name SEPARATOR'||') AS MolecularTraits FROM ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species WHERE ProbeFreeze.TissueId = Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id ORDER BY Tissue.Name) AS molecularTrait FROM InbredSet LEFT JOIN Species ON InbredSet.SpeciesId=Species.Id LEFT JOIN MappingMethod ON InbredSet.MappingMethodId=MappingMethod.Id
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:Inbredset_name -> rdf:type -> gnc:inbredSet 
+gn:Inbredset_name -> rdfs:label -> InbredSet(FullName) 
+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:genotype -> genotypeP 
+gn:Inbredset_name -> gnt:phenotype -> phenotypeP 
+gn:Inbredset_name -> gnt:molecularTrait -> gn:tissue_moleculartrait 
+```
+Here's an example query:
+
+```sparql
+PREFIX gn: <http://genenetwork.org/id/> 
+PREFIX gnc: <http://genenetwork.org/category/> 
+PREFIX owl: <http://www.w3.org/2002/07/owl#> 
+PREFIX gnt: <http://genenetwork.org/term/> 
+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 taxon: <http://purl.uniprot.org/taxonomy/> 
+
+SELECT * WHERE { 
+    ?s rdf:type gnc:inbredSet .
+    ?s rdfs:label "BXD Family" .
+    ?s gnt:geneticType "riset" .
+    ?s gnt:family "Reference Populations (replicate average, SE, N)" .
+    ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:Bxd rdf:type gnc:inbredSet .
+gn:Bxd rdfs:label "BXD Family" .
+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: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 .
+```
+
+
+## 'dump-species'
 
 ## Generated Triples:
 
 The following SQL query was executed:
 
 ```sql
-SELECT Species.Fullname, Species.SpeciesName, Species.MenuName, Species.FullName, Species.Family, Species.TaxonomyId FROM Species
+SELECT Species.Fullname, Species.SpeciesName, Species.Name, Species.MenuName, Species.FullName, Species.Family, Species.TaxonomyId FROM Species
 ```
 
 The above query results to triples that have the form:
 
 ```text
 gn:Species_fullname -> rdf:type -> gnc:species 
-gn:Species_fullname -> gnt:name -> Species(SpeciesName) 
+gn:Species_fullname -> skos:label -> Species(SpeciesName) 
+gn:Species_fullname -> skos:altLabel -> Species(Name) 
 gn:Species_fullname -> rdfs:label -> Species(MenuName) 
 gn:Species_fullname -> gnt:binomialName -> Species(FullName) 
 gn:Species_fullname -> gnt:family -> Species(Family) 
@@ -26,14 +211,15 @@ PREFIX gn: <http://genenetwork.org/id/>
 PREFIX gnc: <http://genenetwork.org/category/> 
 PREFIX owl: <http://www.w3.org/2002/07/owl#> 
 PREFIX gnt: <http://genenetwork.org/term/> 
+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 taxon: <http://purl.uniprot.org/taxonomy/> 
 
 SELECT * WHERE { 
     ?s rdf:type gnc:species .
-    ?s gnt:name "Mouse" .
-    ?s rdfs:label "Mouse (Mus musculus, mm10)" .
+    ?s skos:label "Mouse" .
+    ?s skos:altLabel "mouse" .
     ?s ?p ?o .
 }
 ```
@@ -42,22 +228,23 @@ Expected Result:
 
 ```rdf
 gn:Mus_musculus rdf:type gnc:species .
-gn:Mus_musculus gnt:name "Mouse" .
+gn:Mus_musculus skos:label "Mouse" .
+gn:Mus_musculus skos:altLabel "mouse" .
 gn:Mus_musculus rdfs:label "Mouse (Mus musculus, mm10)" .
 gn:Mus_musculus gnt:binomialName "Mus musculus" .
 gn:Mus_musculus gnt:family "Vertebrates" .
 gn:Mus_musculus gnt:organism taxon:10090 .
 ```
 
-## 'dump-strain'
 
+## 'dump-strain'
 
 ## Generated Triples:
 
 The following SQL query was executed:
 
 ```sql
-SELECT CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARCHAR(15000)) AS StrainName, Species.Fullname, Strain.Name, IF ((Strain.Name2 != Strain.Name), Strain.Name2, '') AS Name2, IF ((Strain.Alias != Strain.Name), Strain.Alias, '') AS Alias, IF ((Strain.Symbol != Strain.Name), Strain.Alias, '') AS Symbol FROM Strain LEFT JOIN Species ON Strain.SpeciesId = Species.SpeciesId
+SELECT CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARCHAR(15000)) AS StrainName, Species.Fullname, Strain.Name, IF ((Strain.Name2 != Strain.Name), Strain.Name2, '') AS Name2, IF ((Strain.Alias != Strain.Name), Strain.Alias, '') AS Alias, IF ((Strain.Symbol != Strain.Name), Strain.Symbol, '') AS Symbol FROM Strain LEFT JOIN Species ON Strain.SpeciesId = Species.SpeciesId
 ```
 
 The above query results to triples that have the form:
@@ -77,6 +264,7 @@ PREFIX gn: <http://genenetwork.org/id/>
 PREFIX gnc: <http://genenetwork.org/category/> 
 PREFIX owl: <http://www.w3.org/2002/07/owl#> 
 PREFIX gnt: <http://genenetwork.org/term/> 
+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 taxon: <http://purl.uniprot.org/taxonomy/> 
@@ -97,8 +285,8 @@ gn:B6d2f1 gnt:species gn:Mus_musculus .
 gn:B6d2f1 rdfs:label "B6D2F1" .
 ```
 
-## 'dump-mapping-method'
 
+## 'dump-mapping-method'
 
 ## Generated Triples:
 
@@ -121,6 +309,7 @@ PREFIX gn: <http://genenetwork.org/id/>
 PREFIX gnc: <http://genenetwork.org/category/> 
 PREFIX owl: <http://www.w3.org/2002/07/owl#> 
 PREFIX gnt: <http://genenetwork.org/term/> 
+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 taxon: <http://purl.uniprot.org/taxonomy/> 
@@ -139,8 +328,8 @@ gn:mappingMethod_qtlreaper rdf:type gnc:mappingMethod .
 gn:mappingMethod_qtlreaper rdfs:label "qtlreaper" .
 ```
 
-## 'dump-avg-method'
 
+## 'dump-avg-method'
 
 ## Generated Triples:
 
@@ -163,6 +352,7 @@ PREFIX gn: <http://genenetwork.org/id/>
 PREFIX gnc: <http://genenetwork.org/category/> 
 PREFIX owl: <http://www.w3.org/2002/07/owl#> 
 PREFIX gnt: <http://genenetwork.org/term/> 
+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 taxon: <http://purl.uniprot.org/taxonomy/>