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diff --git a/rdf-documentation/species-metadata.md b/rdf-documentation/species-metadata.md new file mode 100644 index 0000000..79e897c --- /dev/null +++ b/rdf-documentation/species-metadata.md @@ -0,0 +1,375 @@ +# Species Metadata +## 'inbred-set' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT InbredSet.Name, InbredSet.FullName, InbredSet.Name, 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:setInbredset_name -> rdf:type -> gnc:set +gn:setInbredset_name -> rdfs:label -> InbredSet(FullName) +gn:setInbredset_name -> skos:altLabel -> InbredSet(Name) +gn:setInbredset_name -> gnt:geneticType -> InbredSet(GeneticType) +gn:setInbredset_name -> gnt:family -> InbredSet(Family) +gn:setInbredset_name -> gnt:mappingMethod -> MappingMethod(Name) +gn:setInbredset_name -> gnt:code -> InbredSet(InbredSetCode) +gn:setInbredset_name -> gnt:belongsToSpecies -> gn:Species_fullname +gn:setInbredset_name -> gnt:genotype -> genotypeP +gn:setInbredset_name -> gnt:phenotype -> phenotypeP +gn:setInbredset_name -> gnt:hasTissue -> 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:set . + ?s rdfs:label "BXD Family" . + ?s skos:altLabel "BXD" . + ?s gnt:geneticType "riset" . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:setBxd rdf:type gnc:set . +gn:setBxd rdfs:label "BXD Family" . +gn:setBxd skos:altLabel "BXD" . +gn:setBxd gnt:geneticType "riset" . +gn:setBxd gnt:family "Reference Populations (replicate average, SE, N)" . +gn:setBxd gnt:mappingMethod "BXD" . +gn:setBxd gnt:code "BXD" . +gn:setBxd gnt:belongsToSpecies gn:Mus_musculus . +gn:setBxd gnt:genotype "Traits and Cofactors" . +gn:setBxd gnt:phenotype "DNA Markers and SNPs" . +gn:setBxd gnt:hasTissue gn:tissue_a1c . +gn:setBxd gnt:hasTissue gn:tissue_acc . +gn:setBxd gnt:hasTissue gn:tissue_adr . +gn:setBxd gnt:hasTissue gn:tissue_amg . +gn:setBxd gnt:hasTissue gn:tissue_bebv . +gn:setBxd gnt:hasTissue gn:tissue_bla . +gn:setBxd gnt:hasTissue gn:tissue_brmet . +gn:setBxd gnt:hasTissue gn:tissue_brmicrorna . +gn:setBxd gnt:hasTissue gn:tissue_brn . +gn:setBxd gnt:hasTissue gn:tissue_cart . +gn:setBxd gnt:hasTissue gn:tissue_cb . +gn:setBxd gnt:hasTissue gn:tissue_cbc . +gn:setBxd gnt:hasTissue gn:tissue_ctx . +gn:setBxd gnt:hasTissue gn:tissue_dfc . +gn:setBxd gnt:hasTissue gn:tissue_drg . +gn:setBxd gnt:hasTissue gn:tissue_ec . +gn:setBxd gnt:hasTissue gn:tissue_emb . +gn:setBxd gnt:hasTissue gn:tissue_eye . +gn:setBxd gnt:hasTissue gn:tissue_fat . +gn:setBxd gnt:hasTissue gn:tissue_fecmet . +gn:setBxd gnt:hasTissue gn:tissue_femur . +gn:setBxd gnt:hasTissue gn:tissue_gtex_aor . +gn:setBxd gnt:hasTissue gn:tissue_gtex_atr . +gn:setBxd gnt:hasTissue gn:tissue_gtex_blo . +gn:setBxd gnt:hasTissue gn:tissue_gtex_bonm . +gn:setBxd gnt:hasTissue gn:tissue_gtex_bre . +gn:setBxd gnt:hasTissue gn:tissue_gtex_cau . +gn:setBxd gnt:hasTissue gn:tissue_gtex_cer . +gn:setBxd gnt:hasTissue gn:tissue_gtex_cerv . +gn:setBxd gnt:hasTissue gn:tissue_gtex_cml . +gn:setBxd gnt:hasTissue gn:tissue_gtex_col . +gn:setBxd gnt:hasTissue gn:tissue_gtex_colsig . +gn:setBxd gnt:hasTissue gn:tissue_gtex_cor . +gn:setBxd gnt:hasTissue gn:tissue_gtex_ebv . +gn:setBxd gnt:hasTissue gn:tissue_gtex_eso . +gn:setBxd gnt:hasTissue gn:tissue_gtex_esogas . +gn:setBxd gnt:hasTissue gn:tissue_gtex_fal . +gn:setBxd gnt:hasTissue gn:tissue_gtex_fro . +gn:setBxd gnt:hasTissue gn:tissue_gtex_muc . +gn:setBxd gnt:hasTissue gn:tissue_gtex_ner . +gn:setBxd gnt:hasTissue gn:tissue_gtex_pan . +gn:setBxd gnt:hasTissue gn:tissue_gtex_put . +gn:setBxd gnt:hasTissue gn:tissue_gtex_sintter . +gn:setBxd gnt:hasTissue gn:tissue_gtex_skinex . +gn:setBxd gnt:hasTissue gn:tissue_gtex_skisex . +gn:setBxd gnt:hasTissue gn:tissue_gtex_sn . +gn:setBxd gnt:hasTissue gn:tissue_gtex_sto . +gn:setBxd gnt:hasTissue gn:tissue_gtex_sub . +gn:setBxd gnt:hasTissue gn:tissue_gtex_tf . +gn:setBxd gnt:hasTissue gn:tissue_gtex_thy . +gn:setBxd gnt:hasTissue gn:tissue_gtex_tib . +gn:setBxd gnt:hasTissue gn:tissue_gtex_vag . +gn:setBxd gnt:hasTissue gn:tissue_gtex_ven . +gn:setBxd gnt:hasTissue gn:tissue_gtex_vis . +gn:setBxd gnt:hasTissue gn:tissue_gtex_who . +gn:setBxd gnt:hasTissue gn:tissue_gut . +gn:setBxd gnt:hasTissue gn:tissue_hea . +gn:setBxd gnt:hasTissue gn:tissue_hip . +gn:setBxd gnt:hasTissue gn:tissue_hippreccel . +gn:setBxd gnt:hasTissue gn:tissue_hipprot . +gn:setBxd gnt:hasTissue gn:tissue_hip_mirna . +gn:setBxd gnt:hasTissue gn:tissue_hsc . +gn:setBxd gnt:hasTissue gn:tissue_hyp . +gn:setBxd gnt:hasTissue gn:tissue_ifra_ctx . +gn:setBxd gnt:hasTissue gn:tissue_ipc . +gn:setBxd gnt:hasTissue gn:tissue_isl . +gn:setBxd gnt:hasTissue gn:tissue_itc . +gn:setBxd gnt:hasTissue gn:tissue_kid . +gn:setBxd gnt:hasTissue gn:tissue_lathab . +gn:setBxd gnt:hasTissue gn:tissue_lcm_brreg . +gn:setBxd gnt:hasTissue gn:tissue_leaf . +gn:setBxd gnt:hasTissue gn:tissue_liv . +gn:setBxd gnt:hasTissue gn:tissue_livdnam . +gn:setBxd gnt:hasTissue gn:tissue_livmet . +gn:setBxd gnt:hasTissue gn:tissue_livpro . +gn:setBxd gnt:hasTissue gn:tissue_lung . +gn:setBxd gnt:hasTissue gn:tissue_m1c . +gn:setBxd gnt:hasTissue gn:tissue_mam . +gn:setBxd gnt:hasTissue gn:tissue_mamtum . +gn:setBxd gnt:hasTissue gn:tissue_mbr . +gn:setBxd gnt:hasTissue gn:tissue_md . +gn:setBxd gnt:hasTissue gn:tissue_methyl . +gn:setBxd gnt:hasTissue gn:tissue_mfc . +gn:setBxd gnt:hasTissue gn:tissue_musmet . +gn:setBxd gnt:hasTissue gn:tissue_nac . +gn:setBxd gnt:hasTissue gn:tissue_nbcb . +gn:setBxd gnt:hasTissue gn:tissue_neutrophil . +gn:setBxd gnt:hasTissue gn:tissue_ocl . +gn:setBxd gnt:hasTissue gn:tissue_ofc . +gn:setBxd gnt:hasTissue gn:tissue_of_ctx . +gn:setBxd gnt:hasTissue gn:tissue_ova . +gn:setBxd gnt:hasTissue gn:tissue_pcg . +gn:setBxd gnt:hasTissue gn:tissue_pfc . +gn:setBxd gnt:hasTissue gn:tissue_pg . +gn:setBxd gnt:hasTissue gn:tissue_pln . +gn:setBxd gnt:hasTissue gn:tissue_pl_ctx . +gn:setBxd gnt:hasTissue gn:tissue_pons . +gn:setBxd gnt:hasTissue gn:tissue_pro . +gn:setBxd gnt:hasTissue gn:tissue_ret . +gn:setBxd gnt:hasTissue gn:tissue_ret_mirna . +gn:setBxd gnt:hasTissue gn:tissue_ret_sc-rna-s . +gn:setBxd gnt:hasTissue gn:tissue_s1c . +gn:setBxd gnt:hasTissue gn:tissue_sal . +gn:setBxd gnt:hasTissue gn:tissue_sg . +gn:setBxd gnt:hasTissue gn:tissue_skm . +gn:setBxd gnt:hasTissue gn:tissue_spi . +gn:setBxd gnt:hasTissue gn:tissue_spl . +gn:setBxd gnt:hasTissue gn:tissue_stc . +gn:setBxd gnt:hasTissue gn:tissue_str . +gn:setBxd gnt:hasTissue gn:tissue_tc . +gn:setBxd gnt:hasTissue gn:tissue_tes . +gn:setBxd gnt:hasTissue gn:tissue_tes_dna_met . +gn:setBxd gnt:hasTissue gn:tissue_thelp . +gn:setBxd gnt:hasTissue gn:tissue_thy . +gn:setBxd gnt:hasTissue gn:tissue_treg . +gn:setBxd gnt:hasTissue gn:tissue_ute . +gn:setBxd gnt:hasTissue gn:tissue_v1 . +gn:setBxd gnt:hasTissue gn:tissue_vfc . +gn:setBxd gnt:hasTissue gn:tissue_vta . +gn:setBxd gnt:hasTissue gn:tissue_wb . +gn:setBxd gnt:hasTissue gn:tissue_wbc . +gn:setBxd gnt:hasTissue gn:tissue_wbpr . +gn:setBxd gnt:hasTissue gn:tissue_wfat . +gn:setBxd gnt:hasTissue gn:tissue_wfat_pro . +``` + + +## 'species' + +## Generated Triples: + +The following SQL query was executed: + +```sql +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 -> 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) +gn:Species_fullname -> gnt:organism -> taxon:Species(TaxonomyId) +``` +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:species . + ?s skos:label "Mouse" . + ?s skos:altLabel "mouse" . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:Mus_musculus rdf:type gnc:species . +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 . +``` + + +## 'strain' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT Strain.Name, 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: + +```text +gn:Strain_name_ -> rdf:type -> gnc:strain +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 +gn:Strain_name_ -> gnt:symbol -> Symbol +``` +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:strain . + ?s gnt:belongsToSpecies gn:Mus_musculus . + ?s rdfs:label "B6D2F1" . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:B6d2f1 rdf:type gnc:strain . +gn:B6d2f1 gnt:belongsToSpecies gn:Mus_musculus . +gn:B6d2f1 rdfs:label "B6D2F1" . +``` + + +## 'mapping-method' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT MappingMethod.Name, MappingMethod.Name FROM MappingMethod +``` + +The above query results to triples that have the form: + +```text +gn:mappingMethod_mappingmethod_name -> rdf:type -> gnc:mappingMethod +gn:mappingMethod_mappingmethod_name -> rdfs:label -> MappingMethod(Name) +``` +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:mappingMethod . + ?s rdfs:label "qtlreaper" . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:mappingMethod_qtlreaper rdf:type gnc:mappingMethod . +gn:mappingMethod_qtlreaper rdfs:label "qtlreaper" . +``` + + +## 'avg-method' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT AvgMethod.Name, AvgMethod.Normalization FROM AvgMethod +``` + +The above query results to triples that have the form: + +```text +gn:avgmethod_avgmethod_name -> rdf:type -> gnc:avgMethod +gn:avgmethod_avgmethod_name -> rdfs:label -> AvgMethod(Normalization) +``` +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:avgMethod . + ?s rdfs:label "MAS5" . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:avgmethod_mas5 rdf:type gnc:avgMethod . +gn:avgmethod_mas5 rdfs:label "MAS5" . +``` + |