diff options
Diffstat (limited to 'rdf-documentation/dump-species-metadata.md')
| -rw-r--r-- | rdf-documentation/dump-species-metadata.md | 373 |
1 files changed, 0 insertions, 373 deletions
diff --git a/rdf-documentation/dump-species-metadata.md b/rdf-documentation/dump-species-metadata.md deleted file mode 100644 index 160cf44..0000000 --- a/rdf-documentation/dump-species-metadata.md +++ /dev/null @@ -1,373 +0,0 @@ -# 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:belongsToSpecies -> gn:Species_fullname -gn:Inbredset_name -> gnt:genotype -> genotypeP -gn:Inbredset_name -> gnt:phenotype -> phenotypeP -gn:Inbredset_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: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:belongsToSpecies gn:Mus_musculus . -gn:Bxd gnt:genotype "Traits and Cofactors" . -gn:Bxd gnt:phenotype "DNA Markers and SNPs" . -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 . -``` - - -## 'dump-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 . -``` - - -## 'dump-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" . -``` - - -## 'dump-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" . -``` - - -## 'dump-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" . -``` - |