From 0cb6d0eedd2be519b52ff3a9b8fe4a339d427f02 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 31 Jul 2023 17:21:40 +0300 Subject: Update docs for species matadata dump --- rdf-documentation/dump-species-metadata.md | 120 +++++++++++++++-------------- 1 file changed, 63 insertions(+), 57 deletions(-) diff --git a/rdf-documentation/dump-species-metadata.md b/rdf-documentation/dump-species-metadata.md index a35e1b1..4c0e123 100644 --- a/rdf-documentation/dump-species-metadata.md +++ b/rdf-documentation/dump-species-metadata.md @@ -1,5 +1,4 @@ -# Species Metadata -## 'dump-species' +# Species Metadata## 'dump-species' ## Generated Triples: @@ -7,32 +6,34 @@ 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.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 -> gn:species -gn:Species_fullname -> gn-term:name -> Species(SpeciesName) -gn:Species_fullname -> gn-term:displayName -> Species(MenuName) -gn:Species_fullname -> gn-term:binomialName -> Species(FullName) -gn:Species_fullname -> gn-term:family -> Species(Family) -gn:Species_fullname -> gn-term:organism -> taxon:Species(TaxonomyId) +gn:Species_fullname -> rdf:type -> gnc:species +gn:Species_fullname -> gnt:name -> Species(SpeciesName) +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: -PREFIX gn-term: -PREFIX rdf: +PREFIX gnc: +PREFIX owl: +PREFIX gnt: +PREFIX rdf: PREFIX rdfs: PREFIX taxon: -SELECT ?s ?p ?o WHERE { - ?s rdf:type gn:species . - ?s gn-term:name "Mouse" . - ?s gn-term:displayName "Mouse (Mus musculus, mm10)" . +SELECT * WHERE { + ?s rdf:type gnc:species . + ?s gnt:name "Mouse" . + ?s rdfs:label "Mouse (Mus musculus, mm10)" . ?s ?p ?o . } ``` @@ -40,15 +41,14 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn:Mus_musculus rdf:type gn:species . -gn:Mus_musculus gn-term:name "Mouse" . -gn:Mus_musculus gn-term:displayName "Mouse (Mus musculus, mm10)" . -gn:Mus_musculus gn-term:binomialName "Mus musculus" . -gn:Mus_musculus gn-term:family "Vertebrates" . -gn:Mus_musculus gn-term:organism taxon:10090 . +gn:Mus_musculus rdf:type gnc:species . +gn:Mus_musculus gnt:name "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' @@ -57,32 +57,34 @@ gn:Mus_musculus gn-term:organism taxon:10090 . 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, Strain.Name2, Strain.Alias, Strain.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.Alias, '') AS Symbol FROM Strain LEFT JOIN Species ON Strain.SpeciesId = Species.SpeciesId ``` The above query results to triples that have the form: ```text -gn:Strainname -> rdf:type -> gn:strain -gn:Strainname -> gn-term:strainOfSpecies -> gn:Species_fullname -gn:Strainname -> gn-term:name -> StrainName -gn:Strainname -> gn-term:name2 -> StrainName2 -gn:Strainname -> gn-term:alias -> StrainAlias -gn:Strainname -> gn-term:symbol -> Strain(Symbol) +gn:Strainname -> rdf:type -> gnc:strain +gn:Strainname -> gnt:species -> gn:Species_fullname +gn:Strainname -> rdfs:label -> StrainName +gn:Strainname -> rdfs:label -> Name2 +gn:Strainname -> gnt:alias -> Alias +gn:Strainname -> gnt:symbol -> Symbol ``` Here's an example query: ```sparql PREFIX gn: -PREFIX gn-term: -PREFIX rdf: +PREFIX gnc: +PREFIX owl: +PREFIX gnt: +PREFIX rdf: PREFIX rdfs: PREFIX taxon: -SELECT ?s ?p ?o WHERE { - ?s rdf:type gn:strain . - ?s gn-term:strainOfSpecies gn:Mus_musculus . - ?s gn-term:name "B6D2F1" . +SELECT * WHERE { + ?s rdf:type gnc:strain . + ?s gnt:species gn:Mus_musculus . + ?s rdfs:label "B6D2F1" . ?s ?p ?o . } ``` @@ -90,13 +92,11 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn:B6d2f1 rdf:type gn:strain . -gn:B6d2f1 gn-term:strainOfSpecies gn:Mus_musculus . -gn:B6d2f1 gn-term:name "B6D2F1" . -gn:B6d2f1 gn-term:name2 "B6D2F1" . +gn:B6d2f1 rdf:type gnc:strain . +gn:B6d2f1 gnt:species gn:Mus_musculus . +gn:B6d2f1 rdfs:label "B6D2F1" . ``` - ## 'dump-mapping-method' @@ -105,25 +105,29 @@ gn:B6d2f1 gn-term:name2 "B6D2F1" . The following SQL query was executed: ```sql -SELECT MappingMethod.Name FROM MappingMethod +SELECT MappingMethod.Name, MappingMethod.Name FROM MappingMethod ``` The above query results to triples that have the form: ```text -gn:mappingMethod_mappingmethod_name -> rdf:type -> gn:mappingMethod +gn:mappingMethod_mappingmethod_name -> rdf:type -> gnc:mappingMethod +gn:mappingMethod_mappingmethod_name -> rdfs:label -> MappingMethod(Name) ``` Here's an example query: ```sparql PREFIX gn: -PREFIX gn-term: -PREFIX rdf: +PREFIX gnc: +PREFIX owl: +PREFIX gnt: +PREFIX rdf: PREFIX rdfs: PREFIX taxon: -SELECT ?s ?p ?o WHERE { - ?s rdf:type gn:mappingMethod . +SELECT * WHERE { + ?s rdf:type gnc:mappingMethod . + ?s rdfs:label "qtlreaper" . ?s ?p ?o . } ``` @@ -131,10 +135,10 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn:mappingMethod_qtlreaper rdf:type gn:mappingMethod . +gn:mappingMethod_qtlreaper rdf:type gnc:mappingMethod . +gn:mappingMethod_qtlreaper rdfs:label "qtlreaper" . ``` - ## 'dump-avg-method' @@ -149,21 +153,23 @@ SELECT AvgMethod.Name, AvgMethod.Normalization FROM AvgMethod The above query results to triples that have the form: ```text -gn:avgmethod_avgmethod_name -> rdf:type -> gn:avgMethod -gn:avgmethod_avgmethod_name -> gn-term:normalization -> AvgMethod(Normalization) +gn:avgmethod_avgmethod_name -> rdf:type -> gnc:avgMethod +gn:avgmethod_avgmethod_name -> rdfs:label -> AvgMethod(Normalization) ``` Here's an example query: ```sparql PREFIX gn: -PREFIX gn-term: -PREFIX rdf: +PREFIX gnc: +PREFIX owl: +PREFIX gnt: +PREFIX rdf: PREFIX rdfs: PREFIX taxon: -SELECT ?s ?p ?o WHERE { - ?s rdf:type gn:avgMethod . - ?s gn-term:normalization "MAS5" . +SELECT * WHERE { + ?s rdf:type gnc:avgMethod . + ?s rdfs:label "MAS5" . ?s ?p ?o . } ``` @@ -171,7 +177,7 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn:avgmethod_mas5 rdf:type gn:avgMethod . -gn:avgmethod_mas5 gn-term:normalization "MAS5" . +gn:avgmethod_mas5 rdf:type gnc:avgMethod . +gn:avgmethod_mas5 rdfs:label "MAS5" . ``` -- cgit v1.2.3