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diff --git a/rdf-documentation/dump-genotype.md b/rdf-documentation/dump-genotype.md new file mode 100644 index 0000000..cc35bc4 --- /dev/null +++ b/rdf-documentation/dump-genotype.md @@ -0,0 +1,112 @@ +# Genotype Metadata +## 'dump-genofreeze' + + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT GenoFreeze.Name, GenoFreeze.Name, GenoFreeze.FullName, GenoFreeze.ShortName, GenoFreeze.CreateTime, InbredSet.Name AS InbredSetName FROM GenoFreeze LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = GenoFreeze.Name LEFT JOIN InbredSet ON GenoFreeze.InbredSetId = InbredSet.InbredSetId WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL +``` + +The above query results to triples that have the form: + +```text +gn:Genofreeze_name_ -> rdf:type -> gn:genotypeDataset +gn:Genofreeze_name_ -> gn-term:name -> GenoFreeze(Name) +gn:Genofreeze_name_ -> gn-term:fullName -> GenoFreeze(FullName) +gn:Genofreeze_name_ -> gn-term:shortName -> GenoFreeze(ShortName) +gn:Genofreeze_name_ -> dct:created -> "GenoFreeze(CreateTime)"^^xsd:date +gn:Genofreeze_name_ -> gn-term:datasetOfInbredSet -> gn:_inbredset_inbredsetname +``` +Here's an example query: + +```sparql +@prefix gn: <http://genenetwork.org/id/> . +@prefix gn-term: <http://genenetwork.org/term/> . +@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#> . + +SELECT ?s ?p ?o WHERE { + ?s rdf:type gn:genotypeDataset . + ?s gn-term:name "B6D2RIGeno" . + ?s gn-term:fullName "B6D2RI Genotypes" . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:B6d2rigeno rdf:type gn:genotypeDataset . +gn:B6d2rigeno gn-term:name "B6D2RIGeno" . +gn:B6d2rigeno gn-term:fullName "B6D2RI Genotypes" . +gn:B6d2rigeno gn-term:shortName "B6D2RIGeno" . +gn:B6d2rigeno dct:created "2022-10-24"^^xsd:date . +gn:B6d2rigeno gn-term:datasetOfInbredSet gn:_b6d2ri . +``` + + +## 'dump-genotypes' + + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, ':')), Geno.Name) AS abbrev, Geno.Name, Geno.Marker_Name, Geno.Chr, IFNULL(Geno.Mb, '') AS Mb, Geno.Sequence, Geno.Source, Geno.Source2, IFNULL(GenoFreeze.Name, '') AS DatasetName, IFNULL(Geno.chr_num, '') AS chr_num, CAST(CONVERT(BINARY CONVERT(Geno.Comments USING latin1) USING utf8) AS VARCHAR(255)) AS Comments, IFNULL(GenoXRef.cM, '') AS Chr_mm8 FROM Geno LEFT JOIN GenoXRef ON Geno.Id = GenoXRef.GenoId LEFT JOIN GenoFreeze ON GenoFreeze.Id = GenoXRef.GenoFreezeId LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = GenoFreeze.Name +``` + +The above query results to triples that have the form: + +```text +gn:Abbrev -> rdf:type -> gn:genotype +gn:Abbrev -> gn-term:name -> GenoName +gn:Abbrev -> gn-term:markerName -> GenoMarker_Name +gn:Abbrev -> gn-term:chr -> Geno(Chr) +gn:Abbrev -> gn-term:mb -> "Mb"^^xsd:double +gn:Abbrev -> gn-term:sequence -> Geno(Sequence) +gn:Abbrev -> gn-term:source -> Geno(Source) +gn:Abbrev -> gn-term:source2 -> Geno(Source2) +gn:Abbrev -> gn-term:genotypeOfDataset -> gn:Datasetname +gn:Abbrev -> gn-term:chrNum -> "chr_num"^^xsd:int +gn:Abbrev -> gn:comments -> Comments +gn:Abbrev -> gn-term:cM -> "Chr_mm8"^^xsd:int +``` +Here's an example query: + +```sparql +@prefix gn: <http://genenetwork.org/id/> . +@prefix gn-term: <http://genenetwork.org/term/> . +@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#> . + +SELECT ?s ?p ?o WHERE { + ?s rdf:type gn:genotype . + ?s gn-term:name "D1Mit296" . + ?s gn-term:markerName "D1Mit296" . + ?s gn-term:chr "1" . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:Axbxageno:d1mit296 rdf:type gn:genotype . +gn:Axbxageno:d1mit296 gn-term:name "D1Mit296" . +gn:Axbxageno:d1mit296 gn-term:markerName "D1Mit296" . +gn:Axbxageno:d1mit296 gn-term:chr "1" . +gn:Axbxageno:d1mit296 gn-term:mb "9.749729"^^xsd:double . +gn:Axbxageno:d1mit296 gn-term:sequence "CTTGCATGCCTGCGGNTNCGNACTCTAGAGGATCTCCCTATTATTNTNACATNACTTTNAATTAAAATAATAATCAGATAACTTCAACNNNNTGNNCACTTCTGTCAAGTGGACAGAAATAAACATAGAGCCTAATTATCCTGAATTTNAGAGAAAAGAGTGTGTTTANCACAANAGAACAGTTATAGATCTACACACACACACACACACACACACACACACACATACAGTTTGAAAAATGCATCAGTTGAGACC" . +gn:Axbxageno:d1mit296 gn-term:source "Mit" . +gn:Axbxageno:d1mit296 gn-term:source2 "Mit" . +gn:Axbxageno:d1mit296 gn-term:genotypeOfDataset gn:Axbxageno . +gn:Axbxageno:d1mit296 gn-term:chrNum "1"^^xsd:int . +gn:Axbxageno:d1mit296 gn-term:cM "0"^^xsd:int . +``` + |