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Diffstat (limited to 'rdf-documentation/dump-genotype.md')
| -rw-r--r-- | rdf-documentation/dump-genotype.md | 52 |
1 files changed, 25 insertions, 27 deletions
diff --git a/rdf-documentation/dump-genotype.md b/rdf-documentation/dump-genotype.md index 07533f9..2f5edbc 100644 --- a/rdf-documentation/dump-genotype.md +++ b/rdf-documentation/dump-genotype.md @@ -59,25 +59,24 @@ gn:B6d2rigeno gnt:belongsToInbredSet gn:_b6d2ri . The following SQL query was executed: ```sql -SELECT CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, '_')), Geno.Name) AS abbrev, Geno.Name, Geno.Chr, IFNULL(Geno.Mb, '') AS Mb, IFNULL(Geno.Mb_mm8, '') AS Mb_mm8, IFNULL(Geno.Mb_2016, '') AS Mb_2016, Geno.Sequence, Geno.Source, IF((Source2 = Source), NULL, Source2) AS Source2, IFNULL(GenoFreeze.Name, '') AS DatasetName, Geno.chr_num, Geno.Comments, GenoXRef.cM FROM Geno LEFT JOIN GenoXRef ON Geno.Id = GenoXRef.GenoId LEFT JOIN GenoFreeze ON GenoFreeze.Id = GenoXRef.GenoFreezeId LEFT JOIN InbredSet ON InbredSet.InbredSetId = GenoFreeze.InbredSetId LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = GenoFreeze.Name +SELECT Geno.Name, Geno.Name, Geno.Chr, IFNULL(Geno.Mb, '') AS Mb, IFNULL(Geno.Mb_mm8, '') AS Mb_mm8, IFNULL(Geno.Mb_2016, '') AS Mb_2016, Geno.Sequence, Geno.Source, IF((Source2 = Source), NULL, Source2) AS Source2, Species.Fullname, Geno.chr_num, Geno.Comments FROM Geno LEFT JOIN Species USING (SpeciesId) ``` The above query results to triples that have the form: ```text -gn:Abbrev -> rdf:type -> gnc:genotype -gn:Abbrev -> skos:prefLabel -> GenoName -gn:Abbrev -> gnt:chr -> Geno(Chr) -gn:Abbrev -> gnt:mb -> "Mb"^^xsd:double -gn:Abbrev -> gnt:mbMm8 -> "Mb_mm8"^^xsd:double -gn:Abbrev -> gnt:mb2016 -> "Mb_2016"^^xsd:double -gn:Abbrev -> gnt:hasSequence -> Geno(Sequence) -gn:Abbrev -> gnt:hasSource -> Geno(Source) -gn:Abbrev -> gnt:hasAltSourceName -> Source2 -gn:Abbrev -> gnt:belongsToDataset -> gn:Datasetname -gn:Abbrev -> gnt:chrNum -> "Geno(chr_num)"^^xsd:int -gn:Abbrev -> rdfs:comments -> Geno(Comments) -gn:Abbrev -> gnt:cM -> "GenoXRef(cM)"^^xsd:int +gn:Geno_name_ -> rdf:type -> gnc:genotype +gn:Geno_name_ -> skos:prefLabel -> GenoName +gn:Geno_name_ -> gnt:chr -> Geno(Chr) +gn:Geno_name_ -> gnt:mb -> "Mb"^^xsd:double +gn:Geno_name_ -> gnt:mbMm8 -> "Mb_mm8"^^xsd:double +gn:Geno_name_ -> gnt:mb2016 -> "Mb_2016"^^xsd:double +gn:Geno_name_ -> gnt:hasSequence -> Geno(Sequence) +gn:Geno_name_ -> gnt:hasSource -> Geno(Source) +gn:Geno_name_ -> gnt:hasAltSourceName -> Source2 +gn:Geno_name_ -> gnt:belongsToSpecies -> gn:Species_fullname +gn:Geno_name_ -> gnt:chrNum -> "Geno(chr_num)"^^xsd:int +gn:Geno_name_ -> rdfs:comments -> Geno(Comments) ``` Here's an example query: @@ -94,9 +93,9 @@ PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> SELECT * WHERE { ?s rdf:type gnc:genotype . - ?s skos:prefLabel "D1Mit118" . + ?s skos:prefLabel "D1Mit296" . ?s gnt:chr "1" . - ?s gnt:mb #{"3.968933"^^xsd:double}# . + ?s gnt:mb #{"9.749729"^^xsd:double}# . ?s ?p ?o . } ``` @@ -104,16 +103,15 @@ SELECT * WHERE { Expected Result: ```rdf -gn:B6d2f2geno_d1mit118 rdf:type gnc:genotype . -gn:B6d2f2geno_d1mit118 skos:prefLabel "D1Mit118" . -gn:B6d2f2geno_d1mit118 gnt:chr "1" . -gn:B6d2f2geno_d1mit118 gnt:mb "3.968933"^^xsd:double . -gn:B6d2f2geno_d1mit118 gnt:mbMm8 "3.959096"^^xsd:double . -gn:B6d2f2geno_d1mit118 gnt:mb2016 "3.959014"^^xsd:double . -gn:B6d2f2geno_d1mit118 gnt:hasSequence "TAATACGACTCNCTATAGGGCGAATTGAGGCCCTCTAGATGCATGCTCGANCGGCCGCCAGTGTGCTGGAAAGCCAGCCTGGNCTACAGAGCTCAAGAGACCACATGTGATACTTGCCTTTCTGAGTCTAACATATATAGAATGATCTAATGGTCTCTAATCACACACTTTTTTTTGTGAATGAAACTTATTAAGAGTTTTATATTTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGTGTCTCTGTGTGTGTGT" . -gn:B6d2f2geno_d1mit118 gnt:hasSource "Mit" . -gn:B6d2f2geno_d1mit118 gnt:belongsToDataset gn:B6d2f2geno . -gn:B6d2f2geno_d1mit118 gnt:chrNum "1"^^xsd:int . -gn:B6d2f2geno_d1mit118 gnt:cM "0.0"^^xsd:int . +gn:D1mit296 rdf:type gnc:genotype . +gn:D1mit296 skos:prefLabel "D1Mit296" . +gn:D1mit296 gnt:chr "1" . +gn:D1mit296 gnt:mb "9.749729"^^xsd:double . +gn:D1mit296 gnt:mbMm8 "9.734943"^^xsd:double . +gn:D1mit296 gnt:mb2016 "9.73981"^^xsd:double . +gn:D1mit296 gnt:hasSequence "CTTGCATGCCTGCGGNTNCGNACTCTAGAGGATCTCCCTATTATTNTNACATNACTTTNAATTAAAATAATAATCAGATAACTTCAACNNNNTGNNCACTTCTGTCAAGTGGACAGAAATAAACATAGAGCCTAATTATCCTGAATTTNAGAGAAAAGAGTGTGTTTANCACAANAGAACAGTTATAGATCTACACACACACACACACACACACACACACACACATACAGTTTGAAAAATGCATCAGTTGAGACC" . +gn:D1mit296 gnt:hasSource "Mit" . +gn:D1mit296 gnt:belongsToSpecies gn:Mus_musculus . +gn:D1mit296 gnt:chrNum "1"^^xsd:int . ``` |