From be450b02198f08363986aecfd5227752d2e4ca72 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 15 Aug 2023 21:15:11 +0300 Subject: Update auto-generated docs Signed-off-by: Munyoki Kilyungi --- rdf-documentation/dump-gene-chip.md | 88 ++++++++++++++++++++++--------------- 1 file changed, 52 insertions(+), 36 deletions(-) (limited to 'rdf-documentation/dump-gene-chip.md') diff --git a/rdf-documentation/dump-gene-chip.md b/rdf-documentation/dump-gene-chip.md index 80217d8..abd68d8 100644 --- a/rdf-documentation/dump-gene-chip.md +++ b/rdf-documentation/dump-gene-chip.md @@ -1,37 +1,43 @@ # Probeset freeze metadata ## 'dump-gene-chip' - ## Generated Triples: The following SQL query was executed: ```sql -SELECT GeneChip.Name, GeneChip.GeneChipName, GeneChip.GeoPlatform FROM GeneChip +SELECT GeneChip.Name, GeneChip.GeneChipName, GeneChip.Name, IF(GeneChip.GeneChipName != GeneChip.Title, Title, NULL) AS Title, GeneChip.Go_tree_value, Species.Fullname, GeneChip.GeoPlatform FROM GeneChip LEFT JOIN Species USING (SpeciesId) ``` The above query results to triples that have the form: ```text -gn:platform_genechip_name -> rdf:type -> gn:platform -gn:platform_genechip_name -> gn-term:name -> GeneChip(GeneChipName) -gn:platform_genechip_name -> gn-term:geoPlatform -> geoSeries:GeneChip(GeoPlatform) +gn:platform_genechip_name -> rdf:type -> gnc:geneChip +gn:platform_genechip_name -> rdfs:label -> GeneChip(GeneChipName) +gn:platform_genechip_name -> skos:prefLabel -> GeneChip(Name) +gn:platform_genechip_name -> skos:altLabel -> Title +gn:platform_genechip_name -> gnt:hasGOTreeValue -> GeneChip(Go_tree_value) +gn:platform_genechip_name -> gnt:belongsToSpecies -> gn:Species_fullname +gn:platform_genechip_name -> gnt:hasGeoSeriesId -> geoSeries:GeneChip(GeoPlatform) ``` Here's an example query: ```sparql PREFIX geoSeries: PREFIX gn: -PREFIX dct: <> -PREFIX gn-term: +PREFIX gnc: +PREFIX dct: +PREFIX owl: +PREFIX skos: +PREFIX gnt: PREFIX rdf: PREFIX rdfs: PREFIX xsd: -SELECT ?s ?p ?o WHERE { - ?s rdf:type gn:platform . - ?s gn-term:name "Affy Mouse Genome U74Av2 (GPL81)" . - ?s gn-term:geoPlatform geoSeries:GPL81 . +SELECT * WHERE { + ?s rdf:type gnc:geneChip . + ?s rdfs:label "Affy Mouse Genome U74Av2 (GPL81)" . + ?s skos:prefLabel "MG_U74AV2" . ?s ?p ?o . } ``` @@ -39,50 +45,58 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn:platform_mg_u74av2 rdf:type gn:platform . -gn:platform_mg_u74av2 gn-term:name "Affy Mouse Genome U74Av2 (GPL81)" . -gn:platform_mg_u74av2 gn-term:geoPlatform geoSeries:GPL81 . +gn:platform_mg_u74av2 rdf:type gnc:geneChip . +gn:platform_mg_u74av2 rdfs:label "Affy Mouse Genome U74Av2 (GPL81)" . +gn:platform_mg_u74av2 skos:prefLabel "MG_U74AV2" . +gn:platform_mg_u74av2 gnt:hasGOTreeValue "affy_mg_u74av2" . +gn:platform_mg_u74av2 gnt:belongsToSpecies gn:Mus_musculus . +gn:platform_mg_u74av2 gnt:hasGeoSeriesId geoSeries:GPL81 . ``` ## 'dump-probesetfreeze' - ## Generated Triples: The following SQL query was executed: ```sql -SELECT ProbeSetFreeze.Name, AvgMethod.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.CreateTime, ProbeSetFreeze.DataScale, Tissue.Short_Name, InbredSet.Name AS InbredSetName FROM ProbeSetFreeze LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = ProbeSetFreeze.Name LEFT JOIN ProbeFreeze USING (ProbeFreezeId) LEFT JOIN AvgMethod ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID LEFT JOIN InbredSet ON ProbeFreeze.InbredSetId = InbredSet.Id LEFT JOIN Tissue ON ProbeFreeze.TissueId = Tissue.TissueId WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id +SELECT ProbeSetFreeze.Name, AvgMethod.Name AS AvgMethodName, AvgMethod.Name AS AvgMethodName, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.Name, ProbeSetFreeze.Name2, ProbeSetFreeze.CreateTime, ProbeSetFreeze.DataScale, Tissue.Short_Name, InbredSet.Name AS InbredSetName FROM ProbeSetFreeze LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = ProbeSetFreeze.Name LEFT JOIN ProbeFreeze USING (ProbeFreezeId) LEFT JOIN AvgMethod ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID LEFT JOIN InbredSet ON ProbeFreeze.InbredSetId = InbredSet.Id LEFT JOIN Tissue ON ProbeFreeze.TissueId = Tissue.TissueId WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id ``` The above query results to triples that have the form: ```text -gn:Probesetfreeze_name_ -> rdf:type -> gn:probesetDataset -gn:Probesetfreeze_name_ -> gn-term:avgMethod -> gn:avgmethod_avgmethod_name -gn:Probesetfreeze_name_ -> gn-term:fullName -> ProbeSetFreeze(FullName) -gn:Probesetfreeze_name_ -> gn-term:shortName -> ProbeSetFreeze(ShortName) +gn:Probesetfreeze_name_ -> rdf:type -> gnc:probesetDataset +gn:Probesetfreeze_name_ -> gnt:usesNormalization -> gn:avgmethod_avgmethod_avgmethodname +gn:Probesetfreeze_name_ -> dct:title -> ProbeSetFreeze(FullName) +gn:Probesetfreeze_name_ -> rdfs:label -> ProbeSetFreeze(ShortName) +gn:Probesetfreeze_name_ -> skos:prefLabel -> ProbeSetFreeze(Name) +gn:Probesetfreeze_name_ -> skos:altLabel -> ProbeSetFreeze(Name2) gn:Probesetfreeze_name_ -> dct:created -> "ProbeSetFreeze(CreateTime)"^^xsd:datetime -gn:Probesetfreeze_name_ -> gn-term:dataScale -> ProbeSetFreeze(DataScale) -gn:Probesetfreeze_name_ -> gn-term:tissueName -> gn:tissue_tissue_short_name -gn:Probesetfreeze_name_ -> gn-term:datasetOfInbredSet -> gn:inbredSet_inbredset_inbredsetname +gn:Probesetfreeze_name_ -> gnt:usesDataScale -> ProbeSetFreeze(DataScale) +gn:Probesetfreeze_name_ -> gnt:hasTissue -> gn:tissue_tissue_short_name +gn:Probesetfreeze_name_ -> gnt:belongsToInbredSet -> gn:inbredSet_inbredset_inbredsetname ``` Here's an example query: ```sparql PREFIX geoSeries: PREFIX gn: -PREFIX dct: <> -PREFIX gn-term: +PREFIX gnc: +PREFIX dct: +PREFIX owl: +PREFIX skos: +PREFIX gnt: PREFIX rdf: PREFIX rdfs: PREFIX xsd: -SELECT ?s ?p ?o WHERE { - ?s rdf:type gn:probesetDataset . - ?s gn-term:avgMethod gn:avgmethod_cmmtubcbxdp00cerilm0513 . - ?s gn-term:fullName "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" . +SELECT * WHERE { + ?s rdf:type gnc:probesetDataset . + ?s gnt:usesNormalization gn:avgmethod_rankinv . + ?s dct:title "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" . + ?s rdfs:label "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" . ?s ?p ?o . } ``` @@ -90,13 +104,15 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn:Cmmtubcbxdp00cerilm0513 rdf:type gn:probesetDataset . -gn:Cmmtubcbxdp00cerilm0513 gn-term:avgMethod gn:avgmethod_cmmtubcbxdp00cerilm0513 . -gn:Cmmtubcbxdp00cerilm0513 gn-term:fullName "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" . -gn:Cmmtubcbxdp00cerilm0513 gn-term:shortName "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" . +gn:Cmmtubcbxdp00cerilm0513 rdf:type gnc:probesetDataset . +gn:Cmmtubcbxdp00cerilm0513 gnt:usesNormalization gn:avgmethod_rankinv . +gn:Cmmtubcbxdp00cerilm0513 dct:title "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" . +gn:Cmmtubcbxdp00cerilm0513 rdfs:label "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" . +gn:Cmmtubcbxdp00cerilm0513 skos:prefLabel "CMMTUBCBXDP00CerILM0513" . +gn:Cmmtubcbxdp00cerilm0513 skos:altLabel "CMMTUBCBXDP00CerILMMay13" . gn:Cmmtubcbxdp00cerilm0513 dct:created "2013-04-22"^^xsd:datetime . -gn:Cmmtubcbxdp00cerilm0513 gn-term:dataScale "log2" . -gn:Cmmtubcbxdp00cerilm0513 gn-term:tissueName gn:tissue_cb . -gn:Cmmtubcbxdp00cerilm0513 gn-term:datasetOfInbredSet gn:inbredSet_bxd . +gn:Cmmtubcbxdp00cerilm0513 gnt:usesDataScale "log2" . +gn:Cmmtubcbxdp00cerilm0513 gnt:hasTissue gn:tissue_cb . +gn:Cmmtubcbxdp00cerilm0513 gnt:belongsToInbredSet gn:inbredSet_bxd . ``` -- cgit v1.2.3