From edca04399ae950698a89a64160cd35f6164f4b1c Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Thu, 24 Aug 2023 13:08:59 +0300 Subject: Update autogenerated docs Signed-off-by: Munyoki Kilyungi --- rdf-documentation/probeset-metadata.md | 95 ++++++++++++++++++++++++++++++++++ 1 file changed, 95 insertions(+) create mode 100644 rdf-documentation/probeset-metadata.md (limited to 'rdf-documentation/probeset-metadata.md') diff --git a/rdf-documentation/probeset-metadata.md b/rdf-documentation/probeset-metadata.md new file mode 100644 index 0000000..2387145 --- /dev/null +++ b/rdf-documentation/probeset-metadata.md @@ -0,0 +1,95 @@ +# ProbeSet Metadata +## 'probeset' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name)) AS ProbeSetIdName, ProbeSet.Id, ProbeSet.Name, ProbeSet.alias, IFNULL(GeneChip.Name, '') AS GeneChipName, NULLIF(TRIM(ProbeSet.TargetId), '') AS TargetId, ProbeSet.Symbol, ProbeSet.description, NULLIF(TRIM(ProbeSet.Probe_set_target_region), '') AS Probe_set_target_region, ProbeSet.Chr, IFNULL(ProbeSet.Mb, '') AS Mb, IFNULL(ProbeSet.Mb_mm8, '') AS Mb_mm8, IFNULL(ProbeSet.Mb_2016, '') AS Mb_2016, IFNULL(ProbeSet.Probe_set_specificity, '') AS Probe_set_specificity, IFNULL(ProbeSet.Probe_set_BLAT_score, '') AS Probe_set_BLAT_score, IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '') AS Probe_set_Blat_Mb_start, IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '') AS Probe_set_Blat_Mb_start_2016, IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '') AS Probe_set_Blat_Mb_end, IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '') AS Probe_set_Blat_Mb_start_2016, ProbeSet.BlatSeq, ProbeSet.TargetSeq, IFNULL(ProbeSet.HomoloGeneID, '') AS HomoloGeneID, IFNULL(ProbeSet.UniProtID, '') AS UniProtID, IFNULL(ProbeSet.PubChem_ID, '') AS PubChem_ID, IFNULL(ProbeSet.KEGG_ID, '') AS KEGG_ID, IFNULL(ProbeSet.OMIM, '') AS OMIM, IFNULL(ProbeSet.ChEBI_ID, '') AS ChEBI_ID FROM ProbeSet LEFT JOIN GeneChip ON GeneChip.Id = ProbeSet.ChipId +``` + +The above query results to triples that have the form: + +```text +gn:probeset_probesetidname -> rdf:type -> gnc:probeset +gn:probeset_probesetidname -> rdfs:label -> ProbeSet(Name) +gn:probeset_probesetidname -> skos:altLabel -> ProbeSet(alias) +gn:probeset_probesetidname -> gnt:hasChip -> gn:platform_genechipname +gn:probeset_probesetidname -> gnt:hasTargetId -> TargetId +gn:probeset_probesetidname -> gnt:symbol -> ProbeSet(Symbol) +gn:probeset_probesetidname -> dct:description -> ProbeSetdescription +gn:probeset_probesetidname -> gnt:targetsRegion -> Probe_set_target_region +gn:probeset_probesetidname -> gnt:chr -> ProbeSet(Chr) +gn:probeset_probesetidname -> gnt:mb -> "Mb"^^xsd:double +gn:probeset_probesetidname -> gnt:mbMm8 -> "Mb_mm8"^^xsd:double +gn:probeset_probesetidname -> gnt:mb2016 -> "Mb_2016"^^xsd:double +gn:probeset_probesetidname -> gnt:hasSpecificity -> Probe_set_specificity +gn:probeset_probesetidname -> gnt:hasBlatScore -> Probe_set_BLAT_score +gn:probeset_probesetidname -> gnt:hasBlatMbStart -> "Probe_set_Blat_Mb_start"^^xsd:double +gn:probeset_probesetidname -> gnt:hasBlatMbStart2016 -> "Probe_set_Blat_Mb_start_2016"^^xsd:double +gn:probeset_probesetidname -> gnt:hasBlatMbEnd -> "Probe_set_Blat_Mb_end"^^xsd:double +gn:probeset_probesetidname -> gnt:hasBlatMbEnd2016 -> "Probe_set_Blat_Mb_start_2016"^^xsd:double +gn:probeset_probesetidname -> gnt:hasBlatSeq -> ProbeSetBlatSeq +gn:probeset_probesetidname -> gnt:hasTargetSeq -> ProbeSetTargetSeq +gn:probeset_probesetidname -> gnt:hasHomologeneId -> homologene:HomoloGeneID +gn:probeset_probesetidname -> gnt:hasUniprotId -> uniprot:UniProtID +gn:probeset_probesetidname -> gnt:hasPubChemId -> pubchem:PubChem_ID +gn:probeset_probesetidname -> gnt:hasKeggId -> kegg:KEGG_ID +gn:probeset_probesetidname -> gnt:hasOmimId -> +gn:probeset_probesetidname -> gnt:hasChebiId -> chebi:ChEBI_ID +``` +Here's an example query: + +```sparql +PREFIX gn: +PREFIX probeset: +PREFIX gnc: +PREFIX gnt: +PREFIX rdf: +PREFIX kegg: +PREFIX pubchem: +PREFIX omim: +PREFIX rdfs: +PREFIX uniprot: +PREFIX chebi: +PREFIX dct: +PREFIX owl: +PREFIX homologene: +PREFIX xsd: +PREFIX skos: + +SELECT * WHERE { + ?s rdf:type gnc:probeset . + ?s rdfs:label "100001_at" . + ?s skos:altLabel "T3g; Ctg3; Ctg-3" . + ?s gnt:hasChip gn:platform_mg_u74av2 . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:probeset_100001_at rdf:type gnc:probeset . +gn:probeset_100001_at rdfs:label "100001_at" . +gn:probeset_100001_at skos:altLabel "T3g; Ctg3; Ctg-3" . +gn:probeset_100001_at gnt:hasChip gn:platform_mg_u74av2 . +gn:probeset_100001_at gnt:symbol "Cd3g" . +gn:probeset_100001_at dct:description "CD3d antigen, gamma polypeptide" . +gn:probeset_100001_at gnt:chr "9" . +gn:probeset_100001_at gnt:mb "44.970689"^^xsd:double . +gn:probeset_100001_at gnt:mbMm8 "44.721684"^^xsd:double . +gn:probeset_100001_at gnt:mb2016 "44.778772"^^xsd:double . +gn:probeset_100001_at gnt:hasSpecificity "9.3" . +gn:probeset_100001_at gnt:hasBlatScore "186" . +gn:probeset_100001_at gnt:hasBlatMbStart "44.970689"^^xsd:double . +gn:probeset_100001_at gnt:hasBlatMbStart2016 "44.778772"^^xsd:double . +gn:probeset_100001_at gnt:hasBlatMbEnd "44.971291"^^xsd:double . +gn:probeset_100001_at gnt:hasBlatMbEnd2016 "44.778772"^^xsd:double . +gn:probeset_100001_at gnt:hasBlatSeq "CTCTGTTGCAAAATGAACAGCTGTACAGCCCCTCAAGGACCGGGAATATGACCAGTACAGCCATCTCCAAGGAAACCAACTGAGGAAGAAGTGAACTCAGCAGGACTCAGGGTGTCCCCACAATGCATTTTGGAGAGAGCCCAGACTGCAAGCAGAGAGGAAGAACTGAGGAAAACAAGCACAGCGTGGTGTT" . +gn:probeset_100001_at gnt:hasTargetSeq "ctctgttgcaaaatgaacagctgtaccagcccctcaaggaccgggaatatgaccagtacagccatctccaaggaaaccaactgaggaagaagtgaactcagcaggactcagggtgtccccccttntatccagcacccagaatcaaaacaatgcattttggagagagcccagtagagagattttcaaccctacaggtagactgcaagcagagaggaagaactgtcaaagaaattttggtcttttttttttttttnncaaaataaaataaaagcttggaggagccagtggtatgantnnnnnntgnancanttgtcaaccttgtttggggttnncagcaccccacccccagaccccccaaaaaaattcagtgaaggaaaacaagcacagcgtggtgtt" . +gn:probeset_100001_at gnt:hasHomologeneId homologene:55 . +gn:probeset_100001_at gnt:hasOmimId omim:186740 . +``` + -- cgit v1.2.3