diff options
Diffstat (limited to 'rdf-documentation/probeset-metadata.md')
| -rw-r--r-- | rdf-documentation/probeset-metadata.md | 98 |
1 files changed, 50 insertions, 48 deletions
diff --git a/rdf-documentation/probeset-metadata.md b/rdf-documentation/probeset-metadata.md index 2387145..cde4e43 100644 --- a/rdf-documentation/probeset-metadata.md +++ b/rdf-documentation/probeset-metadata.md @@ -12,32 +12,32 @@ SELECT IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name)) AS P 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 +gn:probesetProbesetidname -> rdf:type -> gnc:Probeset +gn:probesetProbesetidname -> rdfs:label -> ProbeSet(Name) +gn:probesetProbesetidname -> skos:altLabel -> ProbeSet(alias) +gn:probesetProbesetidname -> gnt:hasChip -> gn:platformGenechipname +gn:probesetProbesetidname -> gnt:hasTargetId -> TargetId +gn:probesetProbesetidname -> gnt:symbol -> ProbeSet(Symbol) +gn:probesetProbesetidname -> dct:description -> ProbeSetdescription +gn:probesetProbesetidname -> gnt:targetsRegion -> Probe_set_target_region +gn:probesetProbesetidname -> gnt:chr -> ProbeSet(Chr) +gn:probesetProbesetidname -> gnt:mb -> "Mb"^^xsd:double +gn:probesetProbesetidname -> gnt:mbMm8 -> "Mb_mm8"^^xsd:double +gn:probesetProbesetidname -> gnt:mb2016 -> "Mb_2016"^^xsd:double +gn:probesetProbesetidname -> gnt:hasSpecificity -> Probe_set_specificity +gn:probesetProbesetidname -> gnt:hasBlatScore -> Probe_set_BLAT_score +gn:probesetProbesetidname -> gnt:hasBlatMbStart -> "Probe_set_Blat_Mb_start"^^xsd:double +gn:probesetProbesetidname -> gnt:hasBlatMbStart2016 -> "Probe_set_Blat_Mb_start_2016"^^xsd:double +gn:probesetProbesetidname -> gnt:hasBlatMbEnd -> "Probe_set_Blat_Mb_end"^^xsd:double +gn:probesetProbesetidname -> gnt:hasBlatMbEnd2016 -> "Probe_set_Blat_Mb_start_2016"^^xsd:double +gn:probesetProbesetidname -> gnt:hasBlatSeq -> ProbeSetBlatSeq +gn:probesetProbesetidname -> gnt:hasTargetSeq -> ProbeSetTargetSeq +gn:probesetProbesetidname -> gnt:hasHomologeneId -> homologene:HomoloGeneID +gn:probesetProbesetidname -> gnt:hasUniprotId -> uniprot:UniProtID +gn:probesetProbesetidname -> gnt:hasPubChemId -> pubchem:PubChem_ID +gn:probesetProbesetidname -> gnt:hasKeggId -> kegg:KEGG_ID +gn:probesetProbesetidname -> gnt:hasOmimId -> +gn:probesetProbesetidname -> gnt:hasChebiId -> chebi:ChEBI_ID ``` Here's an example query: @@ -57,13 +57,15 @@ PREFIX dct: <http://purl.org/dc/terms/> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX homologene: <https://bio2rdf.org/homologene:> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> +PREFIX qb: <http://purl.org/linked-data/cube#> +PREFIX sdmx-measure: <http://purl.org/linked-data/sdmx/2009/measure#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> SELECT * WHERE { - ?s rdf:type gnc:probeset . + ?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 gnt:hasChip gn:platformMg_u74av2 . ?s ?p ?o . } ``` @@ -71,25 +73,25 @@ SELECT * WHERE { 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 . +gn:probeset100001_at rdf:type gnc:Probeset . +gn:probeset100001_at rdfs:label "100001_at" . +gn:probeset100001_at skos:altLabel "T3g; Ctg3; Ctg-3" . +gn:probeset100001_at gnt:hasChip gn:platformMg_u74av2 . +gn:probeset100001_at gnt:symbol "Cd3g" . +gn:probeset100001_at dct:description "CD3d antigen, gamma polypeptide" . +gn:probeset100001_at gnt:chr "9" . +gn:probeset100001_at gnt:mb "44.970689"^^xsd:double . +gn:probeset100001_at gnt:mbMm8 "44.721684"^^xsd:double . +gn:probeset100001_at gnt:mb2016 "44.778772"^^xsd:double . +gn:probeset100001_at gnt:hasSpecificity "9.3" . +gn:probeset100001_at gnt:hasBlatScore "186" . +gn:probeset100001_at gnt:hasBlatMbStart "44.970689"^^xsd:double . +gn:probeset100001_at gnt:hasBlatMbStart2016 "44.778772"^^xsd:double . +gn:probeset100001_at gnt:hasBlatMbEnd "44.971291"^^xsd:double . +gn:probeset100001_at gnt:hasBlatMbEnd2016 "44.778772"^^xsd:double . +gn:probeset100001_at gnt:hasBlatSeq "CTCTGTTGCAAAATGAACAGCTGTACAGCCCCTCAAGGACCGGGAATATGACCAGTACAGCCATCTCCAAGGAAACCAACTGAGGAAGAAGTGAACTCAGCAGGACTCAGGGTGTCCCCACAATGCATTTTGGAGAGAGCCCAGACTGCAAGCAGAGAGGAAGAACTGAGGAAAACAAGCACAGCGTGGTGTT" . +gn:probeset100001_at gnt:hasTargetSeq "ctctgttgcaaaatgaacagctgtaccagcccctcaaggaccgggaatatgaccagtacagccatctccaaggaaaccaactgaggaagaagtgaactcagcaggactcagggtgtccccccttntatccagcacccagaatcaaaacaatgcattttggagagagcccagtagagagattttcaaccctacaggtagactgcaagcagagaggaagaactgtcaaagaaattttggtcttttttttttttttnncaaaataaaataaaagcttggaggagccagtggtatgantnnnnnntgnancanttgtcaaccttgtttggggttnncagcaccccacccccagaccccccaaaaaaattcagtgaaggaaaacaagcacagcgtggtgtt" . +gn:probeset100001_at gnt:hasHomologeneId homologene:55 . +gn:probeset100001_at gnt:hasOmimId omim:186740 . ``` |