aboutsummaryrefslogtreecommitdiff
path: root/rdf-documentation/probeset-metadata.md
diff options
context:
space:
mode:
Diffstat (limited to 'rdf-documentation/probeset-metadata.md')
-rw-r--r--rdf-documentation/probeset-metadata.md98
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 .
```
generated by cgit v1.2.3 (git 2.44.0) at 2024-09-19 21:36:38 +0000