From 0e9401165a0c3ad2b891c01efc485431f3229ef8 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Thu, 20 Jul 2023 09:25:18 +0300
Subject: Update metadata information

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 rdf-documentation/dump-probeset-metadata.md | 58 +++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 rdf-documentation/dump-probeset-metadata.md

(limited to 'rdf-documentation/dump-probeset-metadata.md')

diff --git a/rdf-documentation/dump-probeset-metadata.md b/rdf-documentation/dump-probeset-metadata.md
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+# Probeset Metadata
+## 'dump-probeset-metadata'
+
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT CONCAT(ProbeSetFreeze.Name,':',IFNULL(ProbeSet.Name, ProbeSet.Id)) AS ProbeSetName, IFNULL(ProbeSet.Name, ProbeSet.Id) AS name, ProbeSetFreeze.Name, IFNULL(ProbeSetXRef.mean, '') AS mean, IFNULL(ProbeSetXRef.se, '') AS se, ProbeSetXRef.Locus, IFNULL(ProbeSetXRef.LRS, '') AS LRS, IFNULL(ProbeSetXRef.pValue, '') AS pValue, IFNULL(ProbeSetXRef.additive, '') AS additive, IFNULL(ProbeSetXRef.h2, '') AS h2 FROM ProbeSetXRef LEFT JOIN ProbeSet ON ProbeSetXRef.ProbeSetId = ProbeSet.Id LEFT JOIN ProbeSetFreeze ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:probesetData_probesetname -> rdf:type -> gn:probesetData 
+gn:probesetData_probesetname -> gn-term:hasProbeset -> probeset:name 
+gn:probesetData_probesetname -> gn-term:probesetOfDataset -> probeset:ProbeSetFreeze_Name_ 
+gn:probesetData_probesetname -> gn-term:mean -> "mean"^^xsd:double 
+gn:probesetData_probesetname -> gn-term:se -> "se"^^xsd:double 
+gn:probesetData_probesetname -> gn-term:locus -> ProbeSetXRef(Locus) 
+gn:probesetData_probesetname -> gn:LRS -> "LRS"^^xsd:double 
+gn:probesetData_probesetname -> gn-term:pValue -> "pValue"^^xsd:double 
+gn:probesetData_probesetname -> gn-term:additive -> "additive"^^xsd:double 
+gn:probesetData_probesetname -> gn-term:h2 -> "h2"^^xsd:float 
+```
+Here's an example query:
+
+```sparql
+@prefix gn: <http://genenetwork.org/id/> .
+@prefix gn-term: <http://genenetwork.org/id/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+SELECT ?s ?p ?o WHERE { 
+    ?s rdf:type gn:probesetData .
+    ?s gn-term:hasProbeset probeset:100001_at .
+    ?s gn-term:probesetOfDataset probeset:HC_U_0304_R .
+    ?s gn-term:mean #{"8.14033666666667"^^xsd:double}# .
+    ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:probesetData_hc_u_0304_r:100001_at rdf:type gn:probesetData .
+gn:probesetData_hc_u_0304_r:100001_at gn-term:hasProbeset probeset:100001_at .
+gn:probesetData_hc_u_0304_r:100001_at gn-term:probesetOfDataset probeset:HC_U_0304_R .
+gn:probesetData_hc_u_0304_r:100001_at gn-term:mean "8.14033666666667"^^xsd:double .
+gn:probesetData_hc_u_0304_r:100001_at gn-term:se "0.023595817125580502"^^xsd:double .
+gn:probesetData_hc_u_0304_r:100001_at gn-term:locus "rsm10000021399" .
+gn:probesetData_hc_u_0304_r:100001_at gn:LRS "12.2805314427567"^^xsd:double .
+gn:probesetData_hc_u_0304_r:100001_at gn-term:pValue "0.118"^^xsd:double .
+gn:probesetData_hc_u_0304_r:100001_at gn-term:additive "0.0803547619047631"^^xsd:double .
+```
+
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