From 52bfc164eb2ee3b1f0e7b831af4123d17f399c5e Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Fri, 22 Dec 2023 12:00:19 +0300
Subject: Refactor gene symbol handling and add references to probeset.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 gn3/api/metadata.py | 27 ++++++++++++++++++---------
 1 file changed, 18 insertions(+), 9 deletions(-)

(limited to 'gn3/api')

diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index 45b731e..cb61227 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -904,30 +904,39 @@ $prefix
 
 CONSTRUCT {
         ?probeset ?predicate ?object ;
-                  gnt:geneSymbol ?symbol .
-        ?symbol ?symbolPred ?symbolObj .
+                  gnt:geneSymbol ?gene ;
+                  dct:references ?probesetResource .
+        ?gene ?genePred ?geneObj .
         ?resource rdfs:label ?resourceLabel ;
                   rdfs:comments ?resourceComments .
+        ?probesetResource rdfs:label ?probesetResourceLabel ;
+                          rdfs:comments ?probesetResourceComments .
         ?chip rdfs:label ?chipName .
 } WHERE {
         ?probeset rdf:type gnc:Probeset ;
                   rdfs:label "$name" ;
                   ?predicate ?object .
-        FILTER (!regex(str(?predicate), '(geneSymbol)', 'i')) .
         OPTIONAL {
            ?probeset gnt:geneSymbol ?symbolName .
-           ?symbol gnt:geneSymbol ?symbolName ;
-                   rdf:type gnc:Gene ;
-                   ?symbolPred ?symbolObj .
-           ?resource ^dct:references ?symbol ;
+           ?gene gnt:geneSymbol ?symbolName ;
+                 rdf:type gnc:Gene ;
+                 ?genePred ?geneObj .
+           ?resource ^dct:references ?gene ;
                      a ?resourceLink .
-           ?resourceLink rdfs:label ?resourceLabel ;
+           ?resourceLink rdfs:Class gnc:ResourceLink ;
+                         rdfs:label ?resourceLabel ;
                          rdfs:comments ?resourceComments .
         } .
-        OPTIONAL{
+        OPTIONAL {
             ?probeset gnt:hasChip ?chip .
             ?chip rdfs:label ?chipName .
         } .
+        OPTIONAL {
+            ?probesetResource ^dct:references ?probeset ;
+                              a ?probesetResourceLink .
+            ?probesetResourceLink rdfs:label ?probesetResourceLabel ;
+                                  rdfs:comments ?probesetResourceComments .
+        } .
 }
 """).substitute(prefix=RDF_PREFIXES, name=name)
         _context = {
-- 
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