From 9459aa993cc8809f5cb29df73aa8cd86e10c3775 Mon Sep 17 00:00:00 2001
From: tarcisio_adm <tarcisio_adm@wl1s-80-66.unil.ch>
Date: Mon, 2 Dec 2024 13:59:36 +0100
Subject: [PATCH 1/2] change endpoint

---
 examples/dbgi/001.ttl | 2 +-
 examples/dbgi/002.ttl | 2 +-
 examples/dbgi/003.ttl | 2 +-
 examples/dbgi/004.ttl | 2 +-
 examples/dbgi/005.ttl | 2 +-
 examples/dbgi/006.ttl | 2 +-
 examples/dbgi/007.ttl | 2 +-
 examples/dbgi/008.ttl | 2 +-
 examples/dbgi/009.ttl | 2 +-
 9 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/examples/dbgi/001.ttl b/examples/dbgi/001.ttl
index b5303a716..60d7f750b 100644
--- a/examples/dbgi/001.ttl
+++ b/examples/dbgi/001.ttl
@@ -53,5 +53,5 @@ WHERE
         }
     }
 }""" ;
-    schema:target <https://biosoda.unil.ch/graphdb/repositories/emi-dbgi> ;
+    schema:target <https://biosoda.unil.ch/emi/sparql/> ;
     spex:federatesWith <https://query.wikidata.org/sparql> .
diff --git a/examples/dbgi/002.ttl b/examples/dbgi/002.ttl
index 4a406127c..6ab6e0cd4 100644
--- a/examples/dbgi/002.ttl
+++ b/examples/dbgi/002.ttl
@@ -39,5 +39,5 @@ WHERE {
         }
     }
 }""" ;
-    schema:target <https://biosoda.unil.ch/graphdb/repositories/emi-dbgi> ;
+    schema:target <https://biosoda.unil.ch/emi/sparql/> ;
     spex:federatesWith <https://idsm.elixir-czech.cz/sparql/endpoint/wikidata> .
diff --git a/examples/dbgi/003.ttl b/examples/dbgi/003.ttl
index ac29a1697..5dec623a6 100644
--- a/examples/dbgi/003.ttl
+++ b/examples/dbgi/003.ttl
@@ -47,5 +47,5 @@ WHERE {
     FILTER(((?rt - ?rt_tol) < ?rt_opp) && ((?rt + ?rt_tol) > ?rt_opp))
     FILTER((?pm_opp > ((?pm - 2.014) - ((?ppm * 0.000001) * (?pm - 2.014)))) && (?pm_opp < ((?pm - 2.014) + ((?ppm * 0.000001) * (?pm - 2.014)))))
 }""" ;
-    schema:target <https://biosoda.unil.ch/graphdb/repositories/emi-dbgi> .
+    schema:target <https://biosoda.unil.ch/emi/sparql/> .
 
diff --git a/examples/dbgi/004.ttl b/examples/dbgi/004.ttl
index d548762f0..3e9eb04e2 100644
--- a/examples/dbgi/004.ttl
+++ b/examples/dbgi/004.ttl
@@ -45,5 +45,5 @@ WHERE {
     ?activity_opp prov:wasAssociatedWith <https://bio.informatik.uni-jena.de/software/sirius> .
     FILTER(((?rt - ?rt_tol) < ?rt_opp) && ((?rt + ?rt_tol) > ?rt_opp))
 }""" ;
-    schema:target <https://biosoda.unil.ch/graphdb/repositories/emi-dbgi> .
+    schema:target <https://biosoda.unil.ch/emi/sparql/> .
 
diff --git a/examples/dbgi/005.ttl b/examples/dbgi/005.ttl
index ec695ff5a..4a7739ba8 100644
--- a/examples/dbgi/005.ttl
+++ b/examples/dbgi/005.ttl
@@ -30,5 +30,5 @@ WHERE {
             emi:hasChemicalStructure ?isdb_ik2d .
     FILTER(?isdb_ik2d = ?sirius_ik2d) .
 }""" ;
-    schema:target <https://biosoda.unil.ch/graphdb/repositories/emi-dbgi> .
+    schema:target <https://biosoda.unil.ch/emi/sparql/> .
 
diff --git a/examples/dbgi/006.ttl b/examples/dbgi/006.ttl
index 8f3a9538d..2781703c4 100644
--- a/examples/dbgi/006.ttl
+++ b/examples/dbgi/006.ttl
@@ -74,6 +74,6 @@ WHERE {
     }
 } GROUP BY ?family_name ?genus_name ?species_name ?wd_sp ?feature ?sub_rt ?sub_parent_mass ?count
 ORDER BY DESC(?count)""" ;
-    schema:target <https://biosoda.unil.ch/graphdb/repositories/emi-dbgi> ;
+    schema:target <https://biosoda.unil.ch/emi/sparql/> ;
     spex:federatesWith <https://query.wikidata.org/sparql> .
 
diff --git a/examples/dbgi/007.ttl b/examples/dbgi/007.ttl
index 9532975ad..a882ebcb7 100644
--- a/examples/dbgi/007.ttl
+++ b/examples/dbgi/007.ttl
@@ -53,6 +53,6 @@ WHERE {
         }
     }
 }""" ;
-    schema:target <https://biosoda.unil.ch/graphdb/repositories/emi-dbgi> ;
+    schema:target <https://biosoda.unil.ch/emi/sparql/> ;
     spex:federatesWith <https://query.wikidata.org/sparql> .
 
diff --git a/examples/dbgi/008.ttl b/examples/dbgi/008.ttl
index 72153ff7a..b588d90e7 100644
--- a/examples/dbgi/008.ttl
+++ b/examples/dbgi/008.ttl
@@ -33,5 +33,5 @@ WHERE {
         }
     }
 } GROUP BY ?feature ?massive_doi ORDER BY DESC(?count)""" ;
-    schema:target <https://biosoda.unil.ch/graphdb/repositories/emi-dbgi> .
+    schema:target <https://biosoda.unil.ch/emi/sparql/> .
 
diff --git a/examples/dbgi/009.ttl b/examples/dbgi/009.ttl
index 8025cb22f..bb8147663 100644
--- a/examples/dbgi/009.ttl
+++ b/examples/dbgi/009.ttl
@@ -50,6 +50,6 @@ WHERE {
         } GROUP BY ?extract ORDER BY DESC(?count_of_selected_class)
     }
 }""" ;
-    schema:target <https://biosoda.unil.ch/graphdb/repositories/emi-dbgi> ;
+    schema:target <https://biosoda.unil.ch/emi/sparql/> ;
     spex:federatesWith <https://query.wikidata.org/sparql> .
 

From af57efd4da7036894e56fd49e28200d9fc167c17 Mon Sep 17 00:00:00 2001
From: tarcisio_adm <tarcisio_adm@vit-422.local>
Date: Wed, 4 Dec 2024 08:50:24 +0100
Subject: [PATCH 2/2] change prefix ex:

---
 examples/dbgi/001.ttl | 6 +++---
 examples/dbgi/002.ttl | 2 +-
 examples/dbgi/003.ttl | 2 +-
 examples/dbgi/004.ttl | 2 +-
 examples/dbgi/005.ttl | 2 +-
 examples/dbgi/006.ttl | 2 +-
 examples/dbgi/007.ttl | 2 +-
 examples/dbgi/008.ttl | 2 +-
 examples/dbgi/009.ttl | 6 +++---
 9 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/examples/dbgi/001.ttl b/examples/dbgi/001.ttl
index 60d7f750b..3578f7d61 100644
--- a/examples/dbgi/001.ttl
+++ b/examples/dbgi/001.ttl
@@ -1,4 +1,4 @@
-@prefix ex: <https://sib-swiss.github.io/sparql-examples/examples/dbgi/> .
+@prefix ex: <https://biosoda.unil.ch/emi/sparql/.well-known/sparql-examples/> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
@@ -40,7 +40,7 @@ WHERE
                 sosa:isSampleOf ?organe .
             ?organe emi:inTaxon ?wd_sp .
             ?wd_sp rdfs:label "tabernaemontana coffeoides" .
-            OPTIONAL {
+           # OPTIONAL {
                 SERVICE <https://query.wikidata.org/sparql> {
                     ?wd_sp wdt:P225 ?species_name .
                     ?genus wdt:P31 wd:Q16521 ;
@@ -49,7 +49,7 @@ WHERE
                     ?childtaxa wdt:P171* ?genus .
                     ?wd_id wdt:P703 ?childtaxa
                 }
-            }
+           # }
         }
     }
 }""" ;
diff --git a/examples/dbgi/002.ttl b/examples/dbgi/002.ttl
index 6ab6e0cd4..67f9ff4ab 100644
--- a/examples/dbgi/002.ttl
+++ b/examples/dbgi/002.ttl
@@ -1,4 +1,4 @@
-@prefix ex: <https://sib-swiss.github.io/sparql-examples/examples/dbgi/> .
+@prefix ex: <https://biosoda.unil.ch/emi/sparql/.well-known/sparql-examples> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
diff --git a/examples/dbgi/003.ttl b/examples/dbgi/003.ttl
index 5dec623a6..1ad616233 100644
--- a/examples/dbgi/003.ttl
+++ b/examples/dbgi/003.ttl
@@ -1,4 +1,4 @@
-@prefix ex: <https://sib-swiss.github.io/sparql-examples/examples/dbgi/> .
+@prefix ex: <https://biosoda.unil.ch/emi/sparql/.well-known/sparql-examples/> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
diff --git a/examples/dbgi/004.ttl b/examples/dbgi/004.ttl
index 3e9eb04e2..5ab339ccf 100644
--- a/examples/dbgi/004.ttl
+++ b/examples/dbgi/004.ttl
@@ -1,4 +1,4 @@
-@prefix ex: <https://sib-swiss.github.io/sparql-examples/examples/dbgi/> .
+@prefix ex: <https://biosoda.unil.ch/emi/sparql/.well-known/sparql-examples/> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
diff --git a/examples/dbgi/005.ttl b/examples/dbgi/005.ttl
index 4a7739ba8..7b1bccc84 100644
--- a/examples/dbgi/005.ttl
+++ b/examples/dbgi/005.ttl
@@ -1,4 +1,4 @@
-@prefix ex: <https://sib-swiss.github.io/sparql-examples/examples/dbgi/> .
+@prefix ex: <https://biosoda.unil.ch/emi/sparql/.well-known/sparql-examples/> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
diff --git a/examples/dbgi/006.ttl b/examples/dbgi/006.ttl
index 2781703c4..a9bc9ae31 100644
--- a/examples/dbgi/006.ttl
+++ b/examples/dbgi/006.ttl
@@ -1,4 +1,4 @@
-@prefix ex: <https://sib-swiss.github.io/sparql-examples/examples/dbgi/> .
+@prefix ex: <https://biosoda.unil.ch/emi/sparql/.well-known/sparql-examples/> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
diff --git a/examples/dbgi/007.ttl b/examples/dbgi/007.ttl
index a882ebcb7..23ce4cc4b 100644
--- a/examples/dbgi/007.ttl
+++ b/examples/dbgi/007.ttl
@@ -1,4 +1,4 @@
-@prefix ex: <https://sib-swiss.github.io/sparql-examples/examples/dbgi/> .
+@prefix ex: <https://biosoda.unil.ch/emi/sparql/.well-known/sparql-examples/> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
diff --git a/examples/dbgi/008.ttl b/examples/dbgi/008.ttl
index b588d90e7..9622363f2 100644
--- a/examples/dbgi/008.ttl
+++ b/examples/dbgi/008.ttl
@@ -1,4 +1,4 @@
-@prefix ex: <https://sib-swiss.github.io/sparql-examples/examples/dbgi/> .
+@prefix ex: <https://biosoda.unil.ch/emi/sparql/.well-known/sparql-examples/> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
diff --git a/examples/dbgi/009.ttl b/examples/dbgi/009.ttl
index bb8147663..223378016 100644
--- a/examples/dbgi/009.ttl
+++ b/examples/dbgi/009.ttl
@@ -1,4 +1,4 @@
-@prefix ex: <https://sib-swiss.github.io/sparql-examples/examples/dbgi/> .
+@prefix ex: <https://biosoda.unil.ch/emi/sparql/.well-known/sparql-examples/> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
@@ -20,7 +20,7 @@ WHERE {
     ?material sosa:hasSample ?extract ;
         sosa:isSampleOf ?organe .
     ?organe emi:inTaxon ?wd_sp .
-    OPTIONAL {
+    #OPTIONAL {
         SERVICE <https://query.wikidata.org/sparql> {
             ?wd_sp wdt:P225 ?species_name .
             ?family wdt:P31 wd:Q16521 ;
@@ -32,7 +32,7 @@ WHERE {
                 wdt:P225 ?genus_name ;
                 ^wdt:P171* ?wd_sp .
         }
-    }
+    #}
     {
         SELECT ?extract (COUNT(DISTINCT ?feature) AS ?count_of_selected_class)
         WHERE {