Merge pull request #144 from sib-swiss/tarcisio_dev

fix dbgi endpoint and prefix
sib-swiss · Dec 4, 2024 · b0e7689 · b0e7689
2 parents 0ab43af + af57efd
commit b0e7689
Show file tree

Hide file tree

Showing 9 changed files with 22 additions and 22 deletions.
diff --git 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 ;
@@ -49,9 +49,9 @@ WHERE
                     ?childtaxa wdt:P171* ?genus .
                     ?wd_id wdt:P703 ?childtaxa
                 }
-            }
+           # }
         }
     }
 }""" ;
-    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
@@ -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#> .
@@ -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
@@ -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#> .
@@ -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
@@ -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#> .
@@ -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
@@ -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#> .
@@ -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
@@ -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#> .
@@ -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
@@ -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#> .
@@ -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
@@ -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#> .
@@ -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
@@ -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 {
@@ -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> .