Fix bugs in the mapping rules of the interactions

frmichel · Jul 30, 2024 · 9f48f92 · 9f48f92
1 parent 644b75d
commit 9f48f92
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Showing 3 changed files with 20 additions and 9 deletions.
diff --git a/src/xr2rml/xr2rml_interactions_source_taxon.ttl b/src/xr2rml/xr2rml_interactions_source_taxon.ttl
@@ -37,10 +37,10 @@
     rr:class owl:Class.
 
 <#TPL_intersectionOf_BN>
-    rr:template "intersectionOf_{$._id}_{$.taxon.referenceId}_{$.taxonStage}_{$.taxonSex}"; rr:termType rr:BlankNode.
+    rr:template "intersectionOf_{$.taxon.referenceId}_{$.taxonStage}_{$.taxonSex}"; rr:termType rr:BlankNode.
 
 <#TPL_intersectionOf_list1>
-    rr:template "list1_{$.taxon.referenceId}_{$._id}_stage_{$.taxonStage}_sex_{$.taxonSex}"; rr:termType rr:BlankNode.
+    rr:template "list1_{$.taxon.referenceId}_stage_{$.taxonStage}_sex_{$.taxonSex}"; rr:termType rr:BlankNode.
 
 
 # Stage and no sex
@@ -90,7 +90,7 @@
     rr:predicateObjectMap [ rr:predicate rdf:rest;  rr:objectMap <#TPL_intersectionOf_list2_taxon_stage> ].
 
 <#TPL_intersectionOf_list2_taxon_stage>
-    rr:template "list2_{$._id}_{$.taxon.referenceId}_stage_{$.taxonStage}"; rr:termType rr:BlankNode.
+    rr:template "list2_{$.taxon.referenceId}_stage_{$.taxonStage}"; rr:termType rr:BlankNode.
 
 <#TM_intersectionOf_list2_taxon_stage>
     a rr:TriplesMap;
@@ -111,7 +111,7 @@
     rr:predicateObjectMap [ rr:predicate rdf:rest;  rr:objectMap <#TPL_intersectionOf_list2_taxon_sex> ].
 
 <#TPL_intersectionOf_list2_taxon_sex>
-    rr:template "list2_{$._id}_{$.taxon.referenceId}_sex_{$.taxonSex}"; rr:termType rr:BlankNode.
+    rr:template "list2_{$.taxon.referenceId}_sex_{$.taxonSex}"; rr:termType rr:BlankNode.
 
 <#TM_intersectionOf_list2_taxon_sex>
     a rr:TriplesMap;
@@ -132,7 +132,7 @@
     rr:predicateObjectMap [ rr:predicate rdf:rest;  rr:objectMap <#TPL_intersectionOf_list2_taxon_stage_sex> ].
 
 <#TPL_intersectionOf_list2_taxon_stage_sex>
-    rr:template "list2_{$._id}_{$.taxon.referenceId}_stage_{$.taxonStage}_sex_{$.taxonSex}"; rr:termType rr:BlankNode.
+    rr:template "list2_{$.taxon.referenceId}_stage_{$.taxonStage}_sex_{$.taxonSex}"; rr:termType rr:BlankNode.
 
 <#TM_intersectionOf_list2_taxon_stage_sex>
     a rr:TriplesMap;
@@ -143,7 +143,7 @@
     rr:predicateObjectMap [ rr:predicate rdf:rest;  rr:objectMap <#TPL_intersectionOf_list3_taxon_stage_sex> ].
 
 <#TPL_intersectionOf_list3_taxon_stage_sex>
-    rr:template "list3_{$._id}_{$.taxon.referenceId}_stage_{$.taxonStage}_sex_{$.taxonSex}"; rr:termType rr:BlankNode.
+    rr:template "list3_{$.taxon.referenceId}_stage_{$.taxonStage}_sex_{$.taxonSex}"; rr:termType rr:BlankNode.
 
 <#TM_intersectionOf_list3_taxon_stage_sex>
     a rr:TriplesMap;

diff --git a/src/xr2rml/xr2rml_interactions_target_taxon.ttl b/src/xr2rml/xr2rml_interactions_target_taxon.ttl
@@ -36,10 +36,10 @@
     rr:class owl:Class.
 
 <#TPL_intersectionOf_BN>
-    rr:template "intersectionOf_{$._id}_{$.target.referenceId}_{$.targetStage}"; rr:termType rr:BlankNode.
+    rr:template "intersectionOf_{$.target.referenceId}_{$.targetStage}"; rr:termType rr:BlankNode.
 
 <#TPL_intersectionOf_list1>
-    rr:template "list_{$._id}_{$.target.referenceId}_{$.targetStage}"; rr:termType rr:BlankNode.
+    rr:template "list_{$.target.referenceId}_{$.targetStage}"; rr:termType rr:BlankNode.
 
 
 <#LS_Extd_Stage> xrr:query """db.interactions.find({'targetStage': {$ne: null}})""".
@@ -64,7 +64,7 @@
     rr:predicateObjectMap [ rr:predicate rdf:rest;  rr:objectMap <#TPL_intersectionOf_list2_taxon_stage> ].
 
 <#TPL_intersectionOf_list2_taxon_stage>
-    rr:template "sublist_{$._id}_{$.target.referenceId}_{$.targetStage}"; rr:termType rr:BlankNode.
+    rr:template "sublist_{$.target.referenceId}_{$.targetStage}"; rr:termType rr:BlankNode.
 
 <#TM_intersectionOf_list2_taxon_stage>
     a rr:TriplesMap;

diff --git a/src/xr2rml/xr2rml_taxonomy_concepts.ttl b/src/xr2rml/xr2rml_taxonomy_concepts.ttl
@@ -126,6 +126,17 @@
 	.
 
 
+<#TM_Name_In_Collection>
+    a rr:TriplesMap;
+    xrr:logicalSource [ xrr:query """db.taxonomy.find()"""; ];
+    rr:subject taxref:TaxonomicNameCollection;
+    rr:predicateObjectMap [
+        rr:predicate skos:member;
+        rr:objectMap [ rr:template "http://taxref.mnhn.fr/lod/name/{$.id}"; rr:termType rr:IRI; ];
+    ].
+
+
+
 # ---------------------------------------------------------------------------------
 # Taxonomical rank for names
 # ---------------------------------------------------------------------------------