Merge pull request #1143 from EBISPOT/sssom_predicates_update

Added missing SSSOM predicates

Author: henrietteharmse

dataload/extras/json2sssom/src/main/java/CurieMap.java

@@ -23,6 +23,7 @@ public static class CurieMapping {
     public CurieMap() {
         addMapping("semapv", "https://w3id.org/semapv/vocab/");
         addMapping("owl", "http://www.w3.org/2002/07/owl#");
+        addMapping("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
         addMapping("skos", "http://www.w3.org/2004/02/skos/core#");
         addMapping("oboInOwl", "http://www.geneontology.org/formats/oboInOwl#");
         addMapping("chebi", "http://purl.obolibrary.org/obo/chebi/");
@@ -31,10 +32,37 @@ public CurieMap() {
         addMapping("smiles", "https://bioregistry.io/smiles:");
     }
 
+
+    private static boolean isIRI(String str) {
+        if (str == null || str.trim().isEmpty()) {
+            return false;
+        }
+        
+        String trimmed = str.trim();
+        
+        if (!trimmed.contains(":")) {
+            return false;
+        }
+        
+        int colonIndex = trimmed.indexOf(':');
+        if (colonIndex == 0 || colonIndex == trimmed.length() - 1) {
+            return false;
+        }
+        
+        String scheme = trimmed.substring(0, colonIndex);
+        if (scheme.isEmpty() || !scheme.matches("^[a-zA-Z][a-zA-Z0-9+.-]*$")) {
+            return false;
+        }
+        
+        return true;
+    }
+
+
     public CurieMapping mapEntity(JsonObject entityOrLinkedEntity) {
 
         String iriOrUrl = null;
 
+
         if(entityOrLinkedEntity.has("iri")) {
             iriOrUrl = entityOrLinkedEntity.get("iri").getAsString();
         } else if(entityOrLinkedEntity.has("url")) {
@@ -122,4 +150,102 @@ private void addMapping(String curiePrefix, String curieNamespace) {
     }
 
 
+    public CurieMapping mapEntity(JsonObject entityOrLinkedEntity, String valueIRIOrUrl) {
+
+        String iriOrUrl = null;
+
+
+        if(entityOrLinkedEntity.has("iri")) {
+            iriOrUrl = entityOrLinkedEntity.get("iri").getAsString();
+        } else if(entityOrLinkedEntity.has("url")) {
+            iriOrUrl = entityOrLinkedEntity.get("url").getAsString();
+        }
+
+        if(!entityOrLinkedEntity.has("curie")) {
+            if(iriOrUrl == null) {
+                return null;
+            }
+            CurieMapping mapping = new CurieMapping();
+            mapping.iriOrUrl = iriOrUrl;
+            return mapping;
+        }
+
+        String curie = JsonHelper.getFirstStringValue(entityOrLinkedEntity.get("curie"));
+
+        if(!curie.contains(":")) {
+            if (curie.length() > 100) {
+                curie = curie.substring(0, 100);
+                System.out.println("Curie provided by OLS " + curie + 
+                    " does not look like a curie, in entity/linkedEntity: " + gson.toJson(entityOrLinkedEntity) + 
+                    " . Curie truncated to 100 characters.");
+            } else {
+                System.out.println("Curie provided by OLS " + curie + 
+
+                    " does not look like a curie, in entity/linkedEntity: " + gson.toJson(entityOrLinkedEntity));
+            }
+            // TODO ???
+            return null;
+        }
+
+        String curiePrefix = curie.split(":")[0];
+        String curieLocalPart = curie.split(":")[1];
+        if (iriOrUrl == null && isIRI(valueIRIOrUrl)) {
+            iriOrUrl = valueIRIOrUrl;
+        }
+        if(iriOrUrl == null || !iriOrUrl.endsWith(curieLocalPart)) {
+            System.out.println(iriOrUrl + " does not end with local part of curie " + curie + ". This mapping will be omitted from the results.");
+
+            // We can't print the iri/url in SSSOM and we can't put the CURIE in the prefix map
+            // TODO: Currently we just drop the mapping, maybe a better way to approach this.
+            //
+            return null;
+//            CurieMapping mapping = new CurieMapping();
+//            mapping.curiePrefix = curiePrefix;
+//            mapping.curieLocalPart = curieLocalPart;
+//            mapping.curie = curie;
+//            return mapping;
+        }
+
+        String curieNamespace = iriOrUrl.substring(0, iriOrUrl.length() - curieLocalPart.length());
+
+        if(curiePrefixToNamespace.containsKey(curiePrefix)) {
+
+            String existingNs = curiePrefixToNamespace.get(curiePrefix);
+
+            if(!existingNs.equals(curieNamespace)) {
+
+                String origCurieForDebugLog = curiePrefix;
+
+                // try to find a different curie prefix for this namespace
+                String nsToCp = namespaceToCuriePrefix.get(curieNamespace);
+                if(nsToCp != null) {
+                    curiePrefix = nsToCp;
+                    curie = curiePrefix + ":" + curieLocalPart;
+                } else {
+                    // establish this namespace as a curie prefix
+                    int n = 2;
+                    while(curiePrefixToNamespace.containsKey(curiePrefix + "_" + n)) {
+                        ++ n;
+                    }
+                    curiePrefix = curiePrefix + "_" + n;
+                    curie = curiePrefix + ":" + curieLocalPart;
+                    addMapping(curiePrefix, curieNamespace);
+                }
+//                System.out.println("Namespace " + curieNamespace + " did not match existing namespace " + existingNs + " for curie prefix " + origCurieForDebugLog + ". Using " + curiePrefix + " instead. In entity/linkedEntity: " + gson.toJson(entityOrLinkedEntity));
+            }
+
+        } else {
+            addMapping(curiePrefix, curieNamespace);
+        }
+
+        CurieMapping mapping = new CurieMapping();
+        mapping.iriOrUrl = iriOrUrl;
+        mapping.curie = curie;
+        mapping.curiePrefix = curiePrefix;
+        mapping.curieLocalPart = curieLocalPart;
+        mapping.curieNamespace = curieNamespace;
+        return mapping;
+    }
+
+
 }

dataload/extras/json2sssom/src/main/java/JSON2SSSOM.java

@@ -157,15 +157,55 @@ public static void writeMappingsForEntity(JsonObject entity, CSVPrinter writer,
         JsonElement exactMatch = entity.get("http://www.w3.org/2004/02/skos/core#exactMatch");
         if(exactMatch != null) {
             writeMappingsForEntity(entity, "skos:exactMatch", exactMatch, null, null, ontologyProperties, writer, curieMap);
+        }        
+        JsonElement narrowMatch = entity.get("http://www.w3.org/2004/02/skos/core#narrowMatch");
+        if(narrowMatch != null) {
+            writeMappingsForEntity(entity, "skos:narrowMatch", narrowMatch, null, null, ontologyProperties, writer, curieMap);
         }
+        JsonElement broadMatch = entity.get("http://www.w3.org/2004/02/skos/core#broadMatch");
+        if(broadMatch != null) {
+            writeMappingsForEntity(entity, "skos:broadMatch", broadMatch, null, null, ontologyProperties, writer, curieMap);
+        }
+        JsonElement relatedMatch = entity.get("http://www.w3.org/2004/02/skos/core#relatedMatch");
+        if(relatedMatch != null) {
+            writeMappingsForEntity(entity, "skos:relatedMatch", relatedMatch, null, null, ontologyProperties, writer, curieMap);
+        }   
+        JsonElement closeMatch = entity.get("http://www.w3.org/2004/02/skos/core#closeMatch");
+        if(closeMatch != null) {
+            writeMappingsForEntity(entity, "skos:closeMatch", closeMatch, null, null, ontologyProperties, writer, curieMap);
+        }                
+
         JsonElement hasDbXref = entity.get("http://www.geneontology.org/formats/oboInOwl#hasDbXref");
         if(hasDbXref != null) {
             writeMappingsForEntity(entity, "oboInOwl:hasDbXref", hasDbXref, null, null, ontologyProperties, writer, curieMap);
         }
+
+
         JsonElement equivalentClass = entity.get("http://www.w3.org/2002/07/owl#equivalentClass");
         if(equivalentClass != null) {
             writeMappingsForEntity(entity, "owl:equivalentClass", equivalentClass, null, null, ontologyProperties, writer, curieMap);
+
         }
+        JsonElement equivalentProperty = entity.get("http://www.w3.org/2002/07/owl#equivalentProperty");
+        if(equivalentProperty != null) {
+            writeMappingsForEntity(entity, "owl:equivalentProperty", equivalentProperty, null, null, ontologyProperties, writer, curieMap);
+        }     
+        JsonElement sameAs = entity.get("http://www.w3.org/2002/07/owl#sameAs");
+        if(sameAs != null) {
+            writeMappingsForEntity(entity, "owl:sameAs", sameAs, null, null, ontologyProperties, writer, curieMap);
+        }     
+        
+        JsonElement subClassOf = entity.get("http://www.w3.org/2000/01/rdf-schema#subClassOf");
+        if(subClassOf != null) {
+            writeMappingsForEntity(entity, "rdfs:subClassOf", subClassOf, null, null, ontologyProperties, writer, curieMap);
+
+        }
+        JsonElement subPropertyOf = entity.get("http://www.w3.org/2000/01/rdf-schema#subPropertyOf");
+        if(subPropertyOf != null) {
+            writeMappingsForEntity(entity, "rdfs:subPropertyOf", subPropertyOf, null, null, ontologyProperties, writer, curieMap);
+
+        }        
+        
 
         // hacky special cases for chemical specific mapping predicates
         //
@@ -269,7 +309,7 @@ public static void writeMappingsForEntity(
 
                 JsonObject linkedEntity = linkedEntityElem.getAsJsonObject();
 
-                CurieMap.CurieMapping objCurie = curieMap.mapEntity(linkedEntity);
+                CurieMap.CurieMapping objCurie = curieMap.mapEntity(linkedEntity, value);
 
                 if(objCurie == null) {
                     return;
@@ -318,6 +358,9 @@ public static void writeMappingsForEntity(
         }
     }
 
+    private static boolean isNotOWLAxiom(){
+        return true;
+    }