diff --git a/src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java b/src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java
index c3f68a0f..f33eb4bb 100644
--- a/src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java
+++ b/src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java
@@ -233,12 +233,45 @@ public void setUntrackedFiles(Collection<File> files) {
         this.untrackedFiles = files;
     }
 
+    private boolean isKeyUnused(String key, ObjectNode node) {
+        Iterator<Map.Entry<String, JsonNode>> fields = node.fields();
+        while (fields.hasNext()) {
+            Map.Entry<String, JsonNode> entry = fields.next();
+            String fieldName = entry.getKey();
+            if (fieldName.startsWith(key)) {
+                return false;
+            }
+            JsonNode value = entry.getValue();
+            if (value.isObject()) {
+                if (!isKeyUnused(key, (ObjectNode) value)) {
+                    return false;
+                }
+            } else if (value.isArray()) {
+                for (JsonNode element : value) {
+                    if (element.isObject() && !isKeyUnused(key, (ObjectNode) element)) {
+                        return false;
+                    }
+                }
+            }
+        }
+        return true;
+    }
+
+    public boolean cleanupContext() {
+        // TODO we are missing the relations between the pairs and the URL, in order to check if a URL can be removed.
+        var contextUrls = this.metadataContext.getUrls();
+        var contextAllKeys = this.metadataContext.getKeys();
+        var contextExplicitKeys = this.metadataContext.getExplicitKeys();
+    }
+
     @Override
+    @Deprecated(forRemoval = true)
     public void deleteValuePairFromContext(String key) {
         this.metadataContext.deleteValuePairFromContext(key);
     }
 
     @Override
+    @Deprecated(forRemoval = true)
     public void deleteUrlFromContext(String key) {
         this.metadataContext.deleteUrlFromContext(key);
     }
diff --git a/src/main/java/edu/kit/datamanager/ro_crate/context/CrateMetadataContext.java b/src/main/java/edu/kit/datamanager/ro_crate/context/CrateMetadataContext.java
index dfe6548e..b74fa70b 100644
--- a/src/main/java/edu/kit/datamanager/ro_crate/context/CrateMetadataContext.java
+++ b/src/main/java/edu/kit/datamanager/ro_crate/context/CrateMetadataContext.java
@@ -38,12 +38,25 @@ public interface CrateMetadataContext {
    */
   Set<String> getKeys();
 
+  /**
+   * Get an immutable collection of the keys in the metadata context that are
+   * explicitly set, not indirectly using a URL.
+   * @return the explicitly set keys in the metadata context
+   */
+  Set<String> getExplicitKeys();
+
   /**
   * Get an immutable map of the context.
   * @return an immutable map containing the context key-value pairs
   */
   Map<String, String> getPairs();
 
+  /**
+   * Get an immutable collection of the urls in the metadata context.
+   * @return the urls in the metadata context
+   */
+  Set<String> getUrls();
+
   void deleteValuePairFromContext(String key);
 
   void deleteUrlFromContext(String url);
diff --git a/src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java b/src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java
index 731a4c1a..4c08c428 100644
--- a/src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java
+++ b/src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java
@@ -214,6 +214,11 @@ public Set<String> getKeys() {
     return Set.copyOf(merged);
   }
 
+  @Override
+  public Set<String> getExplicitKeys() {
+    return Set.copyOf(this.other.keySet());
+  }
+
   @Override
   public Map<String, String> getPairs() {
     Map<String, String> merged = new HashMap<>();
@@ -222,6 +227,11 @@ public Map<String, String> getPairs() {
     return Map.copyOf(merged);
   }
 
+  @Override
+  public Set<String> getUrls() {
+    return Set.copyOf(this.urls);
+  }
+
 
   @Override
   public void deleteValuePairFromContext(String key) {