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diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/metamodel/MetamodelBuilder.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/metamodel/MetamodelBuilder.java
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+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/metamodel/MetamodelBuilder.java
@@ -0,0 +1,225 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.reasoning.translator.metamodel;
+
+import tools.refinery.store.reasoning.representation.PartialRelation;
+import tools.refinery.store.reasoning.translator.TranslationException;
+import tools.refinery.store.reasoning.translator.containment.ContainmentHierarchyTranslator;
+import tools.refinery.store.reasoning.translator.containment.ContainmentInfo;
+import tools.refinery.store.reasoning.translator.crossreference.DirectedCrossReferenceInfo;
+import tools.refinery.store.reasoning.translator.crossreference.UndirectedCrossReferenceInfo;
+import tools.refinery.store.reasoning.translator.multiplicity.Multiplicity;
+import tools.refinery.store.reasoning.translator.multiplicity.UnconstrainedMultiplicity;
+import tools.refinery.store.reasoning.translator.typehierarchy.TypeInfo;
+
+import java.util.*;
+
+public class MetamodelBuilder {
+        private final ContainedTypeHierarchyBuilder typeHierarchyBuilder = new ContainedTypeHierarchyBuilder();
+        private final Map<PartialRelation, ReferenceInfo> referenceInfoMap = new LinkedHashMap<>();
+        private final Set<PartialRelation> containedTypes = new HashSet<>();
+        private final Map<PartialRelation, ContainmentInfo> containmentHierarchy = new LinkedHashMap<>();
+        private final Map<PartialRelation, DirectedCrossReferenceInfo> directedCrossReferences = new LinkedHashMap<>();
+        private final Map<PartialRelation, UndirectedCrossReferenceInfo> undirectedCrossReferences = new LinkedHashMap<>();
+        private final Map<PartialRelation, PartialRelation> oppositeReferences = new LinkedHashMap<>();
+
+        MetamodelBuilder() {
+                typeHierarchyBuilder.type(ContainmentHierarchyTranslator.CONTAINED_SYMBOL, true);
+        }
+
+        public MetamodelBuilder type(PartialRelation partialRelation, TypeInfo typeInfo) {
+                typeHierarchyBuilder.type(partialRelation, typeInfo);
+                return this;
+
+        }
+
+        public MetamodelBuilder type(PartialRelation partialRelation, boolean abstractType,
+                                                                 PartialRelation... supertypes) {
+                typeHierarchyBuilder.type(partialRelation, abstractType, supertypes);
+                return this;
+        }
+
+        public MetamodelBuilder type(PartialRelation partialRelation, boolean abstractType,
+                                                                 Collection<PartialRelation> supertypes) {
+                typeHierarchyBuilder.type(partialRelation, abstractType, supertypes);
+                return this;
+        }
+
+        public MetamodelBuilder type(PartialRelation partialRelation, PartialRelation... supertypes) {
+                typeHierarchyBuilder.type(partialRelation, supertypes);
+                return this;
+        }
+
+        public MetamodelBuilder type(PartialRelation partialRelation, Collection<PartialRelation> supertypes) {
+                typeHierarchyBuilder.type(partialRelation, supertypes);
+                return this;
+        }
+
+        public MetamodelBuilder types(Collection<Map.Entry<PartialRelation, TypeInfo>> entries) {
+                typeHierarchyBuilder.types(entries);
+                return this;
+        }
+
+        public MetamodelBuilder types(Map<PartialRelation, TypeInfo> map) {
+                typeHierarchyBuilder.types(map);
+                return this;
+        }
+
+        public MetamodelBuilder reference(PartialRelation linkType, ReferenceInfo info) {
+                if (linkType.arity() != 2) {
+                        throw new TranslationException(linkType,
+                                        "Only references of arity 2 are supported, got %s with %d instead".formatted(
+                                                        linkType, linkType.arity()));
+                }
+                var putResult = referenceInfoMap.put(linkType, info);
+                if (putResult != null && !putResult.equals(info)) {
+                        throw new TranslationException(linkType, "Duplicate reference info for partial relation: " + linkType);
+                }
+                return this;
+        }
+
+        public MetamodelBuilder reference(PartialRelation linkType, PartialRelation sourceType, boolean containment,
+                                                                          Multiplicity multiplicity, PartialRelation targetType,
+                                                                          PartialRelation opposite) {
+                return reference(linkType, new ReferenceInfo(containment, sourceType, multiplicity, targetType, opposite));
+        }
+
+        public MetamodelBuilder reference(PartialRelation linkType, PartialRelation sourceType, Multiplicity multiplicity,
+                                                                          PartialRelation targetType, PartialRelation opposite) {
+                return reference(linkType, sourceType, false, multiplicity, targetType, opposite);
+        }
+
+        public MetamodelBuilder reference(PartialRelation linkType, PartialRelation sourceType,
+                                                                          boolean containment, PartialRelation targetType, PartialRelation opposite) {
+                return reference(linkType, sourceType, containment, UnconstrainedMultiplicity.INSTANCE, targetType, opposite);
+        }
+
+        public MetamodelBuilder reference(PartialRelation linkType, PartialRelation sourceType, PartialRelation targetType,
+                                                                          PartialRelation opposite) {
+                return reference(linkType, sourceType, UnconstrainedMultiplicity.INSTANCE, targetType, opposite);
+        }
+
+        public MetamodelBuilder reference(PartialRelation linkType, PartialRelation sourceType, boolean containment,
+                                                                          Multiplicity multiplicity, PartialRelation targetType) {
+                return reference(linkType, sourceType, containment, multiplicity, targetType, null);
+        }
+
+        public MetamodelBuilder reference(PartialRelation linkType, PartialRelation sourceType, Multiplicity multiplicity,
+                                                                          PartialRelation targetType) {
+                return reference(linkType, sourceType, multiplicity, targetType, null);
+        }
+
+        public MetamodelBuilder reference(PartialRelation linkType, PartialRelation sourceType, boolean containment,
+                                                                          PartialRelation targetType) {
+                return reference(linkType, sourceType, containment, targetType, null);
+        }
+
+        public MetamodelBuilder reference(PartialRelation linkType, PartialRelation sourceType,
+                                                                          PartialRelation targetType) {
+                return reference(linkType, sourceType, targetType, null);
+        }
+
+        public MetamodelBuilder references(Collection<Map.Entry<PartialRelation, ReferenceInfo>> entries) {
+                for (var entry : entries) {
+                        reference(entry.getKey(), entry.getValue());
+                }
+                return this;
+        }
+
+        public MetamodelBuilder references(Map<PartialRelation, ReferenceInfo> map) {
+                return references(map.entrySet());
+        }
+
+        public Metamodel build() {
+                for (var entry : referenceInfoMap.entrySet()) {
+                        var linkType = entry.getKey();
+                        var info = entry.getValue();
+                        processReferenceInfo(linkType, info);
+                }
+                typeHierarchyBuilder.setContainedTypes(containedTypes);
+                var typeHierarchy = typeHierarchyBuilder.build();
+                return new Metamodel(typeHierarchy, Collections.unmodifiableMap(containmentHierarchy),
+                                Collections.unmodifiableMap(directedCrossReferences),
+                                Collections.unmodifiableMap(undirectedCrossReferences),
+                                Collections.unmodifiableMap(oppositeReferences));
+        }
+
+        private void processReferenceInfo(PartialRelation linkType, ReferenceInfo info) {
+                if (oppositeReferences.containsKey(linkType) || containmentHierarchy.containsKey(linkType)) {
+                        // We already processed this reference while processing its opposite.
+                        return;
+                }
+                var sourceType = info.sourceType();
+                var targetType = info.targetType();
+                if (typeHierarchyBuilder.isInvalidType(sourceType)) {
+                        throw new TranslationException(linkType, "Source type %s of %s is not in type hierarchy"
+                                        .formatted(sourceType, linkType));
+                }
+                if (typeHierarchyBuilder.isInvalidType(targetType)) {
+                        throw new TranslationException(linkType, "Target type %s of %s is not in type hierarchy"
+                                        .formatted(targetType, linkType));
+                }
+                var opposite = info.opposite();
+                Multiplicity targetMultiplicity = UnconstrainedMultiplicity.INSTANCE;
+                if (opposite != null) {
+                        var oppositeInfo = referenceInfoMap.get(opposite);
+                        validateOpposite(linkType, info, opposite, oppositeInfo);
+                        targetMultiplicity = oppositeInfo.multiplicity();
+                        if (oppositeInfo.containment()) {
+                                // Skip processing this reference and process it once we encounter its containment opposite.
+                                return;
+                        }
+                        if (opposite.equals(linkType)) {
+                                if (!sourceType.equals(targetType)) {
+                                        throw new TranslationException(linkType,
+                                                        "Target %s of undirected reference %s differs from source %s".formatted(
+                                                                        targetType, linkType, sourceType));
+                                }
+                                undirectedCrossReferences.put(linkType, new UndirectedCrossReferenceInfo(sourceType,
+                                                info.multiplicity()));
+                                return;
+                        }
+                        oppositeReferences.put(opposite, linkType);
+                }
+                if (info.containment()) {
+                        if (!UnconstrainedMultiplicity.INSTANCE.equals(targetMultiplicity)) {
+                                throw new TranslationException(opposite, "Invalid opposite %s with multiplicity %s of containment %s"
+                                                .formatted(opposite, targetMultiplicity, linkType));
+                        }
+                        containedTypes.add(targetType);
+                        containmentHierarchy.put(linkType, new ContainmentInfo(sourceType, info.multiplicity(), targetType));
+                        return;
+                }
+                directedCrossReferences.put(linkType, new DirectedCrossReferenceInfo(sourceType, info.multiplicity(),
+                                targetType, targetMultiplicity));
+        }
+
+        private static void validateOpposite(PartialRelation linkType, ReferenceInfo info, PartialRelation opposite,
+                                                                                 ReferenceInfo oppositeInfo) {
+                var sourceType = info.sourceType();
+                var targetType = info.targetType();
+                if (oppositeInfo == null) {
+                        throw new TranslationException(linkType, "Opposite %s of %s is not defined"
+                                        .formatted(opposite, linkType));
+                }
+                if (!linkType.equals(oppositeInfo.opposite())) {
+                        throw new TranslationException(opposite, "Expected %s to have opposite %s, got %s instead"
+                                        .formatted(opposite, linkType, oppositeInfo.opposite()));
+                }
+                if (!targetType.equals(oppositeInfo.sourceType())) {
+                        throw new TranslationException(linkType, "Expected %s to have source type %s, got %s instead"
+                                        .formatted(opposite, targetType, oppositeInfo.sourceType()));
+                }
+                if (!sourceType.equals(oppositeInfo.targetType())) {
+                        throw new TranslationException(linkType, "Expected %s to have target type %s, got %s instead"
+                                        .formatted(opposite, sourceType, oppositeInfo.targetType()));
+                }
+                if (oppositeInfo.containment() && info.containment()) {
+                        throw new TranslationException(opposite, "Opposite %s of containment %s cannot be containment"
+                                        .formatted(opposite, linkType));
+                }
+        }
+}