diff --git a/schema_salad/metaschema/metaschema.yml b/schema_salad/metaschema/metaschema.yml
index d4ec75b51..3de1f9dcc 100644
--- a/schema_salad/metaschema/metaschema.yml
+++ b/schema_salad/metaschema/metaschema.yml
@@ -194,10 +194,8 @@ $graph:
   fields:
     - name: doc
       type:
-        - "null"
-        - string
-        - type: array
-          items: string
+        - string?
+        - string[]?
       doc: "A documentation string for this type, or an array of strings which should be concatenated."
       jsonldPredicate: "sld:doc"
 
@@ -212,10 +210,8 @@ $graph:
 
     - name: docChild
       type:
-        - "null"
-        - string
-        - type: array
-          items: string
+        - string?
+        - string[]?
       doc: |
         Hint to indicate that during documentation generation, documentation
         for `docChild` should appear in a subsection under this type.
@@ -236,19 +232,18 @@ $graph:
 
 - name: SchemaDefinedType
   type: record
-  extends: "#DocType"
+  extends: DocType
   doc: |
     Abstract base for schema-defined types.
   abstract: true
   fields:
     - name: jsonldPredicate
       type:
-        - "null"
-        - string
-        - "#JsonldPredicate"
+        - string?
+        - JsonldPredicate?
       doc: |
         Annotate this type with linked data context.
-      jsonldPredicate: "sld:jsonldPredicate"
+      jsonldPredicate: sld:jsonldPredicate
 
     - name: documentRoot
       type: boolean?
@@ -259,7 +254,7 @@ $graph:
 
 - name: RecordField
   type: record
-  doc: "A field of a record."
+  doc: A field of a record.
   fields:
     - name: name
       type: string
@@ -275,36 +270,36 @@ $graph:
 
     - name: type
       type:
-        - "#PrimitiveType"
-        - "#RecordSchema"
-        - "#EnumSchema"
-        - "#ArraySchema"
+        - PrimitiveType
+        - RecordSchema
+        - EnumSchema
+        - ArraySchema
         - string
         - type: array
           items:
-            - "#PrimitiveType"
-            - "#RecordSchema"
-            - "#EnumSchema"
-            - "#ArraySchema"
+            - PrimitiveType
+            - RecordSchema
+            - EnumSchema
+            - ArraySchema
             - string
       jsonldPredicate:
-        _id: "sld:type"
+        _id: sld:type
         _type: "@vocab"
         typeDSL: true
+        refScope: 0
       doc: |
         The field type
 
 
 - name: SaladRecordField
   type: record
-  extends: "#RecordField"
+  extends: RecordField
   doc: "A field of a record."
   fields:
     - name: jsonldPredicate
       type:
-        - "null"
-        - string
-        - "#JsonldPredicate"
+        - string?
+        - JsonldPredicate?
       doc: |
         Annotate this type with linked data context.
       jsonldPredicate: "sld:jsonldPredicate"
@@ -323,19 +318,16 @@ $graph:
         _id: "sld:type"
         _type: "@vocab"
         typeDSL: true
+        refScope: 0
     - name: "fields"
-      type:
-        - "null"
-        - type: "array"
-          items: "#RecordField"
-
+      type: RecordField[]?
       jsonldPredicate: "sld:fields"
       doc: "Defines the fields of the record."
 
 
 - name: SaladRecordSchema
   type: record
-  extends: ["#NamedType", "#RecordSchema", "#SchemaDefinedType"]
+  extends: [NamedType, RecordSchema, SchemaDefinedType]
   documentRoot: true
   specialize:
     specializeFrom: "#RecordField"
@@ -349,22 +341,19 @@ $graph:
 
     - name: extends
       type:
-        - "null"
-        - string
-        - type: array
-          items: string
+        - string?
+        - string[]?
       jsonldPredicate:
         _id: "sld:extends"
         _type: "@id"
+        refScope: 0
       doc: |
         Indicates that this record inherits fields from one or more base records.
 
     - name: specialize
       type:
-        - "null"
-        - "#SpecializeDef"
-        - type: array
-          items: "#SpecializeDef"
+        - SpecializeDef?
+        - SpecializeDef[]?
       doc: |
         Only applies if `extends` is declared.  Apply type specialization using the
         base record as a template.  For each field inherited from the base
@@ -388,10 +377,9 @@ $graph:
         _id: "sld:type"
         _type: "@vocab"
         typeDSL: true
+        refScope: 0
     - name: "symbols"
-      type:
-        - type: "array"
-          items: "string"
+      type: string[]
       jsonldPredicate:
         _id: "sld:symbols"
         _type: "@id"
@@ -401,20 +389,19 @@ $graph:
 
 - name: SaladEnumSchema
   type: record
-  extends: ["#EnumSchema", "#SchemaDefinedType"]
+  extends: [EnumSchema, SchemaDefinedType]
   documentRoot: true
   doc: |
     Define an enumerated type.
   fields:
     - name: extends
       type:
-        - "null"
-        - string
-        - type: array
-          items: string
+        - string?
+        - string[]?
       jsonldPredicate:
         _id: "sld:extends"
         _type: "@id"
+        refScope: 0
       doc: |
         Indicates that this enum inherits symbols from a base enum.
 
@@ -433,29 +420,31 @@ $graph:
         _id: "sld:type"
         _type: "@vocab"
         typeDSL: true
+        refScope: 0
     - name: items
       type:
-        - "#PrimitiveType"
-        - "#RecordSchema"
-        - "#EnumSchema"
-        - "#ArraySchema"
+        - PrimitiveType
+        - RecordSchema
+        - EnumSchema
+        - ArraySchema
         - string
         - type: array
           items:
-            - "#PrimitiveType"
-            - "#RecordSchema"
-            - "#EnumSchema"
-            - "#ArraySchema"
+            - PrimitiveType
+            - RecordSchema
+            - EnumSchema
+            - ArraySchema
             - string
       jsonldPredicate:
         _id: "sld:items"
         _type: "@vocab"
+        refScope: 0
       doc: "Defines the type of the array elements."
 
 
 - name: Documentation
   type: record
-  extends: ["#NamedType", "#DocType"]
+  extends: [NamedType, DocType]
   documentRoot: true
   doc: |
     A documentation section.  This type exists to facilitate self-documenting
@@ -471,4 +460,5 @@ $graph:
       jsonldPredicate:
         _id: "sld:type"
         _type: "@vocab"
-        typeDSL: true
\ No newline at end of file
+        typeDSL: true
+        refScope: 0
diff --git a/schema_salad/ref_resolver.py b/schema_salad/ref_resolver.py
index 0a303ae19..4fac058e0 100644
--- a/schema_salad/ref_resolver.py
+++ b/schema_salad/ref_resolver.py
@@ -110,7 +110,7 @@ def __init__(self, ctx, schemagraph=None, foreign_properties=None,
 
         self.add_context(ctx)
 
-    def expand_url(self, url, base_url, scoped=False, vocab_term=False):
+    def expand_url(self, url, base_url, scoped_id=False, vocab_term=False, scoped_ref=None):
         # type: (Union[str, unicode], Union[str, unicode], bool, bool) -> Union[str, unicode]
         if url in ("@id", "@type"):
             return url
@@ -127,7 +127,7 @@ def expand_url(self, url, base_url, scoped=False, vocab_term=False):
 
         if split.scheme or url.startswith("$(") or url.startswith("${"):
             pass
-        elif scoped and not split.fragment:
+        elif scoped_id and not split.fragment:
             splitbase = urlparse.urlsplit(base_url)
             frg = ""
             if splitbase.fragment:
@@ -136,6 +136,8 @@ def expand_url(self, url, base_url, scoped=False, vocab_term=False):
                 frg = split.path
             url = urlparse.urlunsplit(
                 (splitbase.scheme, splitbase.netloc, splitbase.path, splitbase.query, frg))
+        elif scoped_ref is not None and not split.fragment:
+            pass
         else:
             url = urlparse.urljoin(base_url, url)
 
@@ -219,6 +221,8 @@ def add_context(self, newcontext, baseuri=""):
             elif isinstance(value, dict) and value.get("@type") == "@vocab":
                 self.url_fields.add(key)
                 self.vocab_fields.add(key)
+                if "refScope" in value:
+                    self.scoped_ref_fields[key] = value["refScope"]
                 if value.get("typeDSL"):
                     self.type_dsl_fields.add(key)
             if isinstance(value, dict) and value.get("noLinkCheck"):
@@ -236,7 +240,7 @@ def add_context(self, newcontext, baseuri=""):
                 self.vocab[key] = value
 
         for k, v in self.vocab.items():
-            self.rvocab[self.expand_url(v, "", scoped=False)] = k
+            self.rvocab[self.expand_url(v, "", scoped_id=False)] = k
 
         _logger.debug("identifiers is %s", self.identifiers)
         _logger.debug("identity_links is %s", self.identity_links)
@@ -282,7 +286,7 @@ def resolve_ref(self, ref, base_url=None, checklinks=True):
         if not isinstance(ref, (str, unicode)):
             raise ValueError("Must be string: `%s`" % str(ref))
 
-        url = self.expand_url(ref, base_url, scoped=(obj is not None))
+        url = self.expand_url(ref, base_url, scoped_id=(obj is not None))
 
         # Has this reference been loaded already?
         if url in self.idx:
@@ -364,7 +368,6 @@ def _type_dsl(self, t):
                  "items": r}
         if m.group(3):
             r = ["null", r]
-        print t, "DSL to", r
         return r
 
     def _resolve_type_dsl(self, document, loader):
@@ -391,7 +394,7 @@ def _resolve_identifier(self, document, loader, base_url):
             if identifer in document:
                 if isinstance(document[identifer], basestring):
                     document[identifer] = loader.expand_url(
-                        document[identifer], base_url, scoped=True)
+                        document[identifer], base_url, scoped_id=True)
                     if document[identifer] not in loader.idx or isinstance(loader.idx[document[identifer]], basestring):
                         loader.idx[document[identifer]] = document
                     base_url = document[identifer]
@@ -408,7 +411,7 @@ def _resolve_identity(self, document, loader, base_url):
                 for n, v in enumerate(document[identifer]):
                     if isinstance(document[identifer][n], basestring):
                         document[identifer][n] = loader.expand_url(
-                            document[identifer][n], base_url, scoped=True)
+                            document[identifer][n], base_url, scoped_id=True)
                         if document[identifer][n] not in loader.idx:
                             loader.idx[document[identifer][
                                 n]] = document[identifer][n]
@@ -416,7 +419,7 @@ def _resolve_identity(self, document, loader, base_url):
     def _normalize_fields(self, document, loader):
         # Normalize fields which are prefixed or full URIn to vocabulary terms
         for d in document:
-            d2 = loader.expand_url(d, "", scoped=False, vocab_term=True)
+            d2 = loader.expand_url(d, "", scoped_id=False, vocab_term=True)
             if d != d2:
                 document[d2] = document[d]
                 del document[d]
@@ -424,17 +427,18 @@ def _normalize_fields(self, document, loader):
     def _resolve_uris(self, document, loader, base_url):
         # Resolve remaining URLs based on document base
         for d in loader.url_fields:
-            if d in self.scoped_ref_fields:
-                continue
             if d in document:
                 if isinstance(document[d], basestring):
                     document[d] = loader.expand_url(
-                        document[d], base_url, scoped=False, vocab_term=(d in loader.vocab_fields))
+                        document[d], base_url, scoped_id=False,
+                        vocab_term=(d in loader.vocab_fields),
+                        scoped_ref=self.scoped_ref_fields.get(d))
                 elif isinstance(document[d], list):
                     document[d] = [
                         loader.expand_url(
-                            url, base_url, scoped=False,
-                            vocab_term=(d in loader.vocab_fields))
+                            url, base_url, scoped_id=False,
+                            vocab_term=(d in loader.vocab_fields),
+                            scoped_ref=self.scoped_ref_fields.get(d))
                         if isinstance(url, (str, unicode))
                         else url for url in document[d]]
 
@@ -531,7 +535,7 @@ def resolve_all(self, document, base_url, file_base=None, checklinks=True):
                 if identifer in metadata:
                     if isinstance(metadata[identifer], (str, unicode)):
                         metadata[identifer] = loader.expand_url(
-                            metadata[identifer], base_url, scoped=True)
+                            metadata[identifer], base_url, scoped_id=True)
                         loader.idx[metadata[identifer]] = document
 
         if checklinks:
@@ -598,6 +602,28 @@ def check_file(self, fn):  # type: (Union[str, unicode]) -> bool
 
     FieldType = TypeVar('FieldType', unicode, List[str], Dict[str, Any])
 
+    def validate_scoped(self, field, link, docid):
+        split = urlparse.urlsplit(docid)
+        sp = split.fragment.split("/")
+        n = self.scoped_ref_fields[field]
+        while n > 0 and len(sp) > 0:
+            sp.pop()
+            n -= 1
+        tried = []
+        while True:
+            sp.append(str(link))
+            url = urlparse.urlunsplit(
+                (split.scheme, split.netloc, split.path, split.query, "/".join(sp)))
+            tried.append(url)
+            if url in self.idx:
+                return url
+            sp.pop()
+            if len(sp) == 0:
+                break
+            sp.pop()
+        raise validate.ValidationException(
+            "Field `%s` contains undefined reference to `%s`, tried %s" % (field, link, tried))
+
     def validate_link(self, field, link, docid):
         # type: (AnyStr, FieldType, AnyStr) -> FieldType
         if field in self.nolinkcheck:
@@ -605,29 +631,14 @@ def validate_link(self, field, link, docid):
         if isinstance(link, (str, unicode)):
             if field in self.vocab_fields:
                 if link not in self.vocab and link not in self.idx and link not in self.rvocab:
-                    if not self.check_file(link):
+                    if field in self.scoped_ref_fields:
+                        return self.validate_scoped(field, link, docid)
+                    elif not self.check_file(link):
                         raise validate.ValidationException(
                             "Field `%s` contains undefined reference to `%s`" % (field, link))
             elif link not in self.idx and link not in self.rvocab:
                 if field in self.scoped_ref_fields:
-                    split = urlparse.urlsplit(docid)
-                    sp = split.fragment.split("/")
-                    n = self.scoped_ref_fields[field]
-                    while n > 0 and len(sp) > 0:
-                        sp.pop()
-                        n -= 1
-                    while True:
-                        sp.append(str(link))
-                        url = urlparse.urlunsplit(
-                            (split.scheme, split.netloc, split.path, split.query, "/".join(sp)))
-                        if url in self.idx:
-                            return url
-                        sp.pop()
-                        if len(sp) == 0:
-                            break
-                        sp.pop()
-                    raise validate.ValidationException(
-                        "Field `%s` contains undefined reference to `%s`" % (field, link))
+                    return self.validate_scoped(field, link, docid)
                 elif not self.check_file(link):
                     raise validate.ValidationException(
                         "Field `%s` contains undefined reference to `%s`" % (field, link))
diff --git a/schema_salad/schema.py b/schema_salad/schema.py
index 9be8ac718..067538f72 100644
--- a/schema_salad/schema.py
+++ b/schema_salad/schema.py
@@ -93,7 +93,8 @@ def get_metaschema():
         "enum": "https://w3id.org/cwl/salad#enum",
         "extends": {
             "@id": "https://w3id.org/cwl/salad#extends",
-            "@type": "@id"
+            "@type": "@id",
+            "refScope": 0
         },
         "fields": "sld:fields",
         "float": "http://www.w3.org/2001/XMLSchema#float",
@@ -101,7 +102,8 @@ def get_metaschema():
         "int": "http://www.w3.org/2001/XMLSchema#int",
         "items": {
             "@id": "https://w3id.org/cwl/salad#items",
-            "@type": "@vocab"
+            "@type": "@vocab",
+            "refScope": 0
         },
         "jsonldPredicate": "sld:jsonldPredicate",
         "long": "http://www.w3.org/2001/XMLSchema#long",
@@ -133,7 +135,8 @@ def get_metaschema():
         "type": {
             "@id": "https://w3id.org/cwl/salad#type",
             "@type": "@vocab",
-            "typeDSL": True
+            "typeDSL": True,
+            "refScope": 0
         },
         "typeDSL": "https://w3id.org/cwl/salad#JsonldPredicate/typeDSL",
         "xsd": "http://www.w3.org/2001/XMLSchema#"
diff --git a/tests/test_examples.py b/tests/test_examples.py
index 2e847d0a2..8a657f445 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -139,7 +139,8 @@ def test_scoped_ref(self):
 
         ra, _ = ldr.resolve_all({
             "inputs": {
-                "inp": "string"
+                "inp": "string",
+                "inp2": "string"
             },
             "outputs": {
                 "out": {
@@ -150,7 +151,9 @@ def test_scoped_ref(self):
             "steps": {
                 "step1": {
                     "in": {
-                        "inp": "inp"
+                        "inp": "inp",
+                        "inp2": "#inp2",
+                        "inp3": ["inp", "inp2"]
                     },
                     "out": ["out"],
                     "scatter": "inp"
@@ -181,6 +184,9 @@ def test_scoped_ref(self):
                     'in': [{
                             'id': 'http://example2.com/#step1/inp',
                             'source': 'http://example2.com/#inp'
+                    }, {
+                            'id': 'http://example2.com/#step1/inp2',
+                            'source': 'http://example2.com/#inp'
                     }],
                     "out": ["http://example2.com/#step1/out"],
             }, {
@@ -223,13 +229,16 @@ def test_typedsl_ref(self):
         })
 
         ra, _ = ldr.resolve_all({"type": "File"}, "")
-        print ra
+        self.assertEqual({'type': 'File'}, ra)
+
         ra, _ = ldr.resolve_all({"type": "File?"}, "")
-        print ra
+        self.assertEqual({'type': ['null', 'File']}, ra)
+
         ra, _ = ldr.resolve_all({"type": "File[]"}, "")
-        print ra
+        self.assertEqual({'type': {'items': 'File', 'type': 'array'}}, ra)
+
         ra, _ = ldr.resolve_all({"type": "File[]?"}, "")
-        print ra
+        self.assertEqual({'type': ['null', {'items': 'File', 'type': 'array'}]}, ra)
 
 if __name__ == '__main__':
     unittest.main()