diff --git a/spacy/gold/example.pyx b/spacy/gold/example.pyx
index 7dfa76221..6119567dc 100644
--- a/spacy/gold/example.pyx
+++ b/spacy/gold/example.pyx
@@ -177,17 +177,19 @@ def _annot2array(vocab, tok_annot, doc_annot):
 
     for key, value in doc_annot.items():
         if key == "entities":
-            words = tok_annot["ORTH"]
-            spaces = tok_annot["SPACY"]
-            ent_iobs, ent_types = _parse_ner_tags(value, vocab, words, spaces)
-            tok_annot["ENT_IOB"] = ent_iobs
-            tok_annot["ENT_TYPE"] = ent_types
+            if value:
+                words = tok_annot["ORTH"]
+                spaces = tok_annot["SPACY"]
+                ent_iobs, ent_types = _parse_ner_tags(value, vocab, words, spaces)
+                tok_annot["ENT_IOB"] = ent_iobs
+                tok_annot["ENT_TYPE"] = ent_types
         elif key == "links":
-            entities = doc_annot.get("entities", {})
-            if value and not entities:
-                raise ValueError(Errors.E981)
-            ent_kb_ids = _parse_links(vocab, words, value, entities)
-            tok_annot["ENT_KB_ID"] = ent_kb_ids
+            if value:
+                entities = doc_annot.get("entities", {})
+                if value and not entities:
+                    raise ValueError(Errors.E981)
+                ent_kb_ids = _parse_links(vocab, words, value, entities)
+                tok_annot["ENT_KB_ID"] = ent_kb_ids
         elif key == "cats":
             pass
         else:
diff --git a/spacy/gold/gold_io.pyx b/spacy/gold/gold_io.pyx
index 83208ad85..1c66ff5e9 100644
--- a/spacy/gold/gold_io.pyx
+++ b/spacy/gold/gold_io.pyx
@@ -38,10 +38,16 @@ def docs_to_json(docs, id=0, ner_missing_tag="O"):
         docs = [docs]
     json_doc = {"id": id, "paragraphs": []}
     for i, doc in enumerate(docs):
-        json_para = {'raw': doc.text, "sentences": [], "cats": []}
+        json_para = {'raw': doc.text, "sentences": [], "cats": [], "entities": [], "links": []}
         for cat, val in doc.cats.items():
             json_cat = {"label": cat, "value": val}
             json_para["cats"].append(json_cat)
+        for ent in doc.ents:
+            ent_tuple = (ent.start_char, ent.end_char, ent.label_)
+            json_para["entities"].append(ent_tuple)
+            if ent.kb_id_:
+                link_dict = {(ent.start_char, ent.end_char): {ent.kb_id_: 1.0}}
+                json_para["links"].append(link_dict)
         ent_offsets = [(e.start_char, e.end_char, e.label_) for e in doc.ents]
         biluo_tags = biluo_tags_from_offsets(doc, ent_offsets, missing=ner_missing_tag)
         for j, sent in enumerate(doc.sents):
@@ -56,7 +62,6 @@ def docs_to_json(docs, id=0, ner_missing_tag="O"):
                 if doc.is_parsed:
                     json_token["head"] = token.head.i-token.i
                     json_token["dep"] = token.dep_
-                json_token["ner"] = biluo_tags[token.i]
                 json_sent["tokens"].append(json_token)
             json_para["sentences"].append(json_sent)
         json_doc["paragraphs"].append(json_para)
@@ -78,7 +83,7 @@ def read_json_file(loc, docs_filter=None, limit=None):
 
 def json_to_annotations(doc):
     """Convert an item in the JSON-formatted training data to the format
-    used by GoldParse.
+    used by Example.
 
     doc (dict): One entry in the training data.
     YIELDS (tuple): The reformatted data - one training example per paragraph
@@ -93,7 +98,6 @@ def json_to_annotations(doc):
         lemmas = []
         heads = []
         labels = []
-        ner = []
         sent_starts = []
         brackets = []
         for sent in paragraph["sentences"]:
@@ -110,7 +114,6 @@ def json_to_annotations(doc):
                 # Ensure ROOT label is case-insensitive
                 if labels[-1].lower() == "root":
                     labels[-1] = "ROOT"
-                ner.append(token.get("ner", "-"))
                 if i == 0:
                     sent_starts.append(1)
                 else:
@@ -119,9 +122,7 @@ def json_to_annotations(doc):
                 brackets.extend((b["first"] + sent_start_i,
                                  b["last"] + sent_start_i, b["label"])
                                  for b in sent["brackets"])
-        cats = {}
-        for cat in paragraph.get("cats", {}):
-            cats[cat["label"]] = cat["value"]
+
         example["token_annotation"] = dict(
             ids=ids,
             words=words,
@@ -131,15 +132,24 @@ def json_to_annotations(doc):
             lemmas=lemmas,
             heads=heads,
             deps=labels,
-            entities=ner,
             sent_starts=sent_starts,
             brackets=brackets
         )
-        example["doc_annotation"] = dict(cats=cats)
+
+        cats = {}
+        for cat in paragraph.get("cats", {}):
+            cats[cat["label"]] = cat["value"]
+        entities = []
+        for start, end, label in paragraph.get("entities", {}):
+            ent_tuple = (start, end, label)
+            entities.append(ent_tuple)
+        example["doc_annotation"] = dict(
+            cats=cats,
+            entities=entities,
+            links=paragraph.get("links", [])   # TODO: fix/test
+        )
         yield example
 
-
-
 def json_iterate(loc):
     # We should've made these files jsonl...But since we didn't, parse out
     # the docs one-by-one to reduce memory usage.
diff --git a/spacy/tests/test_gold.py b/spacy/tests/test_gold.py
index a032cf6e2..5fd060088 100644
--- a/spacy/tests/test_gold.py
+++ b/spacy/tests/test_gold.py
@@ -254,16 +254,15 @@ def test_iob_to_biluo():
 def test_roundtrip_docs_to_json(doc):
     nlp = English()
     text = doc.text
+    idx = [t.idx for t in doc]
     tags = [t.tag_ for t in doc]
     pos = [t.pos_ for t in doc]
     morphs = [t.morph_ for t in doc]
     lemmas = [t.lemma_ for t in doc]
     deps = [t.dep_ for t in doc]
     heads = [t.head.i for t in doc]
-    biluo_tags = iob_to_biluo(
-        [t.ent_iob_ + "-" + t.ent_type_ if t.ent_type_ else "O" for t in doc]
-    )
     cats = doc.cats
+    ents = doc.ents
 
     # roundtrip to JSON
     with make_tempdir() as tmpdir:
@@ -274,12 +273,14 @@ def test_roundtrip_docs_to_json(doc):
         reloaded_example = next(goldcorpus.dev_dataset(nlp=nlp))
         assert len(doc) == goldcorpus.count_train()
     assert text == reloaded_example.predicted.text
+    assert idx == [t.idx for t in reloaded_example.reference]
     assert tags == [t.tag_ for t in reloaded_example.reference]
     assert pos == [t.pos_ for t in reloaded_example.reference]
     assert morphs == [t.morph_ for t in reloaded_example.reference]
     assert lemmas == [t.lemma_ for t in reloaded_example.reference]
     assert deps == [t.dep_ for t in reloaded_example.reference]
     assert heads == [t.head.i for t in reloaded_example.reference]
+    assert ents == reloaded_example.reference.ents
     assert "TRAVEL" in reloaded_example.reference.cats
     assert "BAKING" in reloaded_example.reference.cats
     assert cats["TRAVEL"] == reloaded_example.reference.cats["TRAVEL"]
@@ -394,25 +395,28 @@ def test_align(tokens_a, tokens_b, expected):
 def test_goldparse_startswith_space(en_tokenizer):
     text = " a"
     doc = en_tokenizer(text)
-    g = GoldParse(doc, words=["a"], entities=["U-DATE"], deps=["ROOT"], heads=[0])
-    assert g.words == [" ", "a"]
-    assert g.ner == [None, "U-DATE"]
-    assert g.labels == [None, "ROOT"]
+    gold_words = ["a"]
+    entities = ["U-DATE"]
+    deps = ["ROOT"]
+    heads = [0]
+    example = Example.from_dict(doc, {"words": gold_words, "entities": entities, "deps":deps, "heads": heads})
+    assert example.get_aligned("ENT_IOB") == [None, 3]
+    assert example.get_aligned("ENT_TYPE", as_string=True) == [None, "DATE"]
+    assert example.get_aligned("DEP", as_string=True) == [None, "ROOT"]
 
 
 def test_gold_constructor():
-    """Test that the GoldParse constructor works fine"""
+    """Test that the Example constructor works fine"""
     nlp = English()
     doc = nlp("This is a sentence")
-    gold = GoldParse(doc, cats={"cat1": 1.0, "cat2": 0.0})
-
-    assert gold.cats["cat1"]
-    assert not gold.cats["cat2"]
-    assert gold.words == ["This", "is", "a", "sentence"]
+    example = Example.from_dict(doc, {"cats": {"cat1": 1.0, "cat2": 0.0}})
+    assert example.get_aligned("ORTH", as_string=True) == ["This", "is", "a", "sentence"]
+    assert example.reference.cats["cat1"]
+    assert not example.reference.cats["cat2"]
 
 
 def test_tuple_format_implicit():
-    """Test tuple format with implicit GoldParse creation"""
+    """Test tuple format"""
 
     train_data = [
         ("Uber blew through $1 million a week", {"entities": [(0, 4, "ORG")]}),
@@ -428,7 +432,7 @@ def test_tuple_format_implicit():
 
 @pytest.mark.xfail # TODO
 def test_tuple_format_implicit_invalid():
-    """Test that an error is thrown for an implicit invalid GoldParse field"""
+    """Test that an error is thrown for an implicit invalid field"""
 
     train_data = [
         ("Uber blew through $1 million a week", {"frumble": [(0, 4, "ORG")]}),
diff --git a/spacy/tests/test_new_example.py b/spacy/tests/test_new_example.py
index 0b2846c14..4c44543c4 100644
--- a/spacy/tests/test_new_example.py
+++ b/spacy/tests/test_new_example.py
@@ -169,6 +169,23 @@ def test_Example_from_dict_with_entities(annots):
     assert example.reference[5].ent_type_ == "LOC"
 
 
+@pytest.mark.parametrize(
+    "annots",
+    [
+        {
+            "words": ["I", "like", "New", "York", "and", "Berlin", "."],
+            "entities": [(0, 4, "LOC"), (21, 27, "LOC")],   # not aligned to token boundaries
+        }
+    ],
+)
+def test_Example_from_dict_with_entities_invalid(annots):
+    vocab = Vocab()
+    predicted = Doc(vocab, words=annots["words"])
+    example = Example.from_dict(predicted, annots)
+     # TODO: shouldn't this throw some sort of warning ?
+    assert len(list(example.reference.ents)) == 0
+
+
 @pytest.mark.parametrize(
     "annots",
     [