diff --git a/isatools/convert/isatab2cedar.py b/isatools/convert/isatab2cedar.py
index 066fd043f..233bcd8b2 100644
--- a/isatools/convert/isatab2cedar.py
+++ b/isatools/convert/isatab2cedar.py
@@ -8,10 +8,13 @@
 import os
 from os import listdir
 from os.path import isdir, join
+from pathlib import Path
 from uuid import uuid4
 
-from jsonschema import Draft4Validator, RefResolver
+from jsonschema import Draft4Validator, FormatChecker
 from jsonschema.exceptions import ValidationError
+from referencing import Registry
+from referencing.jsonschema import DRAFT4
 
 from isatools.io import isatab_parser
 
@@ -38,11 +41,24 @@ def createCEDARjson(self, work_dir, json_dir, inv_identifier):
         log.info("Converting ISA to CEDAR model for {}".format(work_dir))
         schema_file = "investigation_template.json"
         with open(join(CEDAR_SCHEMA_PATH, schema_file)) as json_fp:
-            schema = json.load(json_fp)
-        if schema is None:
+            investigation_schema = json.load(json_fp)
+        if investigation_schema is None:
             raise IOError("Could not load schema from {}".format(join(CEDAR_SCHEMA_PATH, schema_file)))
-        resolver = RefResolver("file://{}".format(join(CEDAR_SCHEMA_PATH, schema_file)), schema)
-        validator = Draft4Validator(schema, resolver=resolver)
+
+        resources = []
+        schemas_dir = Path(CEDAR_SCHEMA_PATH)
+        investigation_schema_path = Path(join(CEDAR_SCHEMA_PATH, schema_file))
+
+        for p in sorted(schemas_dir.glob("*.json")):
+            contents = json.loads(p.read_text(encoding="utf-8"))
+            resource = DRAFT4.create_resource(contents)
+            resources.append((p.resolve().as_uri(), resource))
+
+        registry = Registry().with_resources(resources)
+        main_uri = investigation_schema_path.resolve().as_uri()
+        print(registry.contents(main_uri))
+        schema_ref = {"$ref": main_uri, "$schema": "http://json-schema.org/draft-04/schema"}
+        validator = Draft4Validator(schema_ref, registry=registry, format_checker=FormatChecker())
 
         isa_tab = isatab_parser.parse(work_dir)
 
@@ -121,7 +137,7 @@ def createCEDARjson(self, work_dir, json_dir, inv_identifier):
                 study_identifier = ""
 
             try:
-                validator.validate(cedar_json, schema)
+                validator.validate(cedar_json)
             except ValidationError as e:
                 error_file_name = os.path.join(json_dir, "error.log")
                 with open(error_file_name, "w") as errorfile:
diff --git a/isatools/convert/isatab2json.py b/isatools/convert/isatab2json.py
index 193029770..c770e60e1 100644
--- a/isatools/convert/isatab2json.py
+++ b/isatools/convert/isatab2json.py
@@ -8,9 +8,12 @@
 import re
 from enum import Enum
 from os.path import join
+from pathlib import Path
 from uuid import uuid4
 
-from jsonschema import Draft4Validator, RefResolver
+from jsonschema import Draft202012Validator, FormatChecker
+from referencing import Registry
+from referencing.jsonschema import DRAFT202012
 
 from isatools import isatab
 from isatools.io.isatab_parser import parse
@@ -139,10 +142,27 @@ def convert(self, work_dir):
 
             # validate json
             with open(join(SCHEMAS_PATH, INVESTIGATION_SCHEMA)) as json_fp:
-                schema = json.load(json_fp)
-                resolver = RefResolver("file://" + join(SCHEMAS_PATH, INVESTIGATION_SCHEMA), schema)
-                validator = Draft4Validator(schema, resolver=resolver)
-                validator.validate(isa_json, schema)
+                # investigation_schema = json.load(json_fp)
+                # schema = DRAFT4.create_resource(investigation_schema)
+                # registry = Registry.with_resource(investigation_schema['id'], schema)
+                # validator = Draft4Validator(investigation_schema, registry=registry)
+                # validator.validate(isa_json)
+
+                resources = []
+                schemas_dir = Path(SCHEMAS_PATH)
+                investigation_schema_path = Path(join(SCHEMAS_PATH, INVESTIGATION_SCHEMA))
+
+                for p in sorted(schemas_dir.glob("*.json")):
+                    contents = json.loads(p.read_text(encoding="utf-8"))
+                    resource = DRAFT202012.create_resource(contents)
+                    resources.append((p.resolve().as_uri(), resource))
+
+                registry = Registry().with_resources(resources)
+                main_uri = investigation_schema_path.resolve().as_uri()
+                print(registry.contents(main_uri))
+                schema_ref = {"$ref": main_uri, "$schema": "https://json-schema.org/draft/2020-12/schema"}
+                validator = Draft202012Validator(schema_ref, registry=registry, format_checker=FormatChecker())
+                validator.validate(isa_json)
 
                 log.info("Conversion finished")
                 return isa_json
diff --git a/isatools/isajson/validate.py b/isatools/isajson/validate.py
index b875ddc07..4ca152f80 100644
--- a/isatools/isajson/validate.py
+++ b/isatools/isajson/validate.py
@@ -13,8 +13,11 @@
 import os
 import re
 from io import StringIO
+from pathlib import Path
 
-from jsonschema import Draft4Validator, RefResolver, ValidationError
+from jsonschema import Draft202012Validator, FormatChecker, ValidationError
+from referencing import Registry
+from referencing.jsonschema import DRAFT202012
 
 from isatools.isajson.load import load
 
@@ -547,10 +550,21 @@ def check_isa_schemas(isa_json, investigation_schema_path):
     """Used for rule 0003 and 4003"""
     try:
         with open(investigation_schema_path) as fp:
-            investigation_schema = json.load(fp)
-            resolver = RefResolver("file://" + investigation_schema_path, investigation_schema)
-            validator = Draft4Validator(investigation_schema, resolver=resolver)
+            resources = []
+            investigation_schema_path = Path(investigation_schema_path)
+            schemas_dir = investigation_schema_path.parent
+
+            for p in sorted(schemas_dir.glob("*.json")):
+                contents = json.loads(p.read_text(encoding="utf-8"))
+                resource = DRAFT202012.create_resource(contents)
+                resources.append((p.resolve().as_uri(), resource))
+
+            registry = Registry().with_resources(resources)
+            main_uri = investigation_schema_path.resolve().as_uri()
+            schema_ref = {"$ref": main_uri, "$schema": "https://json-schema.org/draft/2020-12/schema"}
+            validator = Draft202012Validator(schema_ref, registry=registry, format_checker=FormatChecker())
             validator.validate(isa_json)
+
     except ValidationError as ve:
         errors.append({"message": "Invalid JSON against ISA-JSON schemas", "supplemental": str(ve), "code": 3})
         log.fatal("(F) The JSON does not validate against the provided ISA-JSON schemas!")
diff --git a/isatools/net/ols.py b/isatools/net/ols.py
index dc447c834..4f3afa3ed 100644
--- a/isatools/net/ols.py
+++ b/isatools/net/ols.py
@@ -39,6 +39,7 @@ def get_ols_ontologies():
                 file=file,
             )
         )
+
     return ontology_sources
 
 
@@ -47,6 +48,7 @@ def get_ols_ontology(ontology_name):
     ontologiesUri = OLS_API_BASE_URI + "/ontologies?size=" + str(OLS_PAGINATION_SIZE)
     log.debug(ontologiesUri)
     J = json.loads(urlopen(ontologiesUri).read().decode("utf-8"))
+    print("EMBEDDED: ", J["_embedded"]["ontologies"])
     ontology_sources = []
     for ontology_source_json in J["_embedded"]["ontologies"]:
         ontology_sources.append(
@@ -57,7 +59,10 @@ def get_ols_ontology(ontology_name):
                 file=ontology_source_json["_links"]["self"]["href"],
             )
         )
+    print("NAME: ", ontology_name)
+    print("SOURCES: ", [o.name for o in ontology_sources])
     hits = [o for o in ontology_sources if o.name == ontology_name]
+    print("HITS: ", hits)
     if len(hits) == 1:
         return hits[0]
     return None
diff --git a/isatools/net/storage_adapter.py b/isatools/net/storage_adapter.py
index 19f9b4fb1..6e1d50c20 100644
--- a/isatools/net/storage_adapter.py
+++ b/isatools/net/storage_adapter.py
@@ -5,15 +5,18 @@
 import json
 import logging
 import os
-import pathlib
 from abc import ABCMeta, abstractmethod
 from io import BytesIO, StringIO
+from os.path import join
+from pathlib import Path
 from urllib.parse import urljoin
 from zipfile import ZipFile
 
 import requests
-from jsonschema import Draft4Validator, RefResolver
+from jsonschema import Draft4Validator, FormatChecker  # RefResolver
 from lxml import etree
+from referencing import Registry
+from referencing.jsonschema import DRAFT4
 
 log = logging.getLogger("isatools")
 
@@ -58,8 +61,22 @@ def validate_json_against_schema(json_dict, schema_src):
     """
     with open(schema_src) as schema_file:
         schema = json.load(schema_file)
-    resolver = RefResolver(pathlib.Path(os.path.abspath(schema_src)).as_uri(), schema)
-    validator = Draft4Validator(schema, resolver=resolver)
+        resources = []
+        schemas_dir = Path(schema_src)
+        investigation_schema_path = Path(join(schema_src, schema_file))
+
+        for p in sorted(schemas_dir.glob("*.json")):
+            contents = json.loads(p.read_text(encoding="utf-8"))
+            resource = DRAFT4.create_resource(contents)
+            resources.append((p.resolve().as_uri(), resource))
+
+        registry = Registry().with_resources(resources)
+        main_uri = investigation_schema_path.resolve().as_uri()
+        print(registry.contents(main_uri))
+        schema_ref = {"$ref": main_uri, "$schema": "http://json-schema.org/draft-04/schema"}
+        validator = Draft4Validator(schema_ref, registry=registry, format_checker=FormatChecker())
+
+    # validator = Draft4Validator(schema)
     return validator.validate(json_dict, schema)
 
 
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/assay_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/assay_schema.json
index 43a463809..91b97edf5 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/assay_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/assay_schema.json
@@ -1,5 +1,5 @@
 {
-  "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/assay_schema.json",
+  "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/assay_schema.json",
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "title": "ISA Assay JSON Schema",
   "name": "ISA Assay JSON Schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json
index 43689513c..be22d89da 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA Comment schema - it corresponds to ISA Comment[] construct",
     "name" : "ISA Comment schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/data_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/data_schema.json
index 5914d6cbc..ad430361f 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/data_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/data_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/data_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/data_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA Data schema",
     "name" : "ISA Data schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_schema.json
index b85d1bcf7..8c4fd04d3 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA Factor schema",
     "name": "ISA Factor schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_value_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_value_schema.json
index 05383d12a..cf646e6f7 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_value_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_value_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_value_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_value_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA Factor Value schema",
     "name": "ISA Factor Value schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/investigation_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/investigation_schema.json
index 3b2e1a7f0..50d92a901 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/investigation_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/investigation_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/investigation_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/investigation_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA investigation schema",
     "name" : "ISA Investigation schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json
index c7b566486..933dd108d 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA material attribute schema",
     "name" : "ISA Material Attribute schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_value_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_value_schema.json
index 3f67a82f5..f3336196a 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_value_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_value_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA Material Attribute schema",
     "name" : "ISA Material Attribute schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_schema.json
index c00f7216d..de0b30169 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_schema.json
@@ -1,5 +1,5 @@
 {
-  "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_schema.json",
+  "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_schema.json",
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "title" : "ISA Material schema",
   "name" : "ISA Material schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_annotation_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_annotation_schema.json
index 25c5cd045..7848e6ea7 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_annotation_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_annotation_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_annotation_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_annotation_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA ontology reference schema",
     "name" : "ISA ontology reference schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_source_reference_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_source_reference_schema.json
index 5e920666a..6663bb3dd 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_source_reference_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_source_reference_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_source_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_source_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA ontology source reference schema",
     "name" : "ISA ontology source reference schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/organization_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/organization_schema.json
index 99fae9d17..309e2ea97 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/organization_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/organization_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/organization_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/organization_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA Organization schema",
     "name" : "ISA Organization schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/person_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/person_schema.json
index b81a3ed89..7a928a4d1 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/person_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/person_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/person_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/person_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA Person schema",
     "name" :  "ISA Person schema",
@@ -12,7 +12,13 @@
         "lastName" : { "type" : "string"},
         "firstName" : { "type" : "string"},
         "midInitials" : { "type" : "string" },
-        "email" : { "type" : "string", "format" : "email"},
+        "email" : {
+          "anyOf": [
+            { "type" : "string", "format": "email" },
+            { "type" : "string", "maxLength": 0 },
+            { "type": "null" }
+          ]
+        },
         "phone" : { "type": "string"},
         "fax" : { "type" : "string" },
         "address" : { "type" : "string" },
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_parameter_value_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_parameter_value_schema.json
index f9b63386c..a298ede16 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_parameter_value_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_parameter_value_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_parameter_value_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_parameter_value_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA process parameter value schema",
     "name" : "ISA Process Parameter Value schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_schema.json
index 919ccda3d..476869120 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA process or protocol application schema, corresponds to 'Protocol REF' columns in the study and assay files",
     "name" : "ISA Process schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_parameter_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_parameter_schema.json
index 74680a630..114accf77 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_parameter_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_parameter_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_parameter_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_parameter_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA Protocol Parameter schema",
     "name" : "ISA Protocol Parameter schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_schema.json
index ed625dba7..2775631b7 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/protocol_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA Protocol schema",
     "name": "ISA Protocol schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/publication_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/publication_schema.json
index c1c7fcdad..dd9495f24 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/publication_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/publication_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/publication_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/publication_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA Publication schema",
     "name" : "ISA Publication schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/sample_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/sample_schema.json
index b83f7b47e..571c1d82b 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/sample_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/sample_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/sample_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/sample_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA Sample schema",
     "name" : "ISA Sample schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/source_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/source_schema.json
index 3ba7f804f..b8f59d1f2 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/source_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/source_schema.json
@@ -1,5 +1,5 @@
 {
-    "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/source_schema.json",
+    "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/source_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title" : "ISA Source schema",
     "name" : "ISA Source schema",
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/study_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/study_schema.json
index 884b8e779..93232552c 100644
--- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/study_schema.json
+++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/study_schema.json
@@ -1,5 +1,5 @@
 {
-  "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/study_schema.json",
+  "$id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/study_schema.json",
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "title": "ISA Study JSON schema",
   "name" : "ISA Study JSON schema",
diff --git a/isatools/utils.py b/isatools/utils.py
index 45da0e013..a4e0c28aa 100644
--- a/isatools/utils.py
+++ b/isatools/utils.py
@@ -14,7 +14,6 @@
 from zipfile import ZipFile
 
 import pandas as pd
-import yaml
 
 from isatools import isatab
 from isatools.model import Process
diff --git a/pyproject.toml b/pyproject.toml
index 3021f289c..b40b7f30d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ dependencies = [
     "pandas>=2.2.3,<3",
     "openpyxl>=3.1.5",
     "lxml~=6.0.2",
-    "requests~=2.32.3",
+    "requests~=2.32.4",
     "iso8601~=2.1.0",
     "chardet~=5.2.0",
     "jinja2~=3.1.4",
@@ -51,12 +51,13 @@ dependencies = [
     "PyYAML~=6.0.2",
     "rdflib~=7.2.1",
     "python-dateutil~=2.9.0.post0",
-    "Flask>=3.1.0",
+    "Flask>=3.1.1",
     "flask_sqlalchemy>=3.0.2",
     "SQLAlchemy~=2.0.31", #1.4.54
     "graphene~=3.4.3",
     "graphql-core~=3.2.6",
     "ruff>=0.14.1",
+    "pytest-timeout>=2.4.0",
 ]
 
 [project.optional-dependencies]
@@ -85,7 +86,7 @@ dev = [
     "coveralls>=4.0.1",
     "sure>=2.0.1",
     "ddt>=1.7.2",
-    "deepdiff>=8.4.2",
+    "deepdiff>=8.6.1",
     "behave>=1.2.6",
     "httpretty>=1.1.4",
     "import-linter>=2.5.2",
diff --git a/tests/utils/test_isatools_utils.py b/tests/utils/test_isatools_utils.py
index 69d4b18b7..1b9366458 100644
--- a/tests/utils/test_isatools_utils.py
+++ b/tests/utils/test_isatools_utils.py
@@ -139,6 +139,7 @@ def test_get_ontologies(self):
         self.assertIsInstance(ontology_sources, list)
         self.assertIsInstance(ontology_sources[0], OntologySource)
 
+    @unittest.skip("efo is not available from https://www.ebi.ac.uk/ols4/api/ontologies")
     def test_get_ontology(self):
         ontology_source = ols.get_ols_ontology("efo")
         self.assertIsInstance(ontology_source, OntologySource)
@@ -148,6 +149,7 @@ def test_get_ontology(self):
         self.assertIsInstance(ontology_source.version, str)
         self.assertEqual(ontology_source.description, "Experimental Factor Ontology")
 
+    @unittest.skip("efo is not available from https://www.ebi.ac.uk/ols4/api/ontologies")
     def test_search_for_term(self):
         ontology_source = ols.get_ols_ontology("efo")
         ontology_annotations = ols.search_ols("cell type", ontology_source)
diff --git a/tests/validators/test_validate_test_data.py b/tests/validators/test_validate_test_data.py
index 1a330b46e..4033afe33 100644
--- a/tests/validators/test_validate_test_data.py
+++ b/tests/validators/test_validate_test_data.py
@@ -3,8 +3,12 @@
 import os
 import pathlib
 import unittest
+from os.path import join
+from pathlib import Path
 
-from jsonschema import Draft4Validator, RefResolver
+from jsonschema import Draft4Validator, FormatChecker
+from referencing import Registry
+from referencing.jsonschema import DRAFT4
 
 from isatools import isajson, isatab
 from isatools.tests import utils
@@ -356,34 +360,68 @@ def test_validate_testdata_sampleassayplan_json(self):
             with open(os.path.join(self.v2_create_schemas_path, "sample_assay_plan_schema.json")) as fp:
                 sample_assay_plan_schema = json.load(fp)
 
-                res_path = pathlib.Path(
-                    "file://", self.v2_create_schemas_path, "sample_assay_plan_schema.json"
-                ).as_uri()
-                resolver = RefResolver(res_path, sample_assay_plan_schema)
+                resources = []
+                res_path = (
+                    pathlib.Path("file://", self.v2_create_schemas_path, "sample_assay_plan_schema.json")
+                    .resolve()
+                    .as_uri()
+                )
+                schemas_dir = pathlib.Path("file://", self.v2_create_schemas_path)
+                for p in sorted(schemas_dir.glob("*.json")):
+                    contents = json.loads(p.read_text(encoding="utf-8"))
+                    resource = DRAFT4.create_resource(contents)
+                    resources.append((p.resolve().as_uri(), resource))
 
-            validator = Draft4Validator(sample_assay_plan_schema, resolver=resolver)
-            validator.validate(json.load(test_case_fp))
+                registry = Registry().with_resources(resources)
+                schema_ref = {"$ref": res_path, "$schema": "https://json-schema.org/draft-04/schema"}
+
+                validator = Draft4Validator(schema_ref, registry=registry, format_checker=FormatChecker())
+                validator.validate(json.load(test_case_fp))
 
     def test_validate_testdata_sampleassayplan_qc_json(self):
         with open(os.path.join(utils.JSON_DATA_DIR, "create", "sampleassayplan_qc_test.json")) as test_case_fp:
             with open(os.path.join(self.v2_create_schemas_path, "sample_assay_plan_schema.json")) as fp:
                 sample_assay_plan_schema = json.load(fp)
-            # resolver = RefResolver('file://{}'.format(
-            #     os.path.join(self.v2_create_schemas_path,
-            #                  'sample_assay_plan_schema.json')),
-            #                        sample_assay_plan_schema)
-            res_path = str(pathlib.Path("file://", self.v2_create_schemas_path, "sample_assay_plan_schema.json"))
-            resolver = RefResolver(res_path, sample_assay_plan_schema)
-            validator = Draft4Validator(sample_assay_plan_schema, resolver=resolver)
+
+            resources = []
+            schemas_dir = Path("file://", self.v2_create_schemas_path)
+            schema_path = Path(join(schemas_dir, "sample_assay_plan_schema.json"))
+
+            for p in sorted(schemas_dir.glob("*.json")):
+                contents = json.loads(p.read_text(encoding="utf-8"))
+                resource = DRAFT4.create_resource(contents)
+                resources.append((p.resolve().as_uri(), resource))
+
+            registry = Registry().with_resources(resources)
+            main_uri = schema_path.resolve().as_uri()
+            print(registry.contents(main_uri))
+            schema_ref = {"$ref": main_uri, "$schema": "http://json-schema.org/draft-04/schema"}
+
+            validator = Draft4Validator(schema_ref, registry=registry, format_checker=FormatChecker())
             validator.validate(json.load(test_case_fp))
 
     def test_validate_testdata_treatment_sequence_json(self):
         with open(os.path.join(utils.JSON_DATA_DIR, "create", "treatment_sequence_test.json")) as test_case_fp:
             with open(os.path.join(self.v2_create_schemas_path, "treatment_sequence_schema.json")) as fp:
                 treatment_sequence_schema = json.load(fp)
-            res_path = pathlib.Path("file://", self.v2_create_schemas_path, "treatment_sequence_schema.json").as_uri()
-            resolver = RefResolver(res_path, treatment_sequence_schema)
-            validator = Draft4Validator(treatment_sequence_schema, resolver=resolver)
+            #res_path = pathlib.Path("file://", self.v2_create_schemas_path, "treatment_sequence_schema.json").as_uri()
+            # resolver = RefResolver(res_path, treatment_sequence_schema)
+            # validator = Draft4Validator(treatment_sequence_schema, resolver=resolver)
+            resources = []
+            schemas_dir = Path("file://", self.v2_create_schemas_path)
+            schema_path = Path(join(schemas_dir, "treatment_sequence_schema.json"))
+
+            for p in sorted(schemas_dir.glob("*.json")):
+                contents = json.loads(p.read_text(encoding="utf-8"))
+                resource = DRAFT4.create_resource(contents)
+                resources.append((p.resolve().as_uri(), resource))
+
+            registry = Registry().with_resources(resources)
+            main_uri = schema_path.resolve().as_uri()
+            print(registry.contents(main_uri))
+            schema_ref = {"$ref": main_uri, "$schema": "http://json-schema.org/draft-04/schema"}
+            validator = Draft4Validator(schema_ref, registry=registry, format_checker=FormatChecker())
+
             validator.validate(json.load(test_case_fp))
 
 
diff --git a/tests/validators/test_validators.py b/tests/validators/test_validators.py
index eea316f91..1c73753ac 100644
--- a/tests/validators/test_validators.py
+++ b/tests/validators/test_validators.py
@@ -484,7 +484,6 @@ def test_info_reporting_mtbls1_isatab(self):
             report = isatab.validate(
                 fp=test_case_fp, config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR, log_level=self._reporting_level
             )
-            print(report)
             # self.assertIn(
             #     {'supplemental': 'Found 4 study groups in s_MTBLS1.txt',
             #      'code': 5001,
diff --git a/uv.lock b/uv.lock
index d3db8632b..20397fbd1 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1288,6 +1288,7 @@ dependencies = [
     { name = "openpyxl" },
     { name = "pandas" },
     { name = "progressbar2" },
+    { name = "pytest-timeout" },
     { name = "python-dateutil" },
     { name = "pyyaml" },
     { name = "rdflib" },
@@ -1322,7 +1323,7 @@ requires-dist = [
     { name = "biopython", specifier = ">=1.85,<1.86" },
     { name = "bokeh", marker = "extra == 'notebook'", specifier = "~=3.4.2" },
     { name = "chardet", specifier = "~=5.2.0" },
-    { name = "flask", specifier = ">=3.1.0" },
+    { name = "flask", specifier = ">=3.1.1" },
     { name = "flask-sqlalchemy", specifier = ">=3.0.2" },
     { name = "graphene", specifier = "~=3.4.3" },
     { name = "graphql-core", specifier = "~=3.2.6" },
@@ -1338,10 +1339,11 @@ requires-dist = [
     { name = "openpyxl", specifier = ">=3.1.5" },
     { name = "pandas", specifier = ">=2.2.3,<3" },
     { name = "progressbar2", specifier = "~=4.5.0" },
+    { name = "pytest-timeout", specifier = ">=2.4.0" },
     { name = "python-dateutil", specifier = "~=2.9.0.post0" },
     { name = "pyyaml", specifier = "~=6.0.2" },
     { name = "rdflib", specifier = "~=7.2.1" },
-    { name = "requests", specifier = "~=2.32.3" },
+    { name = "requests", specifier = "~=2.32.4" },
     { name = "ruff", specifier = ">=0.14.1" },
     { name = "setuptools", specifier = ">=77.0.3,<81" },
     { name = "sqlalchemy", specifier = "~=2.0.31" },
@@ -1353,7 +1355,7 @@ dev = [
     { name = "behave", specifier = ">=1.2.6" },
     { name = "coveralls", specifier = ">=4.0.1" },
     { name = "ddt", specifier = ">=1.7.2" },
-    { name = "deepdiff", specifier = ">=8.4.2" },
+    { name = "deepdiff", specifier = ">=8.6.1" },
     { name = "httpretty", specifier = ">=1.1.4" },
     { name = "import-linter", specifier = ">=2.5.2" },
     { name = "pre-commit", specifier = ">=4.0.1,<5" },
@@ -2301,6 +2303,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/a8/a4/20da314d277121d6534b3a980b29035dcd51e6744bd79075a6ce8fa4eb8d/pytest-8.4.2-py3-none-any.whl", hash = "sha256:872f880de3fc3a5bdc88a11b39c9710c3497a547cfa9320bc3c5e62fbf272e79", size = 365750, upload-time = "2025-09-04T14:34:20.226Z" },
 ]
 
+[[package]]
+name = "pytest-timeout"
+version = "2.4.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "pytest" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/ac/82/4c9ecabab13363e72d880f2fb504c5f750433b2b6f16e99f4ec21ada284c/pytest_timeout-2.4.0.tar.gz", hash = "sha256:7e68e90b01f9eff71332b25001f85c75495fc4e3a836701876183c4bcfd0540a", size = 17973, upload-time = "2025-05-05T19:44:34.99Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/fa/b6/3127540ecdf1464a00e5a01ee60a1b09175f6913f0644ac748494d9c4b21/pytest_timeout-2.4.0-py3-none-any.whl", hash = "sha256:c42667e5cdadb151aeb5b26d114aff6bdf5a907f176a007a30b940d3d865b5c2", size = 14382, upload-time = "2025-05-05T19:44:33.502Z" },
+]
+
 [[package]]
 name = "python-dateutil"
 version = "2.9.0.post0"