diff --git a/json_schema/analysis.json b/json_schema/analysis.json
index 0dd01ab18..adb41dfb1 100644
--- a/json_schema/analysis.json
+++ b/json_schema/analysis.json
@@ -22,7 +22,6 @@
                 "name",
                 "start_time",
                 "stop_time",
-                "log",
                 "disk_size",
                 "docker_image",
                 "cpus",
@@ -87,7 +86,7 @@
         "file": {
             "additionalProperties": false,
             "required": [
-                "checksum",
+                "name",
                 "file_path",
                 "format"
             ],
@@ -101,6 +100,9 @@
                 },
                 "format": {
                     "type": "string"
+                },
+                "name": {
+                    "type": "string"
                 }
             }
         }
@@ -110,7 +112,7 @@
     "properties": {
         "inputs": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json#/definitions/parameter"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json#/definitions/parameter"
             },
             "type": "array",
             "description": "Input parameters used in the pipeline run, these can be files or string values (settings)."
@@ -121,7 +123,7 @@
         },
         "tasks": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json#/definitions/task"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json#/definitions/task"
             },
             "type": "array",
             "description": "Descriptions of tasks in the workflow."
@@ -144,7 +146,7 @@
         },
         "outputs": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json#/definitions/file"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json#/definitions/file"
             },
             "type": "array",
             "description": "Output generated by the pipeline run."
@@ -164,7 +166,7 @@
         },
         "core": {
             "description": "Type and schema for this object.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
         },
         "analysis_run_type": {
             "enum": [
diff --git a/json_schema/analysis_bundle.json b/json_schema/analysis_bundle.json
index f97f1bae4..8d8339fb5 100644
--- a/json_schema/analysis_bundle.json
+++ b/json_schema/analysis_bundle.json
@@ -11,16 +11,16 @@
                 "content": {
                     "type": "object",
                     "description": "Analysis content",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json"
                 },
                 "core": {
                     "description": "Type and schema for this object.",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
                 },
                 "hca_ingest": {
                     "type": "object",
                     "description": "core fields added by HCA ingest service",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ingest.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ingest.json"
                 }
             }
         }
@@ -28,5 +28,5 @@
     "$schema": "http://json-schema.org/draft-04/schema#",
     "type": "object",
     "description": "A schema for a analysis bundle",
-    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis_bundle.json#/definitions/analysis_ingest"
+    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis_bundle.json#/definitions/analysis_ingest"
 }
\ No newline at end of file
diff --git a/json_schema/assay.json b/json_schema/assay.json
index 55ef98dc3..84290c5ac 100644
--- a/json_schema/assay.json
+++ b/json_schema/assay.json
@@ -12,7 +12,7 @@
     "properties": {
         "core": {
             "description": "Type and schema for this object.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
         },
         "name": {
             "type": "string",
@@ -20,19 +20,19 @@
         },
         "seq": {
             "description": "Information about how a cDNA sample was sequenced.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/seq.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/seq.json"
         },
         "rna": {
             "description": "Information about how RNA was converted to cDNA.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/rna.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/rna.json"
         },
         "single_cell": {
             "description": "Information on single-cell aspects of an assay.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/single_cell.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/single_cell.json"
         },
         "imaging": {
             "description": "Information on image based RNA quantification assays",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/imaging.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/imaging.json"
         },
         "assay_id": {
             "type": "string",
diff --git a/json_schema/assay_bundle.json b/json_schema/assay_bundle.json
index 6457c2d24..5045bd908 100644
--- a/json_schema/assay_bundle.json
+++ b/json_schema/assay_bundle.json
@@ -11,19 +11,19 @@
                 "content": {
                     "type": "object",
                     "description": "Assay content",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/assay.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/assay.json"
                 },
                 "derivation_protocols": {
                     "items": {
                         "description": "An array of protocols used in derivation of this sample.",
-                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/protocol.json"
+                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/protocol.json"
                     },
                     "type": "array"
                 },
                 "hca_ingest": {
                     "type": "object",
                     "description": "core fields added by HCA ingest service",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ingest.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ingest.json"
                 },
                 "has_input": {
                     "type": "string",
@@ -38,7 +38,7 @@
                 },
                 "core": {
                     "description": "Type and schema for this object.",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
                 }
             }
         }
@@ -46,5 +46,5 @@
     "$schema": "http://json-schema.org/draft-04/schema#",
     "type": "object",
     "description": "A schema for an assay bundle",
-    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
+    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
 }
\ No newline at end of file
diff --git a/json_schema/cell_suspension.json b/json_schema/cell_suspension.json
index 1313d13bf..f1a58645e 100644
--- a/json_schema/cell_suspension.json
+++ b/json_schema/cell_suspension.json
@@ -4,11 +4,11 @@
     "properties": {
         "well": {
             "description": "Information about wells in a plate or chip used for single-cell isolation.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/well.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/well.json"
         },
         "target_cell_type": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/cell_type_ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/cell_type_ontology.json"
             },
             "type": "array",
             "description": "Cell types present in the suspension."
@@ -21,7 +21,7 @@
         },
         "enrichment": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/enrichment.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/enrichment.json"
             },
             "type": "array",
             "description": "How sample was enriched for specific cell type(s)."
diff --git a/json_schema/death.json b/json_schema/death.json
index a407668a1..f9a79a0a2 100644
--- a/json_schema/death.json
+++ b/json_schema/death.json
@@ -11,7 +11,7 @@
     "properties": {
         "cause_of_death": {
             "description": "Cause of death from death report for human donor, from research lab for mouse.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         },
         "hardy_scale": {
             "minimum": 0,
diff --git a/json_schema/donor.json b/json_schema/donor.json
index 7686c0f6a..2e6e8f9f8 100644
--- a/json_schema/donor.json
+++ b/json_schema/donor.json
@@ -22,7 +22,7 @@
         },
         "death": {
             "description": "Information about conditions of death (or info that donor was living at time of collection).",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/death.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/death.json"
         },
         "genotype": {
             "type": "string",
@@ -59,7 +59,7 @@
         },
         "disease": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/disease_ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/disease_ontology.json"
             },
             "type": "array",
             "description": "Short description of disease status of individual."
@@ -84,14 +84,14 @@
         },
         "strain": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
             },
             "type": "array",
             "description": "The name of the mouse inbred strain. e.g. C57BL/6."
         },
         "ancestry": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
             },
             "type": "array",
             "description": "An array of ontology terms from EMBL-EBI's Ancestry Ontology describing ancestral groups, uncategorised ancestral groups, and population isolates."
@@ -111,14 +111,14 @@
         },
         "medication": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
             },
             "type": "array",
             "description": "List of medications the donor was currently taking at time of sample donation."
         },
         "development_stage": {
             "description": "More detailed (especially for embryos) version of life_stage. e.g. \"E9\" or \"P17\" for mouse.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         }
     }
 }
\ No newline at end of file
diff --git a/json_schema/file.json b/json_schema/file.json
index b48a06b78..d8ebb7779 100644
--- a/json_schema/file.json
+++ b/json_schema/file.json
@@ -10,7 +10,7 @@
     "properties": {
         "core": {
             "description": "Type and schema for this object.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
         },
         "filename": {
             "pattern": "^.*.fastq$|^.*.fastq.gz$|^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$",
diff --git a/json_schema/immortalized_cell_line.json b/json_schema/immortalized_cell_line.json
index 35e5a0db5..6ec7544ac 100644
--- a/json_schema/immortalized_cell_line.json
+++ b/json_schema/immortalized_cell_line.json
@@ -11,7 +11,7 @@
         },
         "cell_type": {
             "description": "What cell type the line was derived from. CLO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/cell_type_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/cell_type_ontology.json"
         },
         "date_established": {
             "type": "string",
@@ -24,7 +24,7 @@
         },
         "disease": {
             "description": "A disease associated with the cell line. EFO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/disease_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/disease_ontology.json"
         },
         "passage_number": {
             "minimum": 0,
@@ -34,7 +34,7 @@
         },
         "publication": {
             "description": "The publication in which the cell line creation was cited.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/publication.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/publication.json"
         },
         "karyotype": {
             "type": "string",
@@ -42,7 +42,7 @@
         },
         "cell_cycle": {
             "description": "The cell cycle phase, if known.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         }
     }
 }
\ No newline at end of file
diff --git a/json_schema/organoid.json b/json_schema/organoid.json
index 128d36fdf..517f36a76 100644
--- a/json_schema/organoid.json
+++ b/json_schema/organoid.json
@@ -7,7 +7,7 @@
     "properties": {
         "model_for_organ": {
             "description": "Organ that this organoid is a model system for.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         }
     },
     "title": "organoid"
diff --git a/json_schema/primary_cell_line.json b/json_schema/primary_cell_line.json
index d1d4a2def..c1a471547 100644
--- a/json_schema/primary_cell_line.json
+++ b/json_schema/primary_cell_line.json
@@ -7,7 +7,7 @@
     "properties": {
         "cell_type": {
             "description": "The cell type that the cell line was derived from. Should be a CLO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/cell_type_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/cell_type_ontology.json"
         },
         "date_established": {
             "type": "string",
@@ -16,7 +16,7 @@
         },
         "disease": {
             "description": "Free text describing any disease association to the cell type. Should be found in EFO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/disease_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/disease_ontology.json"
         },
         "passage_number": {
             "minimum": 0,
@@ -26,7 +26,7 @@
         },
         "cell_cycle": {
             "description": "The cell cycle phase if the cell line is synchronized growing cells or the phase is known.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         }
     }
 }
\ No newline at end of file
diff --git a/json_schema/project.json b/json_schema/project.json
index efc780f20..20dd658c9 100644
--- a/json_schema/project.json
+++ b/json_schema/project.json
@@ -19,7 +19,7 @@
     "properties": {
         "core": {
             "description": "type and schema for this object",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
         },
         "related_projects": {
             "items": {
@@ -34,14 +34,14 @@
         },
         "contributors": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/contact.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/contact.json"
             },
             "type": "array",
             "description": "List of people contributing to the project."
         },
         "submitters": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/contact.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/contact.json"
             },
             "type": "array",
             "description": "List of people submitting data to the project."
@@ -66,14 +66,14 @@
         "experimental_design": {
             "items": {
                 "description": "A short description of overall experiment type. e.g. \"single cell RNA sequencing.\"",
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
             },
             "type": "array"
         },
         "publications": {
             "items": {
                 "description": "An array of publication modules.",
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/publication.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/publication.json"
             },
             "type": "array"
         },
diff --git a/json_schema/project_bundle.json b/json_schema/project_bundle.json
index d88ccb371..27eb9afd5 100644
--- a/json_schema/project_bundle.json
+++ b/json_schema/project_bundle.json
@@ -11,16 +11,16 @@
                 "content": {
                     "type": "object",
                     "description": "Project content",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/project.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/project.json"
                 },
                 "core": {
                     "description": "Type and schema for this object.",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
                 },
                 "hca_ingest": {
                     "type": "object",
                     "description": "core fields added by HCA ingest service",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ingest.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ingest.json"
                 }
             }
         }
@@ -28,5 +28,5 @@
     "$schema": "http://json-schema.org/draft-04/schema#",
     "type": "object",
     "description": "A schema for a project bundle",
-    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/project_bundle.json#/definitions/project_ingest"
+    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/project_bundle.json#/definitions/project_ingest"
 }
\ No newline at end of file
diff --git a/json_schema/protocol.json b/json_schema/protocol.json
index f0162f8f7..12be851db 100644
--- a/json_schema/protocol.json
+++ b/json_schema/protocol.json
@@ -13,7 +13,7 @@
     "properties": {
         "core": {
             "description": "type and schema for this object",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
         },
         "retail_name": {
             "type": "string",
@@ -38,7 +38,7 @@
         },
         "type": {
             "description": "The type of protocol. Ideally an EFO term.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         },
         "name": {
             "type": "string",
diff --git a/json_schema/sample.json b/json_schema/sample.json
index 2d4eb6eca..6414f1889 100644
--- a/json_schema/sample.json
+++ b/json_schema/sample.json
@@ -53,24 +53,24 @@
     "properties": {
         "core": {
             "description": "Type and schema for this object.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
         },
         "immortalized_cell_line": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/immortalized_cell_line.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/immortalized_cell_line.json"
         },
         "description": {
             "type": "string",
             "description": "A general description of the sample."
         },
         "cell_suspension": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/cell_suspension.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/cell_suspension.json"
         },
         "specimen_from_organism": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/specimen_from_organism.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/specimen_from_organism.json"
         },
         "genus_species": {
             "description": "Scientific binomial name of donor species. e.g. Homo sapiens.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         },
         "supplementary_files": {
             "items": {
@@ -97,13 +97,13 @@
             "description": "A unique ID for this sample."
         },
         "donor": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/donor.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/donor.json"
         },
         "primary_cell_line": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/primary_cell_line.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/primary_cell_line.json"
         },
         "organoid": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/organoid.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/organoid.json"
         },
         "sample_accessions": {
             "additionalProperties": false,
diff --git a/json_schema/sample_bundle.json b/json_schema/sample_bundle.json
index 881eed433..f52e8d8fd 100644
--- a/json_schema/sample_bundle.json
+++ b/json_schema/sample_bundle.json
@@ -10,19 +10,19 @@
                 "content": {
                     "type": "object",
                     "description": "Sample content",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/sample.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/sample.json"
                 },
                 "derivation_protocols": {
                     "items": {
                         "description": "An array of protocols used in derivation of this sample.",
-                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/protocol.json"
+                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/protocol.json"
                     },
                     "type": "array"
                 },
                 "hca_ingest": {
                     "type": "object",
                     "description": "core fields added by HCA ingest service",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ingest.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ingest.json"
                 },
                 "derived_from": {
                     "type": "string",
@@ -37,11 +37,11 @@
     "properties": {
         "core": {
             "description": "Type and schema for this object.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
         },
         "samples": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/sample_bundle.json#/definitions/sample_ingest"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/sample_bundle.json#/definitions/sample_ingest"
             },
             "type": "array"
         }
diff --git a/json_schema/seq.json b/json_schema/seq.json
index 465f2be7f..522b0e2b7 100644
--- a/json_schema/seq.json
+++ b/json_schema/seq.json
@@ -53,7 +53,7 @@
             "description": "Was a paired-end sequencing strategy used? Must be either yes or no."
         },
         "lanes": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/seq.json#/definitions/lanes"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/seq.json#/definitions/lanes"
         },
         "insdc_run": {
             "items": {
@@ -88,7 +88,7 @@
         },
         "umi_barcode": {
             "description": "Information about unique molecular identifier (UMI) barcode sequences.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/barcode.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/barcode.json"
         },
         "library_protocol": {
             "pattern": "^P-....-.*$",
diff --git a/json_schema/single_cell.json b/json_schema/single_cell.json
index 24f3307c5..175096cd2 100644
--- a/json_schema/single_cell.json
+++ b/json_schema/single_cell.json
@@ -10,7 +10,7 @@
     "properties": {
         "cell_barcode": {
             "description": "Information about cell identifier barcode.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/barcode.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/barcode.json"
         },
         "cell_handling": {
             "enum": [
diff --git a/json_schema/specimen_from_organism.json b/json_schema/specimen_from_organism.json
index 029703251..84dc5be44 100644
--- a/json_schema/specimen_from_organism.json
+++ b/json_schema/specimen_from_organism.json
@@ -11,15 +11,15 @@
     "properties": {
         "body_part": {
             "description": "A more detailed position within the body than the term given in the organ field.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/body_part_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/body_part_ontology.json"
         },
         "state_of_specimen": {
             "description": "State of body_part at collection and how it was preserved after removal.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/state_of_specimen.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/state_of_specimen.json"
         },
         "organ": {
             "description": "The organ that the sample came from. e.g. liver, spleen. Blood and connective tissue count as organs.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         }
     }
 }
\ No newline at end of file
diff --git a/json_schema/submission.json b/json_schema/submission.json
index 6dc3028e2..a93e5cf31 100644
--- a/json_schema/submission.json
+++ b/json_schema/submission.json
@@ -13,7 +13,7 @@
         "submitted_files": {
             "additionalProperties": false,
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/submission.json#/definitions/file"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/submission.json#/definitions/file"
             },
             "type": "array"
         },
@@ -78,10 +78,10 @@
     "type": "object",
     "properties": {
         "transfer_service_version": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/submission.json#/definitions/transfer_service_version"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/submission.json#/definitions/transfer_service_version"
         },
         "submitted_files": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/submission.json#/definitions/submitted_files"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/submission.json#/definitions/submitted_files"
         }
     }
 }
\ No newline at end of file
diff --git a/schema_test_files/10x_pbmc8k_sample_0.json b/schema_test_files/10x_pbmc8k_sample_0.json
index 26bae044e..d8eaca314 100644
--- a/schema_test_files/10x_pbmc8k_sample_0.json
+++ b/schema_test_files/10x_pbmc8k_sample_0.json
@@ -1,8 +1,8 @@
 {
     "core" : {
-      "schema_version" : "4.5.0",
+      "schema_version" : "4.6.0",
       "type" : "sample",
-      "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/sample.json"
+      "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/sample.json"
     },
     "sample_id": "s1",
     "name": "PBMCs",
diff --git a/schema_test_files/10x_pbmc8k_sample_bundle.json b/schema_test_files/10x_pbmc8k_sample_bundle.json
index 14f779f4b..84cd0574d 100644
--- a/schema_test_files/10x_pbmc8k_sample_bundle.json
+++ b/schema_test_files/10x_pbmc8k_sample_bundle.json
@@ -1,8 +1,8 @@
 {
   "core": {
     "type": "sample_bundle",
-    "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/sample_bundle.json",
-    "schema_version": "4.5.0"
+    "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/sample_bundle.json",
+    "schema_version": "4.6.0"
   },
   "samples": [
     {
@@ -14,9 +14,9 @@
       },
       "content": {
         "core": {
-          "schema_version": "4.5.0",
+          "schema_version": "4.6.0",
           "type": "sample",
-          "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/sample.json"
+          "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/sample.json"
         },
         "sample_id": "d1",
         "donor": {
@@ -40,8 +40,8 @@
       "content": {
         "core": {
           "type": "sample",
-          "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/sample.json",
-          "schema_version": "4.5.0"
+          "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/sample.json",
+          "schema_version": "4.6.0"
         },
         "sample_id": "s1",
         "name": "PBMCs",
diff --git a/schema_tests/sample_bundle/pass/10x_pbmc8k_sample_bundle.json b/schema_tests/sample_bundle/pass/10x_pbmc8k_sample_bundle.json
index 14f779f4b..84cd0574d 100644
--- a/schema_tests/sample_bundle/pass/10x_pbmc8k_sample_bundle.json
+++ b/schema_tests/sample_bundle/pass/10x_pbmc8k_sample_bundle.json
@@ -1,8 +1,8 @@
 {
   "core": {
     "type": "sample_bundle",
-    "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/sample_bundle.json",
-    "schema_version": "4.5.0"
+    "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/sample_bundle.json",
+    "schema_version": "4.6.0"
   },
   "samples": [
     {
@@ -14,9 +14,9 @@
       },
       "content": {
         "core": {
-          "schema_version": "4.5.0",
+          "schema_version": "4.6.0",
           "type": "sample",
-          "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/sample.json"
+          "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/sample.json"
         },
         "sample_id": "d1",
         "donor": {
@@ -40,8 +40,8 @@
       "content": {
         "core": {
           "type": "sample",
-          "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/sample.json",
-          "schema_version": "4.5.0"
+          "schema_url": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/sample.json",
+          "schema_version": "4.6.0"
         },
         "sample_id": "s1",
         "name": "PBMCs",