diff --git a/ingestion_tools/dataset_configs/template.yaml b/ingestion_tools/dataset_configs/template.yaml
index 45960821d..c412f8e34 100644
--- a/ingestion_tools/dataset_configs/template.yaml
+++ b/ingestion_tools/dataset_configs/template.yaml
@@ -8,7 +8,7 @@ annotations: OPTIONAL
     annotation_method: REQUIRED, STRING
     annotation_object: REQUIRED
       description: OPTIONAL, STRING
-      id: REQUIRED, STRING (GO_ID)
+      id: REQUIRED, STRING (GO_ID / UNIPROT_ID)
       name: REQUIRED, STRING
       state: OPTIONAL, STRING
     annotation_publications: OPTIONAL, STRING (DOI / EMPIAR / EMDB / PDB IDs)
diff --git a/schema/api/v1.0.0/codegen/api_models_materialized.yaml b/schema/api/v1.0.0/codegen/api_models_materialized.yaml
index 80f7f904f..378051d4e 100644
--- a/schema/api/v1.0.0/codegen/api_models_materialized.yaml
+++ b/schema/api/v1.0.0/codegen/api_models_materialized.yaml
@@ -295,6 +295,12 @@ types:
     from_schema: cdp-api-models
     base: str
     pattern: ^GO:[0-9]{7}$
+  UNIPROT_ID:
+    name: UNIPROT_ID
+    description: A UniProt identifier
+    from_schema: cdp-api-models
+    base: str
+    pattern: ^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$
   WORMBASE_ID:
     name: WORMBASE_ID
     description: A WormBase identifier
@@ -336,19 +342,19 @@ types:
     description: A Protein Data Bank identifier
     from_schema: cdp-api-models
     base: str
-    pattern: ^pdb[0-9a-zA-Z]{4,8}$
+    pattern: ^PDB-[0-9a-zA-Z]{4,8}$
   EMPIAR_EMDB_PDB_LIST:
     name: EMPIAR_EMDB_PDB_LIST
     description: A list of EMPIAR, EMDB, and PDB identifiers
     from_schema: cdp-api-models
     base: str
-    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$
+    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$
   EMPIAR_EMDB_DOI_PDB_LIST:
     name: EMPIAR_EMDB_DOI_PDB_LIST
     description: A list of EMPIAR, EMDB, DOI, and PDB identifiers
     from_schema: cdp-api-models
     base: str
-    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$
+    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$
 enums:
   tomogram_type:
     name: tomogram_type
@@ -489,6 +495,9 @@ enums:
       JEOL:
         text: JEOL
         description: JEOL Ltd.
+      SIMULATED:
+        text: SIMULATED
+        description: Simulated data
   fiducial_alignment_status_enum:
     name: fiducial_alignment_status_enum
     description: Fiducial Alignment method
@@ -1118,8 +1127,8 @@ classes:
         inlined_as_list: true
       annotation_publication:
         name: annotation_publication
-        description: List of publication IDs (EMPIAR, EMDB, DOI) that describe this
-          annotation method. Comma separated.
+        description: List of publication IDs (EMPIAR, EMDB, DOI, PDB) that describe
+          this annotation method. Comma separated.
         from_schema: cdp-api-models
         exact_mappings:
         - cdp-common:annotation_publications
@@ -1130,7 +1139,7 @@ classes:
         range: EMPIAR_EMDB_DOI_PDB_LIST
         inlined: true
         inlined_as_list: true
-        pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$
+        pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$
       annotation_method:
         name: annotation_method
         description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive
@@ -1173,11 +1182,13 @@ classes:
         owner: Annotation
         domain_of:
         - Annotation
-        range: GO_ID
         required: true
         inlined: true
         inlined_as_list: true
-        pattern: ^GO:[0-9]{7}$
+        pattern: (^GO:[0-9]{7}$)|(^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$)
+        any_of:
+        - range: GO_ID
+        - range: UNIPROT_ID
       object_name:
         name: object_name
         description: Name of the object being annotated (e.g. ribosome, nuclear pore
@@ -2055,7 +2066,7 @@ classes:
         recommended: true
         inlined: true
         inlined_as_list: true
-        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)
+        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)
       related_database_links:
         name: related_database_links
         description: Comma-separated list of related database links for the dataset.
@@ -2487,7 +2498,7 @@ classes:
         required: true
         inlined: true
         inlined_as_list: true
-        pattern: (^FEI$)|(^TFS$)|(^JEOL$)
+        pattern: (^FEI$)|(^TFS$)|(^JEOL$)|(^SIMULATED$)
       microscope_model:
         name: microscope_model
         description: Microscope model name
@@ -3682,7 +3693,7 @@ classes:
         recommended: true
         inlined: true
         inlined_as_list: true
-        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)
+        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)
       related_database_links:
         name: related_database_links
         description: Comma-separated list of related database links for the dataset.
diff --git a/schema/api/v2.0.0/codegen/api_models_materialized.yaml b/schema/api/v2.0.0/codegen/api_models_materialized.yaml
index 634848f5e..2461a9b70 100644
--- a/schema/api/v2.0.0/codegen/api_models_materialized.yaml
+++ b/schema/api/v2.0.0/codegen/api_models_materialized.yaml
@@ -295,6 +295,12 @@ types:
     from_schema: cdp-api
     base: string
     pattern: ^GO:[0-9]{7}$
+  UNIPROT_ID:
+    name: UNIPROT_ID
+    description: A UniProt identifier
+    from_schema: cdp-api
+    base: str
+    pattern: ^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$
   WORMBASE_ID:
     name: WORMBASE_ID
     description: A WormBase identifier
@@ -336,19 +342,19 @@ types:
     description: A Protein Data Bank identifier
     from_schema: cdp-api
     base: string
-    pattern: ^pdb[0-9a-zA-Z]{4,8}$
+    pattern: ^PDB-[0-9a-zA-Z]{4,8}$
   EMPIAR_EMDB_PDB_LIST:
     name: EMPIAR_EMDB_PDB_LIST
     description: A list of EMPIAR, EMDB, and PDB identifiers
     from_schema: cdp-api
     base: string
-    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$
+    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$
   EMPIAR_EMDB_DOI_PDB_LIST:
     name: EMPIAR_EMDB_DOI_PDB_LIST
     description: A list of EMPIAR, EMDB, DOI, and PDB identifiers
     from_schema: cdp-api
     base: string
-    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$
+    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$
 enums:
   annotation_file_source_enum:
     name: annotation_file_source_enum
@@ -492,6 +498,9 @@ enums:
       JEOL:
         text: JEOL
         description: JEOL Ltd.
+      SIMULATED:
+        text: SIMULATED
+        description: Simulated data
   fiducial_alignment_status_enum:
     name: fiducial_alignment_status_enum
     description: Fiducial Alignment method
@@ -737,7 +746,7 @@ classes:
         owner: AuthorEntityMixin
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
       primary_author_status:
@@ -751,7 +760,7 @@ classes:
         owner: AuthorEntityMixin
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
   APIDateStampedEntityMixin:
@@ -1232,7 +1241,7 @@ classes:
         owner: AnnotationAuthor
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
       primary_author_status:
@@ -1246,7 +1255,7 @@ classes:
         owner: AnnotationAuthor
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
   AnnotationFile:
@@ -1537,8 +1546,8 @@ classes:
         inlined_as_list: true
       annotation_publication:
         name: annotation_publication
-        description: List of publication IDs (EMPIAR, EMDB, DOI) that describe this
-          annotation method. Comma separated.
+        description: List of publication IDs (EMPIAR, EMDB, DOI, PDB) that describe
+          this annotation method. Comma separated.
         from_schema: cdp-api
         exact_mappings:
         - cdp-common:annotation_publications
@@ -1549,7 +1558,7 @@ classes:
         range: EMPIAR_EMDB_DOI_PDB_LIST
         inlined: true
         inlined_as_list: true
-        pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$
+        pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$
       annotation_method:
         name: annotation_method
         description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive
@@ -1592,11 +1601,13 @@ classes:
         owner: Annotation
         domain_of:
         - Annotation
-        range: GO_ID
         required: true
         inlined: true
         inlined_as_list: true
-        pattern: ^GO:[0-9]{7}$
+        pattern: (^GO:[0-9]{7}$)|(^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$)
+        any_of:
+        - range: GO_ID
+        - range: UNIPROT_ID
       object_name:
         name: object_name
         description: Name of the object being annotated (e.g. ribosome, nuclear pore
@@ -1957,7 +1968,7 @@ classes:
         owner: DatasetAuthor
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
       primary_author_status:
@@ -1971,7 +1982,7 @@ classes:
         owner: DatasetAuthor
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
   DatasetFunding:
@@ -2458,7 +2469,7 @@ classes:
         recommended: true
         inlined: true
         inlined_as_list: true
-        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)
+        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)
       related_database_links:
         name: related_database_links
         description: Comma-separated list of related database links for the dataset.
@@ -2663,7 +2674,7 @@ classes:
         owner: DepositionAuthor
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
       primary_author_status:
@@ -2677,7 +2688,7 @@ classes:
         owner: DepositionAuthor
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
   Deposition:
@@ -2861,7 +2872,7 @@ classes:
         recommended: true
         inlined: true
         inlined_as_list: true
-        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)
+        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)
       related_database_links:
         name: related_database_links
         description: Comma-separated list of related database links for the dataset.
@@ -3828,7 +3839,7 @@ classes:
         required: true
         inlined: true
         inlined_as_list: true
-        pattern: (^FEI$)|(^TFS$)|(^JEOL$)
+        pattern: (^FEI$)|(^TFS$)|(^JEOL$)|(^SIMULATED$)
       microscope_model:
         name: microscope_model
         description: Microscope model name
@@ -4333,7 +4344,7 @@ classes:
         owner: TomogramAuthor
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
       primary_author_status:
@@ -4347,7 +4358,7 @@ classes:
         owner: TomogramAuthor
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
   TomogramVoxelSpacing:
@@ -5036,7 +5047,7 @@ classes:
         domain_of:
         - DateStampedEntityMixin
         - APIDateStampedEntityMixin
-        range: string
+        range: date
         required: true
         inlined: true
         inlined_as_list: true
@@ -5051,7 +5062,7 @@ classes:
         domain_of:
         - DateStampedEntityMixin
         - APIDateStampedEntityMixin
-        range: string
+        range: date
         required: true
         inlined: true
         inlined_as_list: true
@@ -5067,7 +5078,7 @@ classes:
         domain_of:
         - DateStampedEntityMixin
         - APIDateStampedEntityMixin
-        range: string
+        range: date
         required: true
         inlined: true
         inlined_as_list: true
@@ -5103,7 +5114,7 @@ classes:
         recommended: true
         inlined: true
         inlined_as_list: true
-        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)
+        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)
       related_database_links:
         name: related_database_links
         description: Comma-separated list of related database links for the dataset.
@@ -5212,7 +5223,7 @@ classes:
         owner: AuthorMixin
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
       primary_author_status:
@@ -5226,7 +5237,7 @@ classes:
         owner: AuthorMixin
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
 source_file: api/v2.0.0/api_models.yaml
diff --git a/schema/core/v1.1.0/codegen/metadata_materialized.yaml b/schema/core/v1.1.0/codegen/metadata_materialized.yaml
index 167a50bf9..d65b7f263 100644
--- a/schema/core/v1.1.0/codegen/metadata_materialized.yaml
+++ b/schema/core/v1.1.0/codegen/metadata_materialized.yaml
@@ -312,6 +312,12 @@ types:
     from_schema: metadata
     base: str
     pattern: ^GO:[0-9]{7}$
+  UNIPROT_ID:
+    name: UNIPROT_ID
+    description: A UniProt identifier
+    from_schema: metadata
+    base: str
+    pattern: ^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$
   WORMBASE_ID:
     name: WORMBASE_ID
     description: A WormBase identifier
@@ -353,19 +359,19 @@ types:
     description: A Protein Data Bank identifier
     from_schema: metadata
     base: str
-    pattern: ^pdb[0-9a-zA-Z]{4,8}$
+    pattern: ^PDB-[0-9a-zA-Z]{4,8}$
   EMPIAR_EMDB_PDB_LIST:
     name: EMPIAR_EMDB_PDB_LIST
     description: A list of EMPIAR, EMDB, and PDB identifiers
     from_schema: metadata
     base: str
-    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$
+    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$
   EMPIAR_EMDB_DOI_PDB_LIST:
     name: EMPIAR_EMDB_DOI_PDB_LIST
     description: A list of EMPIAR, EMDB, DOI, and PDB identifiers
     from_schema: metadata
     base: str
-    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$
+    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$
 enums:
   annotation_method_type_enum:
     name: annotation_method_type_enum
@@ -495,6 +501,9 @@ enums:
       JEOL:
         text: JEOL
         description: JEOL Ltd.
+      SIMULATED:
+        text: SIMULATED
+        description: Simulated data
   fiducial_alignment_status_enum:
     name: fiducial_alignment_status_enum
     description: Fiducial Alignment method
@@ -886,7 +895,7 @@ classes:
         recommended: true
         inlined: true
         inlined_as_list: true
-        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)
+        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)
       related_database_links:
         name: related_database_links
         description: Comma-separated list of related database links for the dataset.
@@ -1705,7 +1714,8 @@ classes:
         required: true
         inlined: true
         inlined_as_list: true
-        pattern: (^FEI$)|(^TFS$)|(^JEOL$)|(^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$)
+        pattern: (^FEI$)|(^TFS$)|(^JEOL$)|(^SIMULATED$)|(^[ ]*\{[a-zA-Z0-9_-]+\}[
+          ]*$)
         any_of:
         - description: Name of the microscope manufacturer
           exact_mappings:
@@ -2624,11 +2634,14 @@ classes:
         - CellStrain
         - CellComponent
         - AnnotationObject
-        range: GO_ID
+        range: Any
         required: true
         inlined: true
         inlined_as_list: true
-        pattern: ^GO:[0-9]{7}$
+        pattern: (^GO:[0-9]{7}$)|(^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$)
+        any_of:
+        - range: GO_ID
+        - range: UNIPROT_ID
       name:
         name: name
         description: Name of the object being annotated (e.g. ribosome, nuclear pore
@@ -3272,8 +3285,8 @@ classes:
         inlined_as_list: true
       annotation_publications:
         name: annotation_publications
-        description: List of publication IDs (EMPIAR, EMDB, DOI) that describe this
-          annotation method. Comma separated.
+        description: List of publication IDs (EMPIAR, EMDB, DOI, PDB) that describe
+          this annotation method. Comma separated.
         from_schema: metadata
         exact_mappings:
         - cdp-common:annotation_publications
@@ -3284,7 +3297,7 @@ classes:
         range: EMPIAR_EMDB_DOI_PDB_LIST
         inlined: true
         inlined_as_list: true
-        pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$
+        pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$
       annotation_software:
         name: annotation_software
         description: Software used for generating this annotation
@@ -3510,7 +3523,7 @@ classes:
         recommended: true
         inlined: true
         inlined_as_list: true
-        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)
+        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)
       related_database_links:
         name: related_database_links
         description: Comma-separated list of related database links for the dataset.
diff --git a/schema/core/v1.1.0/codegen/metadata_models.py b/schema/core/v1.1.0/codegen/metadata_models.py
index eecce1ec8..6797660cb 100644
--- a/schema/core/v1.1.0/codegen/metadata_models.py
+++ b/schema/core/v1.1.0/codegen/metadata_models.py
@@ -98,14 +98,14 @@ def __contains__(self, key: str) -> bool:
                 "description": "A list of EMPIAR, " "EMDB, DOI, and PDB " "identifiers",
                 "from_schema": "metadata",
                 "name": "EMPIAR_EMDB_DOI_PDB_LIST",
-                "pattern": "^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$",
+                "pattern": "^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$",
             },
             "EMPIAR_EMDB_PDB_LIST": {
                 "base": "str",
                 "description": "A list of EMPIAR, EMDB, " "and PDB identifiers",
                 "from_schema": "metadata",
                 "name": "EMPIAR_EMDB_PDB_LIST",
-                "pattern": "^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$",
+                "pattern": "^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$",
             },
             "EMPIAR_ID": {
                 "base": "str",
@@ -154,7 +154,7 @@ def __contains__(self, key: str) -> bool:
                 "description": "A Protein Data Bank identifier",
                 "from_schema": "metadata",
                 "name": "PDB_ID",
-                "pattern": "^pdb[0-9a-zA-Z]{4,8}$",
+                "pattern": "^PDB-[0-9a-zA-Z]{4,8}$",
             },
             "StringFormattedString": {
                 "base": "str",
@@ -163,6 +163,13 @@ def __contains__(self, key: str) -> bool:
                 "name": "StringFormattedString",
                 "pattern": "^[ ]*\\{[a-zA-Z0-9_-]+\\}[ " "]*$",
             },
+            "UNIPROT_ID": {
+                "base": "str",
+                "description": "A UniProt identifier",
+                "from_schema": "metadata",
+                "name": "UNIPROT_ID",
+                "pattern": "^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$",
+            },
             "URLorS3URI": {
                 "base": "str",
                 "description": "A URL or S3 URI",
@@ -587,6 +594,8 @@ class TiltseriesMicroscopeManufacturerEnum(str, Enum):
     TFS = "TFS"
     # JEOL Ltd.
     JEOL = "JEOL"
+    # Simulated data
+    SIMULATED = "SIMULATED"
 
 
 class FiducialAlignmentStatusEnum(str, Enum):
@@ -1558,7 +1567,7 @@ class MicroscopeDetails(ConfiguredBaseModel):
 
     @field_validator("manufacturer")
     def pattern_manufacturer(cls, v):
-        pattern = re.compile(r"(^FEI$)|(^TFS$)|(^JEOL$)|(^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$)")
+        pattern = re.compile(r"(^FEI$)|(^TFS$)|(^JEOL$)|(^SIMULATED$)|(^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$)")
         if isinstance(v, list):
             for element in v:
                 if not pattern.match(element):
@@ -2507,6 +2516,7 @@ class AnnotationObject(ConfiguredBaseModel):
         json_schema_extra={
             "linkml_meta": {
                 "alias": "id",
+                "any_of": [{"range": "GO_ID"}, {"range": "UNIPROT_ID"}],
                 "domain_of": ["TissueDetails", "CellType", "CellStrain", "CellComponent", "AnnotationObject"],
                 "exact_mappings": ["cdp-common:annotation_object_id"],
             }
@@ -2558,7 +2568,9 @@ class AnnotationObject(ConfiguredBaseModel):
 
     @field_validator("id")
     def pattern_id(cls, v):
-        pattern = re.compile(r"^GO:[0-9]{7}$")
+        pattern = re.compile(
+            r"(^GO:[0-9]{7}$)|(^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$)"
+        )
         if isinstance(v, list):
             for element in v:
                 if not pattern.match(element):
@@ -3221,7 +3233,7 @@ class Annotation(AuthoredEntity, DateStampedEntity):
     )
     annotation_publications: Optional[str] = Field(
         None,
-        description="""List of publication IDs (EMPIAR, EMDB, DOI) that describe this annotation method. Comma separated.""",
+        description="""List of publication IDs (EMPIAR, EMDB, DOI, PDB) that describe this annotation method. Comma separated.""",
         json_schema_extra={
             "linkml_meta": {
                 "alias": "annotation_publications",
@@ -3335,7 +3347,7 @@ class Annotation(AuthoredEntity, DateStampedEntity):
     @field_validator("annotation_publications")
     def pattern_annotation_publications(cls, v):
         pattern = re.compile(
-            r"^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$"
+            r"^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$"
         )
         if isinstance(v, list):
             for element in v:
@@ -3504,7 +3516,7 @@ def pattern_publications(cls, v):
     @field_validator("related_database_entries")
     def pattern_related_database_entries(cls, v):
         pattern = re.compile(
-            r"(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)"
+            r"(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)"
         )
         if isinstance(v, list):
             for element in v:
@@ -3577,7 +3589,7 @@ def pattern_publications(cls, v):
     @field_validator("related_database_entries")
     def pattern_related_database_entries(cls, v):
         pattern = re.compile(
-            r"(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)"
+            r"(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)"
         )
         if isinstance(v, list):
             for element in v:
diff --git a/schema/core/v1.1.0/common.yaml b/schema/core/v1.1.0/common.yaml
index 0f6fa4849..cb5c0c268 100644
--- a/schema/core/v1.1.0/common.yaml
+++ b/schema/core/v1.1.0/common.yaml
@@ -577,7 +577,7 @@ slots:
     description: Classification of the annotation method based on supervision.
   annotation_publications:
     range: EMPIAR_EMDB_DOI_PDB_LIST
-    description: List of publication IDs (EMPIAR, EMDB, DOI) that describe this annotation method. Comma separated.
+    description: List of publication IDs (EMPIAR, EMDB, DOI, PDB) that describe this annotation method. Comma separated.
   annotation_software:
     range: string
     description: Software used for generating this annotation
@@ -619,7 +619,9 @@ slots:
     range: string
     description: A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state.
   annotation_object_id:
-    range: GO_ID
+    any_of:
+      - range: GO_ID
+      - range: UNIPROT_ID
     required: true
     description: Gene Ontology Cellular Component identifier for the annotation object
   annotation_object_name:
@@ -872,6 +874,8 @@ enums:
         description: Thermo Fisher Scientific
       JEOL:
         description: JEOL Ltd.
+      SIMULATED:
+        description: Simulated data
 
   fiducial_alignment_status_enum:
     description: Fiducial Alignment method
@@ -958,6 +962,11 @@ types:
     base: str
     pattern: '^GO:[0-9]{7}$'
 
+  UNIPROT_ID:
+    description: A UniProt identifier
+    base: str
+    pattern: '^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$'
+
   WORMBASE_ID:
     description: A WormBase identifier
     base: str
@@ -991,17 +1000,17 @@ types:
   PDB_ID:
     description: A Protein Data Bank identifier
     base: str
-    pattern: '^pdb[0-9a-zA-Z]{4,8}$'
+    pattern: '^PDB-[0-9a-zA-Z]{4,8}$'
 
   EMPIAR_EMDB_PDB_LIST:
     description: A list of EMPIAR, EMDB, and PDB identifiers
     base: str
-    pattern: '^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$'
+    pattern: '^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$'
 
   EMPIAR_EMDB_DOI_PDB_LIST:
     description: A list of EMPIAR, EMDB, DOI, and PDB identifiers
     base: str
-    pattern: '^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$'
+    pattern: '^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$'
 
 classes:
   Any:
diff --git a/schema/core/v2.0.0/codegen/metadata_materialized.yaml b/schema/core/v2.0.0/codegen/metadata_materialized.yaml
index 2ca196933..1335b5a1d 100644
--- a/schema/core/v2.0.0/codegen/metadata_materialized.yaml
+++ b/schema/core/v2.0.0/codegen/metadata_materialized.yaml
@@ -312,6 +312,12 @@ types:
     from_schema: metadata
     base: string
     pattern: ^GO:[0-9]{7}$
+  UNIPROT_ID:
+    name: UNIPROT_ID
+    description: A UniProt identifier
+    from_schema: metadata
+    base: str
+    pattern: ^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$
   WORMBASE_ID:
     name: WORMBASE_ID
     description: A WormBase identifier
@@ -353,19 +359,19 @@ types:
     description: A Protein Data Bank identifier
     from_schema: metadata
     base: string
-    pattern: ^pdb[0-9a-zA-Z]{4,8}$
+    pattern: ^PDB-[0-9a-zA-Z]{4,8}$
   EMPIAR_EMDB_PDB_LIST:
     name: EMPIAR_EMDB_PDB_LIST
     description: A list of EMPIAR, EMDB, and PDB identifiers
     from_schema: metadata
     base: string
-    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$
+    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$
   EMPIAR_EMDB_DOI_PDB_LIST:
     name: EMPIAR_EMDB_DOI_PDB_LIST
     description: A list of EMPIAR, EMDB, DOI, and PDB identifiers
     from_schema: metadata
     base: string
-    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$
+    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$
 enums:
   annotation_file_source_enum:
     name: annotation_file_source_enum
@@ -509,6 +515,9 @@ enums:
       JEOL:
         text: JEOL
         description: JEOL Ltd.
+      SIMULATED:
+        text: SIMULATED
+        description: Simulated data
   fiducial_alignment_status_enum:
     name: fiducial_alignment_status_enum
     description: Fiducial Alignment method
@@ -720,7 +729,7 @@ classes:
         owner: Author
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
       primary_author_status:
@@ -734,7 +743,7 @@ classes:
         owner: Author
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
   FundingDetails:
@@ -789,7 +798,7 @@ classes:
         owner: DateStamp
         domain_of:
         - DateStampedEntityMixin
-        range: string
+        range: date
         required: true
         inlined: true
         inlined_as_list: true
@@ -803,7 +812,7 @@ classes:
         owner: DateStamp
         domain_of:
         - DateStampedEntityMixin
-        range: string
+        range: date
         required: true
         inlined: true
         inlined_as_list: true
@@ -818,7 +827,7 @@ classes:
         owner: DateStamp
         domain_of:
         - DateStampedEntityMixin
-        range: string
+        range: date
         required: true
         inlined: true
         inlined_as_list: true
@@ -913,7 +922,7 @@ classes:
         recommended: true
         inlined: true
         inlined_as_list: true
-        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)
+        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)
       related_database_links:
         name: related_database_links
         description: Comma-separated list of related database links for the dataset.
@@ -2468,8 +2477,7 @@ classes:
     attributes:
       id:
         name: id
-        description: Gene Ontology Cellular Component identifier for the annotation
-          object
+        description: A placeholder for any type of data.
         from_schema: metadata
         exact_mappings:
         - cdp-common:annotation_object_id
@@ -2481,11 +2489,14 @@ classes:
         - CellStrain
         - CellComponent
         - AnnotationObject
-        range: GO_ID
+        range: Any
         required: true
         inlined: true
         inlined_as_list: true
-        pattern: ^GO:[0-9]{7}$
+        pattern: (^GO:[0-9]{7}$)|(^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$)
+        any_of:
+        - range: GO_ID
+        - range: UNIPROT_ID
       name:
         name: name
         description: Name of the object being annotated (e.g. ribosome, nuclear pore
@@ -3128,8 +3139,8 @@ classes:
         inlined_as_list: true
       annotation_publications:
         name: annotation_publications
-        description: List of publication IDs (EMPIAR, EMDB, DOI) that describe this
-          annotation method. Comma separated.
+        description: List of publication IDs (EMPIAR, EMDB, DOI, PDB) that describe
+          this annotation method. Comma separated.
         from_schema: metadata
         exact_mappings:
         - cdp-common:annotation_publications
@@ -3140,7 +3151,7 @@ classes:
         range: EMPIAR_EMDB_DOI_PDB_LIST
         inlined: true
         inlined_as_list: true
-        pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$
+        pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$
       annotation_software:
         name: annotation_software
         description: Software used for generating this annotation
@@ -3302,7 +3313,7 @@ classes:
         owner: DateStampedEntityMixin
         domain_of:
         - DateStampedEntityMixin
-        range: string
+        range: date
         required: true
         inlined: true
         inlined_as_list: true
@@ -3316,7 +3327,7 @@ classes:
         owner: DateStampedEntityMixin
         domain_of:
         - DateStampedEntityMixin
-        range: string
+        range: date
         required: true
         inlined: true
         inlined_as_list: true
@@ -3331,7 +3342,7 @@ classes:
         owner: DateStampedEntityMixin
         domain_of:
         - DateStampedEntityMixin
-        range: string
+        range: date
         required: true
         inlined: true
         inlined_as_list: true
@@ -3367,7 +3378,7 @@ classes:
         recommended: true
         inlined: true
         inlined_as_list: true
-        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)
+        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)
       related_database_links:
         name: related_database_links
         description: Comma-separated list of related database links for the dataset.
@@ -3480,7 +3491,7 @@ classes:
         owner: AuthorMixin
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
       primary_author_status:
@@ -3494,7 +3505,7 @@ classes:
         owner: AuthorMixin
         domain_of:
         - AuthorMixin
-        range: string
+        range: boolean
         inlined: true
         inlined_as_list: true
 source_file: core/v2.0.0/metadata.yaml
diff --git a/schema/core/v2.0.0/common.yaml b/schema/core/v2.0.0/common.yaml
index 46618809b..b4162bcfb 100644
--- a/schema/core/v2.0.0/common.yaml
+++ b/schema/core/v2.0.0/common.yaml
@@ -13,7 +13,7 @@ prefixes:
 imports:
   - linkml:types
 default_prefix: cdp-common
-default_range: string
+default_range: Any
 
 
 slots:
@@ -580,7 +580,7 @@ slots:
     description: Classification of the annotation method based on supervision.
   annotation_publications:
     range: EMPIAR_EMDB_DOI_PDB_LIST
-    description: List of publication IDs (EMPIAR, EMDB, DOI) that describe this annotation method. Comma separated.
+    description: List of publication IDs (EMPIAR, EMDB, DOI, PDB) that describe this annotation method. Comma separated.
   annotation_software:
     range: string
     description: Software used for generating this annotation
@@ -622,7 +622,9 @@ slots:
     range: string
     description: A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state.
   annotation_object_id:
-    range: GO_ID
+    any_of:
+      - range: GO_ID
+      - range: UNIPROT_ID
     required: true
     description: Gene Ontology Cellular Component identifier for the annotation object
   annotation_object_name:
@@ -1051,6 +1053,8 @@ enums:
         description: Thermo Fisher Scientific
       JEOL:
         description: JEOL Ltd.
+      SIMULATED:
+        description: Simulated data
 
   fiducial_alignment_status_enum:
     description: Fiducial Alignment method
@@ -1147,6 +1151,11 @@ types:
     base: string
     pattern: '^GO:[0-9]{7}$'
 
+  UNIPROT_ID:
+    description: A UniProt identifier
+    base: str
+    pattern: '^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$'
+
   WORMBASE_ID:
     description: A WormBase identifier
     base: string
@@ -1180,17 +1189,17 @@ types:
   PDB_ID:
     description: A Protein Data Bank identifier
     base: string
-    pattern: '^pdb[0-9a-zA-Z]{4,8}$'
+    pattern: '^PDB-[0-9a-zA-Z]{4,8}$'
 
   EMPIAR_EMDB_PDB_LIST:
     description: A list of EMPIAR, EMDB, and PDB identifiers
     base: string
-    pattern: '^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$'
+    pattern: '^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$'
 
   EMPIAR_EMDB_DOI_PDB_LIST:
     description: A list of EMPIAR, EMDB, DOI, and PDB identifiers
     base: string
-    pattern: '^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$'
+    pattern: '^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$'
 
 classes:
   Any:
diff --git a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.py b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.py
index 4dbbd6175..4e26bf268 100644
--- a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.py
+++ b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.py
@@ -94,14 +94,14 @@ def __contains__(self, key: str) -> bool:
                 "description": "A list of EMPIAR, " "EMDB, DOI, and PDB " "identifiers",
                 "from_schema": "cdp-ingestion-config",
                 "name": "EMPIAR_EMDB_DOI_PDB_LIST",
-                "pattern": "^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$",
+                "pattern": "^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$",
             },
             "EMPIAR_EMDB_PDB_LIST": {
                 "base": "str",
                 "description": "A list of EMPIAR, EMDB, " "and PDB identifiers",
                 "from_schema": "cdp-ingestion-config",
                 "name": "EMPIAR_EMDB_PDB_LIST",
-                "pattern": "^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$",
+                "pattern": "^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$",
             },
             "EMPIAR_ID": {
                 "base": "str",
@@ -150,7 +150,7 @@ def __contains__(self, key: str) -> bool:
                 "description": "A Protein Data Bank identifier",
                 "from_schema": "cdp-ingestion-config",
                 "name": "PDB_ID",
-                "pattern": "^pdb[0-9a-zA-Z]{4,8}$",
+                "pattern": "^PDB-[0-9a-zA-Z]{4,8}$",
             },
             "StringFormattedString": {
                 "base": "str",
@@ -159,6 +159,13 @@ def __contains__(self, key: str) -> bool:
                 "name": "StringFormattedString",
                 "pattern": "^[ ]*\\{[a-zA-Z0-9_-]+\\}[ " "]*$",
             },
+            "UNIPROT_ID": {
+                "base": "str",
+                "description": "A UniProt identifier",
+                "from_schema": "cdp-ingestion-config",
+                "name": "UNIPROT_ID",
+                "pattern": "^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$",
+            },
             "URLorS3URI": {
                 "base": "str",
                 "description": "A URL or S3 URI",
@@ -583,6 +590,8 @@ class TiltseriesMicroscopeManufacturerEnum(str, Enum):
     TFS = "TFS"
     # JEOL Ltd.
     JEOL = "JEOL"
+    # Simulated data
+    SIMULATED = "SIMULATED"
 
 
 class FiducialAlignmentStatusEnum(str, Enum):
@@ -1554,7 +1563,7 @@ class MicroscopeDetails(ConfiguredBaseModel):
 
     @field_validator("manufacturer")
     def pattern_manufacturer(cls, v):
-        pattern = re.compile(r"(^FEI$)|(^TFS$)|(^JEOL$)|(^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$)")
+        pattern = re.compile(r"(^FEI$)|(^TFS$)|(^JEOL$)|(^SIMULATED$)|(^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$)")
         if isinstance(v, list):
             for element in v:
                 if not pattern.match(element):
@@ -2503,6 +2512,7 @@ class AnnotationObject(ConfiguredBaseModel):
         json_schema_extra={
             "linkml_meta": {
                 "alias": "id",
+                "any_of": [{"range": "GO_ID"}, {"range": "UNIPROT_ID"}],
                 "domain_of": ["TissueDetails", "CellType", "CellStrain", "CellComponent", "AnnotationObject"],
                 "exact_mappings": ["cdp-common:annotation_object_id"],
             }
@@ -2554,7 +2564,9 @@ class AnnotationObject(ConfiguredBaseModel):
 
     @field_validator("id")
     def pattern_id(cls, v):
-        pattern = re.compile(r"^GO:[0-9]{7}$")
+        pattern = re.compile(
+            r"(^GO:[0-9]{7}$)|(^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$)"
+        )
         if isinstance(v, list):
             for element in v:
                 if not pattern.match(element):
@@ -3217,7 +3229,7 @@ class Annotation(AuthoredEntity, DateStampedEntity):
     )
     annotation_publications: Optional[str] = Field(
         None,
-        description="""List of publication IDs (EMPIAR, EMDB, DOI) that describe this annotation method. Comma separated.""",
+        description="""List of publication IDs (EMPIAR, EMDB, DOI, PDB) that describe this annotation method. Comma separated.""",
         json_schema_extra={
             "linkml_meta": {
                 "alias": "annotation_publications",
@@ -3331,7 +3343,7 @@ class Annotation(AuthoredEntity, DateStampedEntity):
     @field_validator("annotation_publications")
     def pattern_annotation_publications(cls, v):
         pattern = re.compile(
-            r"^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$"
+            r"^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$"
         )
         if isinstance(v, list):
             for element in v:
@@ -3500,7 +3512,7 @@ def pattern_publications(cls, v):
     @field_validator("related_database_entries")
     def pattern_related_database_entries(cls, v):
         pattern = re.compile(
-            r"(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)"
+            r"(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)"
         )
         if isinstance(v, list):
             for element in v:
@@ -3573,7 +3585,7 @@ def pattern_publications(cls, v):
     @field_validator("related_database_entries")
     def pattern_related_database_entries(cls, v):
         pattern = re.compile(
-            r"(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)"
+            r"(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)"
         )
         if isinstance(v, list):
             for element in v:
diff --git a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.schema.json b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.schema.json
index f4057fea0..10d4fcca4 100644
--- a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.schema.json
+++ b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.schema.json
@@ -13,8 +13,8 @@
                     "description": "Metadata describing the object being annotated."
                 },
                 "annotation_publications": {
-                    "description": "List of publication IDs (EMPIAR, EMDB, DOI) that describe this annotation method. Comma separated.",
-                    "pattern": "^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$",
+                    "description": "List of publication IDs (EMPIAR, EMDB, DOI, PDB) that describe this annotation method. Comma separated.",
+                    "pattern": "^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$",
                     "type": [
                         "string",
                         "null"
@@ -296,9 +296,19 @@
                     ]
                 },
                 "id": {
+                    "$ref": "#/$defs/Any",
+                    "anyOf": [
+                        {
+                            "pattern": "^GO:[0-9]{7}$",
+                            "type": "string"
+                        },
+                        {
+                            "pattern": "^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$",
+                            "type": "string"
+                        }
+                    ],
                     "description": "Gene Ontology Cellular Component identifier for the annotation object",
-                    "pattern": "^GO:[0-9]{7}$",
-                    "type": "string"
+                    "pattern": "(^GO:[0-9]{7}$)|(^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$)"
                 },
                 "name": {
                     "description": "Name of the object being annotated (e.g. ribosome, nuclear pore complex, actin filament, membrane)",
@@ -1089,7 +1099,7 @@
                 },
                 "related_database_entries": {
                     "description": "Comma-separated list of related database entries for the dataset.",
-                    "pattern": "(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)",
+                    "pattern": "(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\\s*,\\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)",
                     "type": [
                         "string",
                         "null"
@@ -2536,7 +2546,7 @@
                         }
                     ],
                     "description": "Name of the microscope manufacturer",
-                    "pattern": "(^FEI$)|(^TFS$)|(^JEOL$)|(^[ ]*\\{[a-zA-Z0-9_-]+\\}[ ]*$)"
+                    "pattern": "(^FEI$)|(^TFS$)|(^JEOL$)|(^SIMULATED$)|(^[ ]*\\{[a-zA-Z0-9_-]+\\}[ ]*$)"
                 },
                 "model": {
                     "description": "Microscope model name",
@@ -3494,7 +3504,8 @@
             "enum": [
                 "FEI",
                 "TFS",
-                "JEOL"
+                "JEOL",
+                "SIMULATED"
             ],
             "title": "TiltseriesMicroscopeManufacturerEnum",
             "type": "string"
diff --git a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml
index a1d86f1ea..8d05673bc 100644
--- a/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml
+++ b/schema/ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml
@@ -296,6 +296,12 @@ types:
     from_schema: cdp-ingestion-config
     base: str
     pattern: ^GO:[0-9]{7}$
+  UNIPROT_ID:
+    name: UNIPROT_ID
+    description: A UniProt identifier
+    from_schema: cdp-ingestion-config
+    base: str
+    pattern: ^UniProtKB:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}+$
   WORMBASE_ID:
     name: WORMBASE_ID
     description: A WormBase identifier
@@ -337,19 +343,19 @@ types:
     description: A Protein Data Bank identifier
     from_schema: cdp-ingestion-config
     base: str
-    pattern: ^pdb[0-9a-zA-Z]{4,8}$
+    pattern: ^PDB-[0-9a-zA-Z]{4,8}$
   EMPIAR_EMDB_PDB_LIST:
     name: EMPIAR_EMDB_PDB_LIST
     description: A list of EMPIAR, EMDB, and PDB identifiers
     from_schema: cdp-ingestion-config
     base: str
-    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$
+    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$
   EMPIAR_EMDB_DOI_PDB_LIST:
     name: EMPIAR_EMDB_DOI_PDB_LIST
     description: A list of EMPIAR, EMDB, DOI, and PDB identifiers
     from_schema: cdp-ingestion-config
     base: str
-    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$
+    pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|PDB-[0-9a-zA-Z]{4,8}))*$
 enums:
   annotation_method_type_enum:
     name: annotation_method_type_enum
@@ -479,6 +485,9 @@ enums:
       JEOL:
         text: JEOL
         description: JEOL Ltd.
+      SIMULATED:
+        text: SIMULATED
+        description: Simulated data
   fiducial_alignment_status_enum:
     name: fiducial_alignment_status_enum
     description: Fiducial Alignment method
@@ -4106,7 +4115,7 @@ classes:
         recommended: true
         inlined: true
         inlined_as_list: true
-        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)
+        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|PDB-[0-9a-zA-Z]{4,8}))*$)
       related_database_links:
         name: related_database_links
         description: Comma-separated list of related database links for the dataset.
diff --git a/schema/ingestion_config/v1.0.0/ingestion_config_models_extended.py b/schema/ingestion_config/v1.0.0/ingestion_config_models_extended.py
index 3fd1a2786..04240178d 100644
--- a/schema/ingestion_config/v1.0.0/ingestion_config_models_extended.py
+++ b/schema/ingestion_config/v1.0.0/ingestion_config_models_extended.py
@@ -69,6 +69,8 @@
 
 validation_exclusions = {}
 CELLULAR_COMPONENT_GO_ID = "GO:0005575"
+GO_ID_REGEX = r"^GO:[0-9]{7}$"
+UNIPROT_ID_REGEX = r"^UniProtKB:[A-Z0-9]+$"
 STRING_FORMATTED_STRING_REGEX = r"^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$"
 VALID_IMAGE_FORMATS = ("image/png", "image/jpeg", "image/jpg", "image/gif")
 # Note that model namees should all be uppercase or pascal case
@@ -275,7 +277,7 @@ async def validate_wormbase_id(id: str) -> Tuple[List[str], bool]:
 
     async with aiohttp.ClientSession() as session, session.get(names_url) as response:
         if response.status >= 400:
-            return names, True
+            return [], True
         data = await response.json()
         if other_names := data.get("other_names", {}).get("data", []):
             names += other_names
@@ -283,6 +285,29 @@ async def validate_wormbase_id(id: str) -> Tuple[List[str], bool]:
     return names, True
 
 
+@alru_cache
+async def validate_uniprot_id(id: str) -> Tuple[List[str], bool]:
+    """
+    Returns a tuple of the ID names and whether or not it is valid.
+    """
+
+    # Strip the UniProtKB: prefix
+    id = id.replace("UniProtKB:", "")
+    url = f"https://rest.uniprot.org/uniprotkb/{id}"
+
+    logger.debug("Getting ID %s at %s", id, url)
+
+    async with aiohttp.ClientSession() as session, session.get(url) as response:
+        if response.status >= 400:
+            return [], False
+        data = await response.json()
+        try:
+            name = data["proteinDescription"]["recommendedName"]["fullName"]["value"]
+            return [name], True
+        except KeyError:
+            return [], True
+
+
 def validate_id_name_object(
     self: Union[AnnotationObject, CellComponent, CellStrain, CellType, OrganismDetails, TissueDetails],
     id: str,
@@ -321,7 +346,8 @@ def validate_id_name_object(
 
     logger.debug("Valid ID, now checking if name '%s' matches ID: %s", name, id)
 
-    valid_name = any(name == retrieved_name for retrieved_name in retrieved_names)
+    # if the retrieved names is empty, we can assume the name is valid
+    valid_name = retrieved_names == [] or any(name == retrieved_name for retrieved_name in retrieved_names)
 
     if not valid_name:
         raise ValueError(f"name '{name}' does not match id: {id}")
@@ -406,6 +432,8 @@ class ExtendedValidationDepositionKeyPhotoSource(DepositionKeyPhotoSource):
 # ==============================================================================
 @alru_cache
 async def lookup_doi(doi: str) -> Tuple[str, bool]:
+    # Remove the doi: prefix if it exists
+    doi = doi.replace("doi:", "")
     url = f"https://api.crossref.org/works/{doi}/agency"
     async with aiohttp.ClientSession() as session, session.head(url) as response:
         return doi, response.status == 200
@@ -427,6 +455,8 @@ async def lookup_emdb(emdb_id: str) -> Tuple[str, bool]:
 
 @alru_cache
 async def lookup_pdb(pdb_id: str) -> Tuple[str, bool]:
+    # Strip the PDB- prefix
+    pdb_id = pdb_id.replace("PDB-", "")
     url = f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}"
     async with aiohttp.ClientSession() as session, session.head(url) as response:
         return pdb_id, response.status == 200
@@ -436,7 +466,7 @@ async def lookup_pdb(pdb_id: str) -> Tuple[str, bool]:
     "doi": (r"^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+$", lookup_doi),
     "empiar": (r"^EMPIAR-[0-9]{5}$", lookup_empiar),
     "emdb": (r"^EMD-[0-9]{4,5}$", lookup_emdb),
-    "pdb": (r"^pdb[0-9a-zA-Z]{4,8}$", lookup_pdb),
+    "pdb": (r"^PDB-[0-9a-zA-Z]{4,8}$", lookup_pdb),
 }
 
 
@@ -444,12 +474,10 @@ async def validate_publication_lists(publication_list: List[str]) -> List[str]:
     tasks = []
 
     for publication in publication_list:
-        for publication_type, (regex, validate_function) in PUBLICATION_REGEXES_AND_FUNCTIONS.items():
+        for _, (regex, validate_function) in PUBLICATION_REGEXES_AND_FUNCTIONS.items():
             if not re.match(regex, publication):
                 continue
-            # edge case for DOI, remove the doi: prefix
-            updated_publication = publication.replace("doi:", "") if publication_type == "doi" else publication
-            tasks.append(validate_function(updated_publication))
+            tasks.append(validate_function(publication))
             break
 
     results = await asyncio.gather(*tasks)
@@ -516,7 +544,10 @@ def validate_sources(source_list: List[DefaultSource] | List[VoxelSpacingSource]
 class ExtendedValidationAnnotationObject(AnnotationObject):
     @model_validator(mode="after")
     def validate_annotation_object(self) -> Self:
-        validate_id_name_object(self, self.id, self.name, ancestor=CELLULAR_COMPONENT_GO_ID)
+        if re.match(GO_ID_REGEX, self.id):
+            validate_id_name_object(self, self.id, self.name, ancestor=CELLULAR_COMPONENT_GO_ID)
+        elif re.match(UNIPROT_ID_REGEX, self.id):
+            validate_id_name_object(self, self.id, self.name, validate_id_function=validate_uniprot_id)
         return self