diff --git a/src/ontogpt/io/template_loader.py b/src/ontogpt/io/template_loader.py
index f21a1d9c5..50fbe543d 100644
--- a/src/ontogpt/io/template_loader.py
+++ b/src/ontogpt/io/template_loader.py
@@ -4,6 +4,7 @@
 import logging
 from pathlib import Path
 
+from linkml.generators.pydanticgen import PydanticGenerator
 from linkml_runtime import SchemaView
 from linkml_runtime.linkml_model import ClassDefinition
 
@@ -17,24 +18,56 @@ def get_template_details(template: TEMPLATE_NAME) -> ClassDefinition:
     """
     Get the LinkML class, module, and schemaview for a template.
 
+    This may be a template already known to ontogpt or the path
+    to a custom template. It is assumed to be the latter if the
+    template input is a path to a YAML file.
     :param template: template name of the form module.ClassName
     :return: tuple of (LinkML class definition, module, specific
     Python class, schemaview)
     """
-    logger.info(f"Loading schema for {template}")
-    if "." in template:
-        module_name, class_name = template.split(".", 1)
-    else:
-        module_name = template
+    # Check if template is a path to a YAML file
+    # If so, this is a custom schema and needs python classes
+    if template.endswith(".yaml"):
+        logger.info(f"Loading custom schema from {template}")
+        path_to_template = Path(template)
+
+        # Check if file exists first
+        if not path_to_template.exists():
+            raise FileNotFoundError(f"Template file not found at {template}")
+        
+        # Copy the schema to the templates directory
+        # So it will have access to imports like the core schema
+        templates_path = this_path.parent / "templates"
+        new_path_to_template = templates_path / path_to_template.name
+        new_path_to_template.write_text(path_to_template.read_text())
+        module_name = new_path_to_template.stem
+        path_to_module = new_path_to_template.with_suffix(".py")
+
+        sv = SchemaView(new_path_to_template)
+
+        gen = PydanticGenerator(str(new_path_to_template), pydantic_version=2)
+        path_to_module.write_text(gen.serialize())
+        
+        mod = importlib.import_module(f"ontogpt.templates.{module_name}")
         class_name = None
-    path_to_template = get_template_path(module_name)
-    sv = SchemaView(path_to_template)
+
+    else:
+        logger.info(f"Loading schema for {template}")
+        if "." in template:
+            module_name, class_name = template.split(".", 1)
+        else:
+            module_name = template
+            class_name = None
+        path_to_template = get_template_path(module_name)
+        sv = SchemaView(path_to_template)
+        mod = importlib.import_module(f"ontogpt.templates.{module_name}")
+
     if class_name is None:
         roots = [c.name for c in sv.all_classes().values() if c.tree_root]
         if len(roots) != 1:
             raise ValueError(f"Template {template} does not have singular root: {roots}")
         class_name = roots[0]
-    mod = importlib.import_module(f"ontogpt.templates.{module_name}")
+
     pyclass = mod.__dict__[class_name]
 
     logger.info(f"Getting class for template {template}")