diff --git a/docs/conf.py b/docs/conf.py
index c56983e..c4286b0 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -39,7 +39,8 @@ intersphinx_mapping = {
     'matplotlib': ('https://matplotlib.org/stable/', None),
     'numpy': ('https://numpy.org/doc/stable/', None),
     'pandas': ('https://pandas.pydata.org/docs/', None),
-    'pydantic': ('https://docs.pydantic.dev/latest/', None)
+    'pydantic': ('https://docs.pydantic.dev/latest/', None),
+    'h5py': ('https://docs.h5py.org/en/stable/', None)
 
 }
 
diff --git a/nwb_linkml/poetry.lock b/nwb_linkml/poetry.lock
index 946195d..cbba7b4 100644
--- a/nwb_linkml/poetry.lock
+++ b/nwb_linkml/poetry.lock
@@ -295,13 +295,13 @@ yaml = ["PyYAML (>=3.10)"]
 
 [[package]]
 name = "curies"
-version = "0.6.0"
+version = "0.6.3"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "curies-0.6.0-py3-none-any.whl", hash = "sha256:0bf79e2176b2e44dee7fefadcd1f2d69e643fea124dc4a8d0dbf47ca5e1589f2"},
-    {file = "curies-0.6.0.tar.gz", hash = "sha256:a31533ae9caeec332f9bb33e21366ab7ec32437c5f347fc9d85aa77cc48093cc"},
+    {file = "curies-0.6.3-py3-none-any.whl", hash = "sha256:fb4e99b011f34fb61f7aa38e0bb32c6c6c529c252d27ad2c8a7031687c6894ea"},
+    {file = "curies-0.6.3.tar.gz", hash = "sha256:37f4763c387a674adcfa5e93d222315d646647a2df198a60382ff877b72963df"},
 ]
 
 [package.dependencies]
@@ -397,17 +397,6 @@ files = [
     {file = "dash_table-5.0.0.tar.gz", hash = "sha256:18624d693d4c8ef2ddec99a6f167593437a7ea0bf153aa20f318c170c5bc7308"},
 ]
 
-[[package]]
-name = "decorator"
-version = "5.1.1"
-description = "Decorators for Humans"
-optional = false
-python-versions = ">=3.5"
-files = [
-    {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
-    {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
-]
-
 [[package]]
 name = "deprecated"
 version = "1.2.14"
@@ -789,20 +778,17 @@ jsonpointer = ">=1.9"
 
 [[package]]
 name = "jsonpath-ng"
-version = "1.5.3"
+version = "1.6.0"
 description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
 optional = false
 python-versions = "*"
 files = [
-    {file = "jsonpath-ng-1.5.3.tar.gz", hash = "sha256:a273b182a82c1256daab86a313b937059261b5c5f8c4fa3fc38b882b344dd567"},
-    {file = "jsonpath_ng-1.5.3-py2-none-any.whl", hash = "sha256:f75b95dbecb8a0f3b86fd2ead21c2b022c3f5770957492b9b6196ecccfeb10aa"},
-    {file = "jsonpath_ng-1.5.3-py3-none-any.whl", hash = "sha256:292a93569d74029ba75ac2dc3d3630fc0e17b2df26119a165fa1d498ca47bf65"},
+    {file = "jsonpath-ng-1.6.0.tar.gz", hash = "sha256:5483f8e9d74c39c9abfab554c070ae783c1c8cbadf5df60d561bc705ac68a07e"},
+    {file = "jsonpath_ng-1.6.0-py3-none-any.whl", hash = "sha256:6fd04833412c4b3d9299edf369542f5e67095ca84efa17cbb7f06a34958adc9f"},
 ]
 
 [package.dependencies]
-decorator = "*"
 ply = "*"
-six = "*"
 
 [[package]]
 name = "jsonpointer"
@@ -817,13 +803,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.19.0"
+version = "4.19.1"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.19.0-py3-none-any.whl", hash = "sha256:043dc26a3845ff09d20e4420d6012a9c91c9aa8999fa184e7efcfeccb41e32cb"},
-    {file = "jsonschema-4.19.0.tar.gz", hash = "sha256:6e1e7569ac13be8139b2dd2c21a55d350066ee3f80df06c608b398cdc6f30e8f"},
+    {file = "jsonschema-4.19.1-py3-none-any.whl", hash = "sha256:cd5f1f9ed9444e554b38ba003af06c0a8c2868131e56bfbef0550fb450c0330e"},
+    {file = "jsonschema-4.19.1.tar.gz", hash = "sha256:ec84cc37cfa703ef7cd4928db24f9cb31428a5d0fa77747b8b51a847458e0bbf"},
 ]
 
 [package.dependencies]
@@ -1035,13 +1021,13 @@ files = [
 
 [[package]]
 name = "nest-asyncio"
-version = "1.5.7"
+version = "1.5.8"
 description = "Patch asyncio to allow nested event loops"
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "nest_asyncio-1.5.7-py3-none-any.whl", hash = "sha256:5301c82941b550b3123a1ea772ba9a1c80bad3a182be8c1a5ae6ad3be57a9657"},
-    {file = "nest_asyncio-1.5.7.tar.gz", hash = "sha256:6a80f7b98f24d9083ed24608977c09dd608d83f91cccc24c9d2cba6d10e01c10"},
+    {file = "nest_asyncio-1.5.8-py3-none-any.whl", hash = "sha256:accda7a339a70599cb08f9dd09a67e0c2ef8d8d6f4c07f96ab203f2ae254e48d"},
+    {file = "nest_asyncio-1.5.8.tar.gz", hash = "sha256:25aa2ca0d2a5b5531956b9e273b45cf664cae2b145101d73b86b199978d48fdb"},
 ]
 
 [[package]]
@@ -1170,13 +1156,13 @@ files = [
 
 [[package]]
 name = "plotly"
-version = "5.16.1"
+version = "5.17.0"
 description = "An open-source, interactive data visualization library for Python"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "plotly-5.16.1-py2.py3-none-any.whl", hash = "sha256:19cc34f339acd4e624177806c14df22f388f23fb70658b03aad959a0e650a0dc"},
-    {file = "plotly-5.16.1.tar.gz", hash = "sha256:295ac25edeb18c893abb71dcadcea075b78fd6fdf07cee4217a4e1009667925b"},
+    {file = "plotly-5.17.0-py2.py3-none-any.whl", hash = "sha256:7c84cdf11da162423da957bb093287134f2d6f170eb9a74f1459f825892247c3"},
+    {file = "plotly-5.17.0.tar.gz", hash = "sha256:290d796bf7bab87aad184fe24b86096234c4c95dcca6ecbca02d02bdf17d3d97"},
 ]
 
 [package.dependencies]
@@ -1486,13 +1472,13 @@ shexjsg = ">=0.8.1"
 
 [[package]]
 name = "pytest"
-version = "7.4.1"
+version = "7.4.2"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-7.4.1-py3-none-any.whl", hash = "sha256:460c9a59b14e27c602eb5ece2e47bec99dc5fc5f6513cf924a7d03a578991b1f"},
-    {file = "pytest-7.4.1.tar.gz", hash = "sha256:2f2301e797521b23e4d2585a0a3d7b5e50fdddaaf7e7d6773ea26ddb17c213ab"},
+    {file = "pytest-7.4.2-py3-none-any.whl", hash = "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002"},
+    {file = "pytest-7.4.2.tar.gz", hash = "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"},
 ]
 
 [package.dependencies]
@@ -1816,13 +1802,13 @@ files = [
 
 [[package]]
 name = "rich"
-version = "13.5.2"
+version = "13.5.3"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "rich-13.5.2-py3-none-any.whl", hash = "sha256:146a90b3b6b47cac4a73c12866a499e9817426423f57c5a66949c086191a8808"},
-    {file = "rich-13.5.2.tar.gz", hash = "sha256:fb9d6c0a0f643c99eed3875b5377a184132ba9be4d61516a55273d3554d75a39"},
+    {file = "rich-13.5.3-py3-none-any.whl", hash = "sha256:9257b468badc3d347e146a4faa268ff229039d4c2d176ab0cffb4c4fbc73d5d9"},
+    {file = "rich-13.5.3.tar.gz", hash = "sha256:87b43e0543149efa1253f485cd845bb7ee54df16c9617b8a893650ab84b4acb6"},
 ]
 
 [package.dependencies]
@@ -1834,108 +1820,108 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
 name = "rpds-py"
-version = "0.10.2"
+version = "0.10.3"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "SQLAlchemy-2.0.21.tar.gz", hash = "sha256:05b971ab1ac2994a14c56b35eaaa91f86ba080e9ad481b20d99d77f381bb6258"},
 ]
 
 [package.dependencies]
@@ -2184,13 +2170,13 @@ doc = ["reno", "sphinx", "tornado (>=4.5)"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.7.1"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+version = "4.8.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
-    {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
+    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
+    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
 ]
 
 [[package]]
@@ -2209,13 +2195,13 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 
 [[package]]
 name = "urllib3"
-version = "2.0.4"
+version = "2.0.5"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "urllib3-2.0.4-py3-none-any.whl", hash = "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4"},
-    {file = "urllib3-2.0.4.tar.gz", hash = "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11"},
+    {file = "urllib3-2.0.5-py3-none-any.whl", hash = "sha256:ef16afa8ba34a1f989db38e1dbbe0c302e4289a47856990d0682e374563ce35e"},
+    {file = "urllib3-2.0.5.tar.gz", hash = "sha256:13abf37382ea2ce6fb744d4dad67838eec857c9f4f57009891805e0b5e123594"},
 ]
 
 [package.extras]
@@ -2381,24 +2367,24 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.16.2"
+version = "3.17.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
-    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
 testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [extras]
 plot = ["dash", "dash-cytoscape"]
-tests = ["coverage", "coveralls", "pytest", "pytest-cov", "pytest-depends", "pytest-emoji", "pytest-md", "pytest-profiling"]
+tests = ["coverage", "coveralls", "pytest", "pytest-cov", "pytest-depends", "pytest-md", "pytest-profiling"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "9ef89b731746d07d428c6cff4a8c8b4771fbfcfcc8f17120ce3c6089e5161eb6"
+content-hash = "7a4e1c3b66143e4f4e8392238051241f25274ebd597183ef64168055949074f4"
diff --git a/nwb_linkml/pyproject.toml b/nwb_linkml/pyproject.toml
index 77ac0db..f43701b 100644
--- a/nwb_linkml/pyproject.toml
+++ b/nwb_linkml/pyproject.toml
@@ -65,11 +65,11 @@ build-backend = "poetry.core.masonry.api"
 
 
 [tool.pytest.ini_options]
-addopts = [
-    "--cov=nwb_linkml",
-    "--cov-append",
-    "--cov-config=.coveragerc"
-]
+#addopts = [
+#    "--cov=nwb_linkml",
+#    "--cov-append",
+#    "--cov-config=.coveragerc"
+#]
 testpaths = [
     "tests",
     'nwb_linkml/tests'
diff --git a/nwb_linkml/src/nwb_linkml/generators/pydantic.py b/nwb_linkml/src/nwb_linkml/generators/pydantic.py
index 3dc2ebb..f66ee7f 100644
--- a/nwb_linkml/src/nwb_linkml/generators/pydantic.py
+++ b/nwb_linkml/src/nwb_linkml/generators/pydantic.py
@@ -19,11 +19,12 @@ The `serialize` method
 import pdb
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import List, Dict, Set, Tuple, Optional, TypedDict
+from typing import List, Dict, Set, Tuple, Optional, TypedDict, Type
 import os, sys
 from types import ModuleType
 from copy import deepcopy, copy
 import warnings
+import inspect
 
 from nwb_linkml.maps import flat_to_npytyping
 from linkml.generators import PydanticGenerator
@@ -48,10 +49,14 @@ from linkml.utils.ifabsent_functions import ifabsent_value_declaration
 from nwb_linkml.maps.naming import module_case, version_module_case
 
 from jinja2 import Template
+from pydantic import BaseModel
+
+class LinkML_Meta(BaseModel):
+    """Extra LinkML Metadata stored as a class attribute"""
+    tree_root: bool = False
 
 
-
-def default_template(pydantic_ver: str = "1") -> str:
+def default_template(pydantic_ver: str = "1", extra_classes:Optional[List[Type[BaseModel]]] = None) -> str:
     """Constructs a default template for pydantic classes based on the version of pydantic"""
     ### HEADER ###
     template = """
@@ -94,7 +99,6 @@ class ConfiguredBaseModel(WeakRefShimBaseModel,
                 extra = {% if allow_extra %}'allow'{% else %}'forbid'{% endif %},
                 arbitrary_types_allowed = True,
                 use_enum_values = True):
-    pass
 """
     else:
         template += """
@@ -104,8 +108,22 @@ class ConfiguredBaseModel(BaseModel,
                 extra = {% if allow_extra %}'allow'{% else %}'forbid'{% endif %},
                 arbitrary_types_allowed = True,
                 use_enum_values = True):
-    pass
 """
+    ### Injected Fields
+    template += """
+{%- if injected_fields != None -%}
+    {% for field in injected_fields %}
+    {{ field }}
+    {% endfor %}
+{%- else -%}
+    pass
+{%- endif -%}
+    """
+    ### Extra classes
+    if extra_classes is not None:
+        template += """{{ '\n\n' }}"""
+        for cls in extra_classes:
+            template += inspect.getsource(cls) + '\n\n'
     ### ENUMS ###
     template += """
 {% for e in enums.values() %}
@@ -142,11 +160,15 @@ class {{ c.name }}
     \"\"\"
     {%- endif %}
     {% for attr in c.attributes.values() if c.attributes -%}
-    {{attr.name}}: {%- if attr.equals_string -%}
+    {{attr.name}}:{{ ' ' }}{%- if attr.equals_string -%}
         Literal[{{ predefined_slot_values[c.name][attr.name] }}]
         {%- else -%}
         {{ attr.annotations['python_range'].value }}
-        {%- endif -%} = Field(
+        {%- endif -%}
+        {%- if attr.annotations['fixed_field'] -%}
+        {{ ' ' }}= {{ attr.annotations['fixed_field'].value }}
+        {%- else -%}
+        {{ ' ' }}= Field(
     {%- if predefined_slot_values[c.name][attr.name] -%}
         {{ predefined_slot_values[c.name][attr.name] }}
     {%- elif attr.required -%}
@@ -159,6 +181,7 @@ class {{ c.name }}
     {%- if attr.minimum_value != None %}, ge={{attr.minimum_value}}{% endif -%}
     {%- if attr.maximum_value != None %}, le={{attr.maximum_value}}{% endif -%}
     )
+    {%- endif %}
     {% else -%}
     None
     {% endfor %}
@@ -192,6 +215,9 @@ class NWBPydanticGenerator(PydanticGenerator):
     # SKIP_SLOTS=('VectorData',)
     SKIP_SLOTS=('',)
     SKIP_CLASSES=('',)
+    INJECTED_FIELDS = (
+        'hdf5_path: Optional[str] = Field(None, description="The absolute path that this object is stored in an NWB file")',
+    )
     # SKIP_CLASSES=('VectorData','VectorIndex')
     split:bool=True
     schema_map:Optional[Dict[str, SchemaDefinition]]=None
@@ -410,6 +436,18 @@ class NWBPydanticGenerator(PydanticGenerator):
         union += '\n' + ' '*4 + ']'
         return union
 
+    def _get_linkml_classvar(self, cls:ClassDefinition) -> SlotDefinition:
+        """A class variable that holds additional linkml attrs"""
+        slot = SlotDefinition(
+            name='linkml_meta'
+        )
+        slot.annotations['python_range'] = Annotation('python_range', 'ClassVar[LinkML_Meta]')
+        meta_fields = {k: getattr(cls, k, None) for k in LinkML_Meta.model_fields.keys()}
+        meta_field_strings = [f'{k}={v}' for k,v in meta_fields.items() if v is not None]
+        meta_field_string = ', '.join(meta_field_strings)
+        slot.annotations['fixed_field'] = Annotation('fixed_field', f'Field(LinkML_Meta({meta_field_string}), frozen=True)')
+
+        return slot
 
     def sort_classes(self, clist: List[ClassDefinition], imports:Dict[str, List[str]]) -> List[ClassDefinition]:
         """
@@ -538,7 +576,8 @@ class NWBPydanticGenerator(PydanticGenerator):
             with open(self.template_file) as template_file:
                 template_obj = Template(template_file.read())
         else:
-            template_obj = Template(default_template(self.pydantic_version))
+            template_obj = Template(default_template(self.pydantic_version,
+                                                     extra_classes=[LinkML_Meta]))
 
         sv: SchemaView
         sv = self.schemaview
@@ -581,6 +620,9 @@ class NWBPydanticGenerator(PydanticGenerator):
             for attribute in list(class_def.attributes.keys()):
                 del class_def.attributes[attribute]
 
+            # make class attr that stores extra linkml attrs
+            class_def.attributes['linkml_meta'] = self._get_linkml_classvar(class_def)
+
             class_name = class_original.name
             predefined_slot_values[camelcase(class_name)] = {}
             for s in class_slots[class_name]:
@@ -632,6 +674,7 @@ class NWBPydanticGenerator(PydanticGenerator):
                     pyrange = f"Optional[{pyrange}]"
                 ann = Annotation("python_range", pyrange)
                 s.annotations[ann.tag] = ann
+
         code = template_obj.render(
             imports=imports,
             schema=pyschema,
@@ -642,6 +685,7 @@ class NWBPydanticGenerator(PydanticGenerator):
             metamodel_version=self.schema.metamodel_version,
             version=self.schema.version,
             class_isa_plus_mixins=self.get_class_isa_plus_mixins(sorted_classes),
+            injected_fields=self.INJECTED_FIELDS
         )
         return code
 
@@ -678,3 +722,4 @@ def compile_python(text_or_fn: str, package_path: Path = None) -> ModuleType:  #
 
     exec(spec, module.__dict__)
     return module
+
diff --git a/nwb_linkml/src/nwb_linkml/io/hdf5.py b/nwb_linkml/src/nwb_linkml/io/hdf5.py
index 8f77f8e..96be760 100644
--- a/nwb_linkml/src/nwb_linkml/io/hdf5.py
+++ b/nwb_linkml/src/nwb_linkml/io/hdf5.py
@@ -1,154 +1,79 @@
 """
 This is a sandbox file that should be split out to its own pydantic-hdf5 package, but just experimenting here to get our bearings
+
+Notes:
+
+    * Rather than a set of recursive build steps as is used elsewhere in the package,
+      since we need to instantiate some models first that are referred to elsewhere, we
+      flatten the hdf5 file and build each from a queue.
+
+Mapping operations (mostly TODO atm)
+
+* Create new models from DynamicTables
+* Handle softlinks as object references and vice versa by adding a ``path`` attr
+
+
+
+Other TODO:
+
+* Read metadata only, don't read all arrays
+* Write, obvi lol.
+
 """
 import pdb
 import typing
+import warnings
 from typing import Optional, List, Dict, overload, Literal, Type, Any
 from pathlib import Path
 from types import ModuleType
-from typing import TypeVar, TYPE_CHECKING
+from typing import TypeVar, TYPE_CHECKING, NamedTuple
 from abc import abstractmethod
 import json
+import subprocess
+import shutil
 
 import h5py
-from pydantic import BaseModel
+from pydantic import BaseModel, Field, ConfigDict
 from dataclasses import dataclass, field
 
 from nwb_linkml.translate import generate_from_nwbfile
 #from nwb_linkml.models.core_nwb_file import NWBFile
 if TYPE_CHECKING:
-    from nwb_linkml.models.core_nwb_file import NWBFile
+    from nwb_linkml.models import NWBFile
 from nwb_linkml.providers.schema import SchemaProvider
 
-@dataclass
-class HDF5Element():
 
-    cls: h5py.Dataset | h5py.Group
-    parent: Type[BaseModel]
-    model: Optional[Any] = None
-    root_model: Optional[Type[BaseModel]] = None
 
-    @abstractmethod
-    def read(self) -> BaseModel | List[BaseModel]:
-        """
-        Constructs the pydantic model from the given hdf5 element
-        """
+class H5SourceItem(BaseModel):
+    """Tuple of items for each element when flattening an hdf5 file"""
+    path: str
+    """Absolute hdf5 path of element"""
+    leaf: bool
+    """If ``True``, this item has no children (and thus we should start instantiating it before ascending to parent classes)"""
+    h5_type: Literal['group', 'dataset']
+    """What kind of hdf5 element this is"""
+    depends: List[str] = Field(default_factory=list)
+    """Paths of other source items that this item depends on before it can be instantiated. eg. from softlinks"""
 
-    @abstractmethod
-    def write(self) -> h5py.Dataset | h5py.Group:
-        """
-        Create the h5py object from the in-memory pydantic model
-        """
 
+
+
+    model_config = ConfigDict(arbitrary_types_allowed=True)
     @property
-    def name(self) -> str:
-        """Just the terminal group name"""
-        return self.cls.name.split('/')[-1]
-
-    def get_model(self) -> Type[BaseModel | dict | list]:
-        """
-        Find our model
-        - If we have a neurodata_type in our attrs, use that
-        - Otherwise, use our parent to resolve the type
-        """
-        if self.model is not None:
-            return self.model
-
-        if 'neurodata_type' in self.cls.attrs.keys():
-            return get_model(self.cls)
-        else:
-            parent_model  = get_model(self.cls.parent)
-            field = parent_model.model_fields.get(self.name)
-            if issubclass(type(field.annotation), BaseModel):
-                return field.annotation
-            else:
-                try:
-                    if issubclass(field.annotation, BaseModel):
-                        return field.annotation
-                except TypeError:
-                    pass
-            # remove any optionals
-            annotation = field.annotation
-            annotation = unwrap_optional(annotation)
-
-            if typing.get_origin(annotation) is list:
-                return list
-
-            else:
-                return dict
-                #raise NotImplementedError('Need to unpack at least listlike annotations')
-
-def unwrap_optional(annotation):
-    if typing.get_origin(annotation) == typing.Union:
-        args = typing.get_args(annotation)
-
-        if len(args) == 2 and args[1].__name__ == 'NoneType':
-            annotation = args[0]
-    return annotation
-
-def take_outer_type(annotation):
-    if typing.get_origin(annotation) is list:
-        return list
-    return annotation
-
-def submodel_by_path(model: BaseModel, path:str) -> Type[BaseModel | dict | list]:
-    """
-    Given a pydantic model and an absolute HDF5 path, get the type annotation
-    """
-
-
-@dataclass
-class H5Dataset(HDF5Element):
-    cls: h5py.Dataset
-
-    def read(self) -> Any:
-        model = self.get_model()
-
-        # TODO: Handle references
-        if self.cls.dtype == h5py.ref_dtype:
-            return None
-
-        if self.cls.shape == ():
-            return self.cls[()]
-        elif model is list:
-            return self.cls[:].tolist()
-        else:
-            return {'array':self.cls[:], 'name': self.cls.name.split('/')[-1]}
-            #raise NotImplementedError('oop')
-
-@dataclass
-class H5Group(HDF5Element):
-    cls: h5py.Group
-
-    def read(self) -> BaseModel:
-        data = {}
-        model = self.get_model()
-
-        model_attrs = {
-            k:v for k, v in self.cls.attrs.items() if k in model.model_fields.keys()
-        }
-        data.update(model_attrs)
-
-
-        for k, v in self.cls.items():
-            child_model = None
-            if isinstance(model, type) and issubclass(model, BaseModel):
-                child_field = model.model_fields.get(k, None)
-                if child_field is not None:
-                    child_model = unwrap_optional(child_field.annotation)
-                    child_model = take_outer_type(child_model)
-            if isinstance(v, h5py.Group):
-                data[k] = H5Group(cls=v, parent=model, model=child_model).read()
-            elif isinstance(v, h5py.Dataset):
-                data[k] = H5Dataset(cls=v, parent=model, model=child_model).read()
-
-
-        if issubclass(model, BaseModel):
-            data['name'] = self.cls.name.split('/')[-1]
-            return model(**data)
-        elif model is list:
-            return list(data.values())
+    def parts(self) -> List[str]:
+        """path split by /"""
+        return self.path.split('/')
 
+class ReadQueue(BaseModel):
+    """Container model to store items as they are built """
+    queue: Dict[str,H5SourceItem] = Field(
+        default_factory=dict,
+        description="Items left to be instantiated, keyed by hdf5 path",
+    )
+    completed: Dict[str, BaseModel] = Field(
+        default_factory=dict,
+        description="Items that have already been instantiated, keyed by hdf5 path"
+    )
 
 class HDF5IO():
 
@@ -169,19 +94,23 @@ class HDF5IO():
     def read(self, path:str) -> BaseModel | Dict[str, BaseModel]: ...
 
     def read(self, path:Optional[str] = None):
+        provider = self.make_provider()
+
         h5f = h5py.File(str(self.path))
-        schema = read_specs(h5f.get('specifications'))
-        # build schema so we have them cached
-
-        provider = SchemaProvider()
-        res = provider.build_from_dicts(schema)
-
         if path:
             src = h5f.get(path)
-            parent = get_model(src)
         else:
             src = h5f
-            parent = provider.get_class('core', 'NWBFile')
+
+        # get all children of selected item
+        if isinstance(src, (h5py.File, h5py.Group)):
+            children = self._flatten_hdf(src)
+        else:
+            raise NotImplementedError('directly read individual datasets')
+
+
+
+
 
         data = {}
         for k, v in src.items():
@@ -199,6 +128,38 @@ class HDF5IO():
 
 
 
+
+
+    def make_provider(self) -> SchemaProvider:
+        """
+        Create a :class:`~.providers.schema.SchemaProvider` by
+        reading specifications from the NWBFile ``/specification`` group and translating
+        them to LinkML and generating pydantic models
+
+        Returns:
+            :class:`~.providers.schema.SchemaProvider` : Schema Provider with correct versions
+                specified as defaults
+        """
+        h5f = h5py.File(str(self.path))
+        schema = read_specs_as_dicts(h5f.get('specifications'))
+
+        # get versions for each namespace
+        versions = {}
+        for ns_schema in schema.values():
+            # each "namespace" can actually contain multiple namespaces which actually contain the version info
+            for inner_ns in ns_schema['namespace']['namespaces']:
+                versions[inner_ns['name']] = inner_ns['version']
+
+        provider = SchemaProvider(versions=versions)
+
+        # build schema so we have them cached
+        provider.build_from_dicts(schema)
+        h5f.close()
+        return provider
+
+
+
+
     def process_group(self, group:h5py.Group|h5py.File) -> dict | list:
         attrs = dict(group.attrs)
 
@@ -233,7 +194,17 @@ class HDF5IO():
 
 
 
-def read_specs(group: h5py.Group) -> dict:
+def read_specs_as_dicts(group: h5py.Group) -> dict:
+    """
+    Utility function to iterate through the `/specifications` group and
+    load
+
+    Args:
+        group:
+
+    Returns:
+
+    """
     spec_dict = {}
     def _read_spec(name, node):
 
@@ -263,4 +234,136 @@ def get_model(cls: h5py.Group | h5py.Dataset) -> Type[BaseModel]:
         return mod.model_fields[cls.name.split('/')[-1]].annotation
 
 
+def truncate_file(source: Path, target: Optional[Path] = None, n:int=10) -> Path:
+    """
+    Create a truncated HDF5 file where only the first few samples are kept.
+
+    Used primarily to create testing data from real data without it being so damn bit
+
+    Args:
+        source (:class:`pathlib.Path`): Source hdf5 file
+        target (:class:`pathlib.Path`): Optional - target hdf5 file to write to. If ``None``, use ``{source}_truncated.hdf5``
+        n (int): The number of items from datasets (samples along the 0th dimension of a dataset) to include
+
+    Returns:
+        :class:`pathlib.Path` path of the truncated file
+    """
+    if target is None:
+        target = source.parent / (source.stem + '_truncated.hdf5')
+    else:
+        target = Path(target)
+
+    source = Path(source)
+
+    # and also a temporary file that we'll make with h5repack
+    target_tmp = target.parent / (target.stem + '_tmp.hdf5')
+
+
+    # copy the whole thing
+    if target.exists():
+        target.unlink()
+    shutil.copy(source, target)
+
+    h5f_target = h5py.File(str(target), 'r+')
+    def _prune_dataset(name:str, obj: h5py.Dataset | h5py.Group):
+
+        if isinstance(obj, h5py.Dataset):
+            if obj.size > 10:
+                try:
+                    obj.resize(n, axis=0)
+                except TypeError:
+                    # contiguous arrays cant be resized directly
+                    # so we have to jank our way through it
+                    tmp_name = obj.name + '__tmp'
+                    original_name = obj.name
+                    obj.parent.move(obj.name, tmp_name)
+                    old_obj = obj.parent.get(tmp_name)
+                    new_obj = obj.parent.create_dataset(original_name, data=old_obj[0:n])
+                    for k, v in old_obj.attrs.items():
+                        new_obj.attrs[k] = v
+                    del new_obj.parent[tmp_name]
+
+
+    h5f_target.visititems(_prune_dataset)
+    h5f_target.flush()
+    h5f_target.close()
+
+    # use h5repack to actually remove the items from the dataset
+    if shutil.which('h5repack') is None:
+        warnings.warn('Truncated file made, but since h5repack not found in path, file wont be any smaller')
+        return target
+
+    res = subprocess.run(
+        ['h5repack', '-f', 'GZIP=9', str(target), str(target_tmp)],
+        capture_output=True
+    )
+    if res.returncode != 0:
+        warnings.warn(f'h5repack did not return 0: {res.stderr} {res.stdout}')
+        # remove the attempt at the repack
+        target_tmp.unlink()
+        return target
+
+    target.unlink()
+    target_tmp.rename(target)
+
+    return target
+
+def unwrap_optional(annotation):
+    if typing.get_origin(annotation) == typing.Union:
+        args = typing.get_args(annotation)
+
+        if len(args) == 2 and args[1].__name__ == 'NoneType':
+            annotation = args[0]
+    return annotation
+
+def take_outer_type(annotation):
+    if typing.get_origin(annotation) is list:
+        return list
+    return annotation
+
+
+
+def submodel_by_path(model: BaseModel, path:str) -> Type[BaseModel | dict | list]:
+    """
+    Given a pydantic model and an absolute HDF5 path, get the type annotation
+    """
+    parts = path.split('/')
+    for part in parts:
+        ann = model.model_fields[part].annotation
+
+
+def flatten_hdf(h5f:h5py.File | h5py.Group, skip='specifications') -> Dict[str, H5SourceItem]:
+    """
+    Flatten all child elements of hdf element into a dict of :class:`.H5SourceItem` s keyed by their path
+
+    Args:
+        h5f (:class:`h5py.File` | :class:`h5py.Group`): HDF file or group to flatten!
+    """
+    items = {}
+    def _itemize(name: str, obj: h5py.Dataset | h5py.Group):
+        if skip in name:
+            return
+        leaf = isinstance(obj, h5py.Dataset) or len(obj.keys()) == 0
+        # get references in attrs and datasets
+        refs = [ref for ref in obj.attrs.values() if isinstance(ref, h5py.h5r.Reference)]
+        if isinstance(obj, h5py.Dataset):
+            h5_type = 'dataset'
+            if obj.shape == ():
+                if isinstance(obj[()], h5py.h5r.Reference):
+                    refs.append(obj[()])
+            elif isinstance(obj[0], h5py.h5r.Reference):
+                refs.extend(obj[:].tolist())
+        else:
+            h5_type = 'group'
+        # dereference and get name of reference
+        depends = list(set([h5f[i].name for i in refs]))
+        items[name] = H5SourceItem.model_construct(
+            path = name,
+            leaf = leaf,
+            depends = depends
+        )
+
+    h5f.visititems(_itemize)
+    return items
+
 
diff --git a/nwb_linkml/src/nwb_linkml/providers/schema.py b/nwb_linkml/src/nwb_linkml/providers/schema.py
index e2323d8..fa58b8d 100644
--- a/nwb_linkml/src/nwb_linkml/providers/schema.py
+++ b/nwb_linkml/src/nwb_linkml/providers/schema.py
@@ -172,7 +172,7 @@ class Provider(ABC):
         return version_path
 
     @property
-    def versions(self) -> Dict[str,List[str]]:
+    def available_versions(self) -> Dict[str,List[str]]:
         """
         Dictionary mapping a namespace to a list of built versions
         """
@@ -511,7 +511,7 @@ class PydanticProvider(Provider):
             path = LinkMLProvider(path=self.config.cache_dir).namespace_path(namespace, version) / 'namespace.yaml'
             if version is None:
                 # Get the most recently built version
-                version = LinkMLProvider(path=self.config.cache_dir).versions[name][-1]
+                version = LinkMLProvider(path=self.config.cache_dir).available_versions[name][-1]
             fn = path.parts[-1]
         else:
             # given a path to a namespace linkml yaml file
@@ -563,10 +563,8 @@ class PydanticProvider(Provider):
         return serialized
 
     @classmethod
-    def module_name(self, namespace:str, version: Optional[str]=None) -> str:
-        name_pieces = ['nwb_linkml', 'models', 'pydantic',  namespace]
-        if version is not None:
-            name_pieces.append(version_module_case(version))
+    def module_name(self, namespace:str, version: str) -> str:
+        name_pieces = ['nwb_linkml', 'models', 'pydantic',  namespace, version_module_case(version), 'namespace']
         module_name = '.'.join(name_pieces)
         return module_name
     def import_module(
@@ -590,7 +588,7 @@ class PydanticProvider(Provider):
         """
         # get latest version if None
         if version is None:
-            version = self.versions[namespace][-1]
+            version = self.available_versions[namespace][-1]
 
         path = self.namespace_path(namespace, version) / 'namespace.py'
         if not path.exists():
@@ -602,7 +600,9 @@ class PydanticProvider(Provider):
         spec.loader.exec_module(module)
         return module
 
-    def get(self, namespace: str, version: Optional[str] = None) -> ModuleType:
+    def get(self, namespace: str,
+            version: Optional[str] = None,
+            allow_repo: bool = True) -> ModuleType:
         """
         Get the imported module for a given namespace and version.
 
@@ -628,22 +628,27 @@ class PydanticProvider(Provider):
             namespace (str): Name of namespace to import. Must have either been previously built with :meth:`.PydanticProvider.build` or
                 a matching namespace/version combo must be available to the :class:`.LinkMLProvider`
             version (Optional[str]): Version to import. If ``None``, get the most recently build module
+            allow_repo (bool): Allow getting modules provided within :mod:`nwb_linkml.models.pydantic`
 
         Returns:
             The imported :class:`types.ModuleType` object that has all the built classes at the root level.
 
         """
+
+        if version is None:
+            version = self.available_versions[namespace][-1]
+
         module_name = self.module_name(namespace, version)
         if module_name in sys.modules:
             return sys.modules[module_name]
 
         try:
-            path = self.namespace_path(namespace, version)
+            path = self.namespace_path(namespace, version, allow_repo)
         except FileNotFoundError:
             path = None
 
         if path is None or not path.exists():
-            _ = self.build(namespace, version)
+            _ = self.build(namespace, version=version)
         module = self.import_module(namespace, version)
         return module
 
@@ -689,6 +694,21 @@ class SchemaProvider(Provider):
     Alias for :meth:`.LinkMLProvider.build_from_dicts` that also builds a pydantic model
     """
 
+    def __init__(
+            self,
+            versions: Optional[Dict[str, str]] = None,
+            **kwargs
+        ):
+        """
+        Args:
+            versions (dict): Dictionary like ``{'namespace': 'v1.0.0'}`` used to specify that this provider should always
+                return models from a specific version of a namespace (unless explicitly requested otherwise
+                in a call to :meth:`.get` ).
+            **kwargs: passed to superclass __init__ (see :class:`.Provider` )
+        """
+        self.versions = versions
+        super(SchemaProvider, self).__init__(**kwargs)
+
     @property
     def path(self) -> Path:
         return self.config.cache_dir
@@ -737,6 +757,9 @@ class SchemaProvider(Provider):
 
         Wrapper around :meth:`.PydanticProvider.get`
         """
+        if version is None and self.versions is not None:
+            version = self.versions.get(namespace, None)
+
         return PydanticProvider(path=self.path).get(namespace, version)
 
     def get_class(self, namespace: str, class_: str, version: Optional[str] = None) -> Type[BaseModel]:
@@ -745,6 +768,9 @@ class SchemaProvider(Provider):
 
         Wrapper around :meth:`.PydanticProvider.get_class`
         """
+        if version is None and self.versions is not None:
+            version = self.versions.get(namespace, None)
+
         return PydanticProvider(path=self.path).get_class(namespace, class_, version)
 
 
diff --git a/nwb_linkml/tests/data/aibs_ecephys.nwb b/nwb_linkml/tests/data/aibs_ecephys.nwb
new file mode 100644
index 0000000..b760cd4
Binary files /dev/null and b/nwb_linkml/tests/data/aibs_ecephys.nwb differ
diff --git a/nwb_linkml/tests/data/sources.txt b/nwb_linkml/tests/data/sources.txt
new file mode 100644
index 0000000..559aafb
--- /dev/null
+++ b/nwb_linkml/tests/data/sources.txt
@@ -0,0 +1,4 @@
+aibs_ecephys.nwb
+    - https://dandiarchive.org/dandiset/000021/
+    - 000021/sub-738651046/sub-738651046_ses-760693773_probe-769322820_ecephys.nwb
+    - truncated datasets to length 10
\ No newline at end of file
diff --git a/nwb_linkml/tests/test_io/test_io_hdf5.py b/nwb_linkml/tests/test_io/test_io_hdf5.py
index 6a336db..6f5cb8a 100644
--- a/nwb_linkml/tests/test_io/test_io_hdf5.py
+++ b/nwb_linkml/tests/test_io/test_io_hdf5.py
@@ -1,11 +1,14 @@
 import pdb
+import h5py
 
 import pytest
 from pathlib import Path
+import numpy as np
 
 from ..fixtures import tmp_output_dir, set_config_vars
 
 from nwb_linkml.io.hdf5 import HDF5IO
+from nwb_linkml.io.hdf5 import truncate_file
 @pytest.mark.skip()
 def test_hdf_read():
     NWBFILE = Path('/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb')
@@ -15,3 +18,73 @@ def test_hdf_read():
     model = io.read('acquisition')
 
     pdb.set_trace()
+
+@pytest.mark.skip()
+def test_truncate_file(tmp_output_dir):
+    source = tmp_output_dir / 'truncate_source.hdf5'
+
+    # create a dang ol hdf5 file with a big dataset and some softlinks and make sure
+    # we truncate the dataset and preserve softlink
+
+    h5f = h5py.File(str(source), 'w')
+    data_group = h5f.create_group('data')
+    dataset_contig = h5f.create_dataset(
+        '/data/dataset_contig',
+        data=np.zeros((1000,30,40), dtype=np.float64),
+        compression = "gzip",
+        compression_opts = 9
+    )
+    dataset_chunked = h5f.create_dataset(
+        '/data/dataset_chunked',
+        data=np.zeros((1000, 40, 50), dtype=np.float64),
+        compression="gzip",
+        compression_opts=9,
+        chunks=True
+    )
+    dataset_contig.attrs['reference_other'] = dataset_chunked.ref
+    dataset_chunked.attrs['reference_other'] = dataset_contig.ref
+    dataset_contig.attrs['anattr'] = 1
+
+    link_group = h5f.create_group('link/child')
+    link_group.attrs['reference_contig'] = dataset_contig.ref
+    link_group.attrs['reference_chunked'] = dataset_chunked.ref
+    h5f.flush()
+    h5f.close()
+
+    source_size = source.stat().st_size
+
+    # do it without providing target to check that we make filename correctly
+    n = 10
+    target_output = truncate_file(source, n=n)
+    assert target_output == source.parent / (source.stem + '_truncated.hdf5')
+    # check that we actually made it smaller
+    target_size = target_output.stat().st_size
+    # empirically, the source dataset is ~125KB and truncated is ~17KB
+    assert target_size < source_size / 5
+
+    # then check that we have what's expected in the file
+    target_h5f = h5py.File(target_output, 'r')
+
+    # truncation happened
+    assert target_h5f['data']['dataset_contig'].shape == (n, 30, 40)
+    assert target_h5f['data']['dataset_chunked'].shape == (n, 40, 50)
+    # references still work
+    # can't directly assess object identity equality with "is"
+    # so this tests if the referenced dereference and that they dereference to the right place
+    assert target_h5f[target_h5f['data']['dataset_contig'].attrs['reference_other']].name == target_h5f['data']['dataset_chunked'].name
+    assert target_h5f[target_h5f['data']['dataset_chunked'].attrs['reference_other']].name == target_h5f['data']['dataset_contig'].name
+    assert target_h5f[target_h5f['link']['child'].attrs['reference_contig']].name == target_h5f['data']['dataset_contig'].name
+    assert target_h5f[target_h5f['link']['child'].attrs['reference_chunked']].name == target_h5f['data']['dataset_chunked'].name
+    assert target_h5f['data']['dataset_contig'].attrs['anattr'] == 1
+
+@pytest.mark.skip()
+def test_flatten_hdf():
+    from nwb_linkml.io.hdf5 import HDF5IO, flatten_hdf
+    path = '/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773_probe-769322820_ecephys.nwb'
+    import h5py
+    h5f = h5py.File(path)
+    flat = flatten_hdf(h5f)
+    assert not any(['specifications' in v.path for v in flat.values()])
+
+    raise NotImplementedError('Just a stub for local testing for now, finish me!')
+
diff --git a/nwb_linkml/tests/test_providers/test_provider_schema.py b/nwb_linkml/tests/test_providers/test_provider_schema.py
index 392dbf1..e8b0f7d 100644
--- a/nwb_linkml/tests/test_providers/test_provider_schema.py
+++ b/nwb_linkml/tests/test_providers/test_provider_schema.py
@@ -1,6 +1,8 @@
 import pdb
 import shutil
 import os
+import sys
+from pathlib import Path
 
 from typing import Optional, Union, List
 from ..fixtures import tmp_output_dir, set_config_vars
@@ -8,6 +10,8 @@ from ..fixtures import tmp_output_dir, set_config_vars
 import pytest
 
 from nwb_linkml.providers.schema import LinkMLProvider, PydanticProvider
+import nwb_linkml
+from nwb_linkml.maps.naming import version_module_case
 
 
 CORE_MODULES = (
@@ -62,14 +66,24 @@ def test_linkml_provider(tmp_output_dir, repo_version, schema_version, schema_di
         })
     ]
 )
-def test_pydantic_provider(tmp_output_dir, class_name, test_fields):
+def test_pydantic_provider_core(tmp_output_dir, class_name, test_fields):
     provider = PydanticProvider(path=tmp_output_dir)
     # clear any prior output
     assert provider.path.parent == tmp_output_dir
     shutil.rmtree(provider.path, ignore_errors=True)
     assert not provider.path.exists()
 
-    core = provider.get('core')
+    # first, we should not build if we're allowed to get core from repo
+    core = provider.get('core', allow_repo=True)
+    assert Path(nwb_linkml.__file__).parent in Path(core.__file__).parents
+    assert not (provider.path / 'core').exists()
+
+    # then, if we're not allowed to get repo versions, we build!
+    del sys.modules[core.__name__]
+    core = provider.get('core', allow_repo=False)
+    # ensure we didn't get the builtin one
+    assert Path(nwb_linkml.__file__).parent not in Path(core.__file__).parents
+    assert (tmp_output_dir / 'pydantic' / 'core' / version_module_case(core.version) / 'namespace.py').exists()
 
     test_class = getattr(core, class_name)
     assert test_class == provider.get_class('core', class_name)