diff --git a/.gitignore b/.gitignore
index 92dd66e..b0802e5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -167,4 +167,5 @@ jupyter_execute
 .pdm-python
 .venv*
 
-requests-cache.sqlite
\ No newline at end of file
+requests-cache.sqlite
+*.pstats
\ No newline at end of file
diff --git a/nwb_linkml/pdm.lock b/nwb_linkml/pdm.lock
index 7627014..7a1aca7 100644
--- a/nwb_linkml/pdm.lock
+++ b/nwb_linkml/pdm.lock
@@ -5,7 +5,7 @@
 groups = ["default", "dev", "plot", "tests"]
 strategy = ["inherit_metadata"]
 lock_version = "4.5.0"
-content_hash = "sha256:3223b7fb1c0ac9877a6d8af33e55f10e54fe8eb3a8b4fa053d3e7082863260ac"
+content_hash = "sha256:f219083028bd024c53bc55626c8b6088d6eb5c2ade56bd694a7a112098aa9bfc"
 
 [[metadata.targets]]
 requires_python = ">=3.10,<3.13"
@@ -582,18 +582,18 @@ files = [
 
 [[package]]
 name = "idna"
-version = "3.7"
-requires_python = ">=3.5"
+version = "3.8"
+requires_python = ">=3.6"
 summary = "Internationalized Domain Names in Applications (IDNA)"
 groups = ["default", "dev", "plot", "tests"]
 files = [
-    {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"},
-    {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
+    {file = "idna-3.8-py3-none-any.whl", hash = "sha256:050b4e5baadcd44d760cedbd2b8e639f2ff89bbc7a5730fcc662954303377aac"},
+    {file = "idna-3.8.tar.gz", hash = "sha256:d838c2c0ed6fced7693d5e8ab8e734d5f8fda53a039c0164afb0b82e771e3603"},
 ]
 
 [[package]]
 name = "importlib-metadata"
-version = "8.2.0"
+version = "8.4.0"
 requires_python = ">=3.8"
 summary = "Read metadata from Python packages"
 groups = ["plot"]
@@ -602,8 +602,8 @@ dependencies = [
     "zipp>=0.5",
 ]
 files = [
-    {file = "importlib_metadata-8.2.0-py3-none-any.whl", hash = "sha256:11901fa0c2f97919b288679932bb64febaeacf289d18ac84dd68cb2e74213369"},
-    {file = "importlib_metadata-8.2.0.tar.gz", hash = "sha256:72e8d4399996132204f9a16dcc751af254a48f8d1b20b9ff0f98d4a8f901e73d"},
+    {file = "importlib_metadata-8.4.0-py3-none-any.whl", hash = "sha256:66f342cc6ac9818fc6ff340576acd24d65ba0b3efabb2b4ac08b598965a4a2f1"},
+    {file = "importlib_metadata-8.4.0.tar.gz", hash = "sha256:9a547d3bc3608b025f93d403fdd1aae741c24fbb8314df4b155675742ce303c5"},
 ]
 
 [[package]]
@@ -809,7 +809,7 @@ version = "0.0.0"
 requires_python = "<4.0.0,>=3.8.1"
 git = "https://github.com/sneakers-the-rat/linkml"
 ref = "nwb-linkml"
-revision = "0a6578bff4713688260f64b3076b197bd6decce9"
+revision = "0247c0b1e1a87366e0e047449e604881870c4e98"
 summary = "Linked Open Data Modeling Language"
 groups = ["default"]
 dependencies = [
@@ -822,7 +822,7 @@ dependencies = [
     "jsonasobj2==1.*,>=1.0.0,>=1.0.3",
     "jsonschema[format]>=4.0.0",
     "linkml-dataops",
-    "linkml-runtime==1.8.0",
+    "linkml-runtime<2.0.0,>=1.8.1",
     "openpyxl",
     "parse",
     "prefixcommons>=0.1.7",
@@ -860,7 +860,7 @@ files = [
 
 [[package]]
 name = "linkml-runtime"
-version = "1.8.0"
+version = "1.8.2"
 requires_python = "<4.0,>=3.8"
 summary = "Runtime environment for LinkML, the Linked open data modeling language"
 groups = ["default"]
@@ -880,8 +880,8 @@ dependencies = [
     "requests",
 ]
 files = [
-    {file = "linkml_runtime-1.8.0-py3-none-any.whl", hash = "sha256:e99a809eda52640633f07a9e8b391d1a9da863eb68a475dfd74a79335b909931"},
-    {file = "linkml_runtime-1.8.0.tar.gz", hash = "sha256:436381a7bf791e9af4ef0a5adcac86762d451b77670fbdb3ba083d2c177fb5f2"},
+    {file = "linkml_runtime-1.8.2-py3-none-any.whl", hash = "sha256:a66d7b5b82cb57b2d6c603c75ca22db4bae0409e0fb2b9e7835f921a23716096"},
+    {file = "linkml_runtime-1.8.2.tar.gz", hash = "sha256:f5067aeeb96c8d3ca1761b55b82d927af88d810459d533fb1f7876a90224b130"},
 ]
 
 [[package]]
@@ -984,42 +984,45 @@ files = [
 
 [[package]]
 name = "numpy"
-version = "2.0.1"
-requires_python = ">=3.9"
+version = "2.1.0"
+requires_python = ">=3.10"
 summary = "Fundamental package for array computing in Python"
 groups = ["default"]
 files = [
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 ]
 
 [[package]]
@@ -1349,13 +1352,13 @@ files = [
 
 [[package]]
 name = "pyparsing"
-version = "3.1.2"
+version = "3.1.4"
 requires_python = ">=3.6.8"
 summary = "pyparsing module - Classes and methods to define and execute parsing grammars"
 groups = ["default"]
 files = [
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 [[package]]
@@ -1679,7 +1682,7 @@ files = [
 
 [[package]]
 name = "rich"
-version = "13.7.1"
+version = "13.8.0"
 requires_python = ">=3.7.0"
 summary = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 groups = ["default"]
@@ -1689,8 +1692,8 @@ dependencies = [
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 ]
 files = [
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 ]
 
 [[package]]
@@ -2161,11 +2164,11 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.20.0"
+version = "3.20.1"
 requires_python = ">=3.8"
 summary = "Backport of pathlib-compatible object wrapper for zip files"
 groups = ["plot"]
 files = [
-    {file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"},
-    {file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"},
+    {file = "zipp-3.20.1-py3-none-any.whl", hash = "sha256:9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064"},
+    {file = "zipp-3.20.1.tar.gz", hash = "sha256:c22b14cc4763c5a5b04134207736c107db42e9d3ef2d9779d465f5f1bcba572b"},
 ]
diff --git a/nwb_linkml/pyproject.toml b/nwb_linkml/pyproject.toml
index c7611e2..41cf80a 100644
--- a/nwb_linkml/pyproject.toml
+++ b/nwb_linkml/pyproject.toml
@@ -16,8 +16,7 @@ dependencies = [
     "rich>=13.5.2",
     #"linkml>=1.7.10",
     "linkml @ git+https://github.com/sneakers-the-rat/linkml@nwb-linkml",
-    # until recursive imports gets released
-    "linkml-runtime @ git+https://github.com/linkml/linkml-runtime@main",
+    "linkml-runtime>=1.8.2",
     "pydantic>=2.3.0",
     "h5py>=3.9.0",
     "pydantic-settings>=2.0.3",
diff --git a/pdm.lock b/pdm.lock
index 0978fa5..540a4df 100644
--- a/pdm.lock
+++ b/pdm.lock
@@ -4,8 +4,11 @@
 [metadata]
 groups = ["default", "dev"]
 strategy = ["cross_platform", "inherit_metadata"]
-lock_version = "4.4.2"
-content_hash = "sha256:3113d2345a99f9287c2a8a545bcfeb5d34b99f44377f211dab8652e78d2f551d"
+lock_version = "4.5.0"
+content_hash = "sha256:a92f0895c7e29aac0736d0ef0a879a33ed0a3ce64b9584d195f88181fd2d16dc"
+
+[[metadata.targets]]
+requires_python = ">=3.10,<3.13"
 
 [[package]]
 name = "alabaster"
@@ -24,6 +27,9 @@ version = "0.7.0"
 requires_python = ">=3.8"
 summary = "Reusable constraint types to use with typing.Annotated"
 groups = ["dev"]
+dependencies = [
+    "typing-extensions>=4.0.0; python_version < \"3.9\"",
+]
 files = [
     {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
     {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
@@ -34,6 +40,9 @@ name = "antlr4-python3-runtime"
 version = "4.9.3"
 summary = "ANTLR 4.9.3 runtime for Python 3.7"
 groups = ["dev"]
+dependencies = [
+    "typing; python_version < \"3.5\"",
+]
 files = [
     {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"},
 ]
@@ -89,6 +98,7 @@ summary = "Annotate AST trees with source code positions"
 groups = ["dev"]
 dependencies = [
     "six>=1.12.0",
+    "typing; python_version < \"3.5\"",
 ]
 files = [
     {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
@@ -97,13 +107,16 @@ files = [
 
 [[package]]
 name = "attrs"
-version = "23.2.0"
+version = "24.2.0"
 requires_python = ">=3.7"
 summary = "Classes Without Boilerplate"
 groups = ["dev"]
+dependencies = [
+    "importlib-metadata; python_version < \"3.8\"",
+]
 files = [
-    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
-    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
+    {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
+    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
 ]
 
 [[package]]
@@ -114,6 +127,7 @@ summary = "Seamlessly integrate pydantic models in your Sphinx documentation."
 groups = ["dev"]
 dependencies = [
     "Sphinx>=4.0",
+    "importlib-metadata>1; python_version <= \"3.8\"",
     "pydantic-settings<3.0.0,>=2.0",
     "pydantic<3.0.0,>=2.0",
 ]
@@ -123,13 +137,16 @@ files = [
 
 [[package]]
 name = "babel"
-version = "2.15.0"
+version = "2.16.0"
 requires_python = ">=3.8"
 summary = "Internationalization utilities"
 groups = ["dev"]
+dependencies = [
+    "pytz>=2015.7; python_version < \"3.9\"",
+]
 files = [
-    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
-    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
+    {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"},
+    {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
 ]
 
 [[package]]
@@ -148,7 +165,7 @@ files = [
 
 [[package]]
 name = "black"
-version = "24.4.2"
+version = "24.8.0"
 requires_python = ">=3.8"
 summary = "The uncompromising code formatter."
 groups = ["dev"]
@@ -162,74 +179,36 @@ dependencies = [
     "typing-extensions>=4.0.1; python_version < \"3.11\"",
 ]
 files = [
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-    {file = "black-24.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eaea3008c281f1038edb473c1aa8ed8143a5535ff18f978a318f10302b254063"},
-    {file = "black-24.4.2-cp310-cp310-win_amd64.whl", hash = "sha256:7768a0dbf16a39aa5e9a3ded568bb545c8c2727396d063bbaf847df05b08cd96"},
-    {file = "black-24.4.2-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:257d724c2c9b1660f353b36c802ccece186a30accc7742c176d29c146df6e474"},
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-]
-
-[[package]]
-name = "blosc2"
-version = "2.7.0"
-requires_python = "<4,>=3.10"
-summary = "Python wrapper for the C-Blosc2 library"
-groups = ["dev"]
-dependencies = [
-    "msgpack",
-    "ndindex>=1.4",
-    "numexpr",
-    "numpy>=1.20.3",
-    "py-cpuinfo",
-]
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+    {file = "black-24.8.0.tar.gz", hash = "sha256:2500945420b6784c38b9ee885af039f5e7471ef284ab03fa35ecdde4688cd83f"},
 ]
 
 [[package]]
 name = "certifi"
-version = "2024.6.2"
+version = "2024.7.4"
 requires_python = ">=3.6"
 summary = "Python package for providing Mozilla's CA Bundle."
 groups = ["dev"]
 files = [
-    {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"},
-    {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"},
+    {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
+    {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
 ]
 
 [[package]]
 name = "cffi"
-version = "1.16.0"
+version = "1.17.0"
 requires_python = ">=3.8"
 summary = "Foreign Function Interface for Python calling C code."
 groups = ["dev"]
@@ -238,39 +217,42 @@ dependencies = [
     "pycparser",
 ]
 files = [
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 dependencies = [
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+    {file = "debugpy-1.8.5.zip", hash = "sha256:b2112cfeb34b4507399d298fe7023a16656fc553ed5246536060ca7bd0e668d0"},
 ]
 
 [[package]]
@@ -511,14 +462,14 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.1"
+version = "1.2.2"
 requires_python = ">=3.7"
 summary = "Backport of PEP 654 (exception groups)"
 groups = ["dev"]
 marker = "python_version < \"3.11\""
 files = [
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-    {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"},
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 ]
 
 [[package]]
@@ -548,25 +499,17 @@ version = "1.5.1"
 requires_python = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4"
 summary = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers"
 groups = ["dev"]
+dependencies = [
+    "cached-property>=1.3.0; python_version < \"3.8\"",
+]
 files = [
     {file = "fqdn-1.5.1-py3-none-any.whl", hash = "sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014"},
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 ]
 
-[[package]]
-name = "fsspec"
-version = "2024.6.1"
-requires_python = ">=3.8"
-summary = "File-system specification"
-groups = ["dev"]
-files = [
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-]
-
 [[package]]
 name = "furo"
-version = "2024.5.6"
+version = "2024.8.6"
 requires_python = ">=3.8"
 summary = "A clean customisable Sphinx documentation theme."
 groups = ["dev"]
@@ -574,11 +517,11 @@ dependencies = [
     "beautifulsoup4",
     "pygments>=2.7",
     "sphinx-basic-ng>=1.0.0.beta2",
-    "sphinx<8.0,>=6.0",
+    "sphinx<9.0,>=6.0",
 ]
 files = [
-    {file = "furo-2024.5.6-py3-none-any.whl", hash = "sha256:490a00d08c0a37ecc90de03ae9227e8eb5d6f7f750edf9807f398a2bdf2358de"},
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+    {file = "furo-2024.8.6-py3-none-any.whl", hash = "sha256:6cd97c58b47813d3619e63e9081169880fbe331f0ca883c871ff1f3f11814f5c"},
+    {file = "furo-2024.8.6.tar.gz", hash = "sha256:b63e4cee8abfc3136d3bc03a3d45a76a850bada4d6374d24c1716b0e01394a01"},
 ]
 
 [[package]]
@@ -636,6 +579,9 @@ version = "0.14.0"
 requires_python = ">=3.7"
 summary = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
 groups = ["dev"]
+dependencies = [
+    "typing-extensions; python_version < \"3.8\"",
+]
 files = [
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@@ -679,13 +625,13 @@ files = [
 
 [[package]]
 name = "idna"
-version = "3.7"
-requires_python = ">=3.5"
+version = "3.8"
+requires_python = ">=3.6"
 summary = "Internationalized Domain Names in Applications (IDNA)"
 groups = ["dev"]
 files = [
-    {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"},
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+    {file = "idna-3.8-py3-none-any.whl", hash = "sha256:050b4e5baadcd44d760cedbd2b8e639f2ff89bbc7a5730fcc662954303377aac"},
+    {file = "idna-3.8.tar.gz", hash = "sha256:d838c2c0ed6fced7693d5e8ab8e734d5f8fda53a039c0164afb0b82e771e3603"},
 ]
 
 [[package]]
@@ -701,16 +647,17 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "8.0.0"
+version = "8.4.0"
 requires_python = ">=3.8"
 summary = "Read metadata from Python packages"
 groups = ["dev"]
 dependencies = [
+    "typing-extensions>=3.6.4; python_version < \"3.8\"",
     "zipp>=0.5",
 ]
 files = [
-    {file = "importlib_metadata-8.0.0-py3-none-any.whl", hash = "sha256:15584cf2b1bf449d98ff8a6ff1abef57bf20f3ac6454f431736cd3e660921b2f"},
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 ]
 
 [[package]]
@@ -776,20 +723,20 @@ files = [
 
 [[package]]
 name = "ipywidgets"
-version = "8.1.3"
+version = "8.1.5"
 requires_python = ">=3.7"
 summary = "Jupyter interactive widgets"
 groups = ["dev"]
 dependencies = [
     "comm>=0.1.3",
     "ipython>=6.1.0",
-    "jupyterlab-widgets~=3.0.11",
+    "jupyterlab-widgets~=3.0.12",
     "traitlets>=4.3.1",
-    "widgetsnbextension~=4.0.11",
+    "widgetsnbextension~=4.0.12",
 ]
 files = [
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+    {file = "ipywidgets-8.1.5.tar.gz", hash = "sha256:870e43b1a35656a80c18c9503bbf2d16802db1cb487eec6fab27d683381dde17"},
 ]
 
 [[package]]
@@ -926,19 +873,21 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.22.0"
+version = "4.23.0"
 requires_python = ">=3.8"
 summary = "An implementation of JSON Schema validation for Python"
 groups = ["dev"]
 dependencies = [
     "attrs>=22.2.0",
+    "importlib-resources>=1.4.0; python_version < \"3.9\"",
     "jsonschema-specifications>=2023.03.6",
+    "pkgutil-resolve-name>=1.3.10; python_version < \"3.9\"",
     "referencing>=0.28.4",
     "rpds-py>=0.7.1",
 ]
 files = [
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+    {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"},
+    {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
 ]
 
 [[package]]
@@ -948,6 +897,7 @@ requires_python = ">=3.8"
 summary = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 groups = ["dev"]
 dependencies = [
+    "importlib-resources>=1.4.0; python_version < \"3.9\"",
     "referencing>=0.31.0",
 ]
 files = [
@@ -957,7 +907,7 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.22.0"
+version = "4.23.0"
 extras = ["format"]
 requires_python = ">=3.8"
 summary = "An implementation of JSON Schema validation for Python"
@@ -967,15 +917,15 @@ dependencies = [
     "idna",
     "isoduration",
     "jsonpointer>1.13",
-    "jsonschema==4.22.0",
+    "jsonschema==4.23.0",
     "rfc3339-validator",
     "rfc3987",
     "uri-template",
     "webcolors>=1.11",
 ]
 files = [
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+    {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"},
+    {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
 ]
 
 [[package]]
@@ -1006,6 +956,7 @@ requires_python = ">=3.8"
 summary = "Jupyter protocol implementation and client libraries"
 groups = ["dev"]
 dependencies = [
+    "importlib-metadata>=4.8.3; python_version < \"3.10\"",
     "jupyter-core!=5.0.*,>=4.12",
     "python-dateutil>=2.8.2",
     "pyzmq>=23.0",
@@ -1035,32 +986,35 @@ files = [
 
 [[package]]
 name = "jupyterlab-widgets"
-version = "3.0.11"
+version = "3.0.13"
 requires_python = ">=3.7"
 summary = "Jupyter interactive widgets for JupyterLab"
 groups = ["dev"]
 files = [
-    {file = "jupyterlab_widgets-3.0.11-py3-none-any.whl", hash = "sha256:78287fd86d20744ace330a61625024cf5521e1c012a352ddc0a3cdc2348becd0"},
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+    {file = "jupyterlab_widgets-3.0.13-py3-none-any.whl", hash = "sha256:e3cda2c233ce144192f1e29914ad522b2f4c40e77214b0cc97377ca3d323db54"},
+    {file = "jupyterlab_widgets-3.0.13.tar.gz", hash = "sha256:a2966d385328c1942b683a8cd96b89b8dd82c8b8f81dda902bb2bc06d46f5bed"},
 ]
 
 [[package]]
 name = "linkml"
-version = "1.7.10"
+version = "0.0.0"
 requires_python = "<4.0.0,>=3.8.1"
+git = "https://github.com/sneakers-the-rat/linkml"
+ref = "nwb-linkml"
+revision = "0247c0b1e1a87366e0e047449e604881870c4e98"
 summary = "Linked Open Data Modeling Language"
 groups = ["dev"]
 dependencies = [
-    "antlr4-python3-runtime<4.10,>=4.9.0",
+    "antlr4-python3-runtime<4.10,==4.*,>=4.9.0",
     "click>=7.0",
     "graphviz>=0.10.1",
     "hbreader",
     "isodate>=0.6.0",
     "jinja2>=3.1.0",
-    "jsonasobj2<2.0.0,>=1.0.3",
+    "jsonasobj2==1.*,>=1.0.0,>=1.0.3",
     "jsonschema[format]>=4.0.0",
     "linkml-dataops",
-    "linkml-runtime>=1.7.4",
+    "linkml-runtime<2.0.0,>=1.8.1",
     "openpyxl",
     "parse",
     "prefixcommons>=0.1.7",
@@ -1074,12 +1028,9 @@ dependencies = [
     "rdflib>=6.0.0",
     "requests>=2.22",
     "sqlalchemy>=1.4.31",
+    "typing-extensions>=4.4.0; python_version < \"3.9\"",
     "watchdog>=0.9.0",
 ]
-files = [
-    {file = "linkml-1.7.10-py3-none-any.whl", hash = "sha256:bf21cce814e9d1509489f1e6e15a7e86e4f11d949490d9a7a5c3f6b5b412ec62"},
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-]
 
 [[package]]
 name = "linkml-dataops"
@@ -1101,7 +1052,7 @@ files = [
 
 [[package]]
 name = "linkml-runtime"
-version = "1.7.7"
+version = "1.8.2"
 requires_python = "<4.0,>=3.8"
 summary = "Runtime environment for LinkML, the Linked open data modeling language"
 groups = ["dev"]
@@ -1121,19 +1072,8 @@ dependencies = [
     "requests",
 ]
 files = [
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-]
-
-[[package]]
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-version = "1.0.0"
-requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-summary = "File-based locks for Python on Linux and Windows"
-groups = ["dev"]
-files = [
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 ]
 
 [[package]]
@@ -1229,49 +1169,6 @@ files = [
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 ]
 
-[[package]]
-name = "msgpack"
-version = "1.0.8"
-requires_python = ">=3.8"
-summary = "MessagePack serializer"
-groups = ["dev"]
-files = [
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+groups = ["dev"]
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 groups = ["dev"]
 dependencies = [
-    "blosc2>=2.2.7",
-    "dask>=2023.9.2",
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+[[package]]
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+editable = true
+path = "./nwb_models"
+summary = "Pydantic/LinkML models for Neurodata Without Borders"
+groups = ["dev"]
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+    "pandas>=2.2.2",
+    "pydantic>=2.3.0",
+]
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 [[package]]
 name = "nwb-schema-language"
 version = "0.1.3"
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+groups = ["dev"]
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 [[package]]
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 version = "1.20.2"
@@ -1571,21 +1486,6 @@ files = [
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-requires_python = ">=3.9"
-summary = "Appendable key-value storage"
-groups = ["dev"]
-dependencies = [
-    "locket",
-    "toolz",
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 [[package]]
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 version = "0.12.1"
@@ -1662,7 +1562,7 @@ files = [
 
 [[package]]
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-version = "0.2.4"
+version = "0.2.5"
 requires_python = "<4.0,>=3.8"
 summary = "A python library for retrieving semantic prefix maps"
 groups = ["dev"]
@@ -1671,8 +1571,8 @@ dependencies = [
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 ]
 
 [[package]]
@@ -1719,22 +1619,12 @@ files = [
 
 [[package]]
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 summary = "Safely evaluate AST nodes without side effects"
 groups = ["dev"]
 files = [
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 [[package]]
@@ -1751,23 +1641,24 @@ files = [
 
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 requires_python = ">=3.8"
 summary = "Data validation using Python type hints"
 groups = ["dev"]
 dependencies = [
     "annotated-types>=0.4.0",
-    "pydantic-core==2.20.0",
+    "pydantic-core==2.20.1",
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 files = [
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 [[package]]
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-version = "2.20.0"
+version = "2.20.1"
 requires_python = ">=3.8"
 summary = "Core functionality for Pydantic validation and serialization"
 groups = ["dev"]
@@ -1775,64 +1666,56 @@ dependencies = [
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 [[package]]
@@ -2705,16 +2584,17 @@ files = [
 
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 requires_python = ">=3.8"
 summary = "The little ASGI library that shines."
 groups = ["dev"]
 dependencies = [
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 groups = ["dev"]
@@ -2781,8 +2650,8 @@ dependencies = [
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 summary = "Measures the displayed width of unicode strings in a terminal"
 groups = ["dev"]
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+    {file = "websockets-13.0.tar.gz", hash = "sha256:b7bf950234a482b7461afdb2ec99eee3548ec4d53f418c7990bb79c620476602"},
 ]
 
 [[package]]
 name = "wheel"
-version = "0.43.0"
+version = "0.44.0"
 requires_python = ">=3.8"
 summary = "A built-package format for Python"
 groups = ["dev"]
 files = [
-    {file = "wheel-0.43.0-py3-none-any.whl", hash = "sha256:55c570405f142630c6b9f72fe09d9b67cf1477fcf543ae5b8dcb1f5b7377da81"},
-    {file = "wheel-0.43.0.tar.gz", hash = "sha256:465ef92c69fa5c5da2d1cf8ac40559a8c940886afcef87dcf14b9470862f1d85"},
+    {file = "wheel-0.44.0-py3-none-any.whl", hash = "sha256:2376a90c98cc337d18623527a97c31797bd02bad0033d41547043a1cbfbe448f"},
+    {file = "wheel-0.44.0.tar.gz", hash = "sha256:a29c3f2817e95ab89aa4660681ad547c0e9547f20e75b0562fe7723c9a2a9d49"},
 ]
 
 [[package]]
 name = "widgetsnbextension"
-version = "4.0.11"
+version = "4.0.13"
 requires_python = ">=3.7"
 summary = "Jupyter interactive widgets for Jupyter Notebook"
 groups = ["dev"]
 files = [
-    {file = "widgetsnbextension-4.0.11-py3-none-any.whl", hash = "sha256:55d4d6949d100e0d08b94948a42efc3ed6dfdc0e9468b2c4b128c9a2ce3a7a36"},
-    {file = "widgetsnbextension-4.0.11.tar.gz", hash = "sha256:8b22a8f1910bfd188e596fe7fc05dcbd87e810c8a4ba010bdb3da86637398474"},
+    {file = "widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71"},
+    {file = "widgetsnbextension-4.0.13.tar.gz", hash = "sha256:ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6"},
 ]
 
 [[package]]
@@ -3099,11 +2961,11 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.19.2"
+version = "3.20.1"
 requires_python = ">=3.8"
 summary = "Backport of pathlib-compatible object wrapper for zip files"
 groups = ["dev"]
 files = [
-    {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
-    {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
+    {file = "zipp-3.20.1-py3-none-any.whl", hash = "sha256:9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064"},
+    {file = "zipp-3.20.1.tar.gz", hash = "sha256:c22b14cc4763c5a5b04134207736c107db42e9d3ef2d9779d465f5f1bcba572b"},
 ]
diff --git a/pyproject.toml b/pyproject.toml
index 99b5e1f..f744e6f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,12 +7,15 @@ requires-python = "<3.13,>=3.10"
 dev = [
     '-e nwb-linkml @ file:///${PROJECT_ROOT}/nwb_linkml',
     '-e nwb-schema-language @ file:///${PROJECT_ROOT}/nwb_schema_language',
-    '-e nwb-models @ file:///${PROJECT_ROOT/nwb_models',
+    '-e nwb-models @ file:///${PROJECT_ROOT}/nwb_models',
     '-e docs @ file:///${PROJECT_ROOT}/docs',
     "ruff>=0.5.0",
     "black>=24.4.2",
 ]
 
+[tool.pdm.scripts]
+build-models = "python scripts/generate_core.py"
+
 [tool.codespell]
 # Ref: https://github.com/codespell-project/codespell#using-a-config-file
 skip = '.git*,*.lock,*.css,./nwb_models/src/nwb_models/models,./nwb_models/src/nwb_models/schema'
diff --git a/scripts/generate_core.py b/scripts/generate_core.py
index 1e03897..221aeaf 100644
--- a/scripts/generate_core.py
+++ b/scripts/generate_core.py
@@ -166,29 +166,17 @@ def generate_versions(
                     pydantic_task = None
 
         if not dry_run:
-            if hdmf_only:
-                shutil.rmtree(yaml_path / "linkml" / "hdmf_common")
-                shutil.rmtree(yaml_path / "linkml" / "hdmf_experimental")
-                shutil.rmtree(pydantic_path / "pydantic" / "hdmf_common")
-                shutil.rmtree(pydantic_path / "pydantic" / "hdmf_experimental")
-                shutil.move(tmp_dir / "linkml" / "hdmf_common", yaml_path / "linkml")
-                shutil.move(tmp_dir / "linkml" / "hdmf_experimental", yaml_path / "linkml")
-                shutil.move(tmp_dir / "pydantic" / "hdmf_common", pydantic_path / "pydantic")
-                shutil.move(tmp_dir / "pydantic" / "hdmf_experimental", pydantic_path / "pydantic")
-            else:
-                shutil.rmtree(yaml_path / "linkml")
-                shutil.rmtree(pydantic_path / "pydantic")
-                shutil.move(tmp_dir / "linkml", yaml_path)
-                shutil.move(tmp_dir / "pydantic", pydantic_path)
+            shutil.copytree(tmp_dir / "linkml", yaml_path, dirs_exist_ok=True)
+            shutil.copytree(tmp_dir / "pydantic", pydantic_path, dirs_exist_ok=True)
+            shutil.rmtree(tmp_dir / "linkml")
+            shutil.rmtree(tmp_dir / "pydantic")
 
             # import the most recent version of the schemaz we built
-            latest_version = sorted(
-                (pydantic_path / "pydantic" / "core").glob("v*"), key=os.path.getmtime
-            )[-1]
+            latest_version = sorted((pydantic_path / "core").glob("v*"), key=os.path.getmtime)[-1]
 
             # make inits to use the schema! we don't usually do this in the
             # provider class because we directly import the files there.
-            with open(pydantic_path / "pydantic" / "__init__.py", "w") as initfile:
+            with open(pydantic_path / "__init__.py", "w") as initfile:
                 initfile.write(" ")
 
             with open(pydantic_path / "__init__.py", "w") as initfile:
@@ -208,13 +196,23 @@ def parser() -> ArgumentParser:
         "--yaml",
         help="directory to export linkML schema to",
         type=Path,
-        default=Path(__file__).parent.parent / "nwb_models" / "src" / "nwb_models" / "schema",
+        default=Path(__file__).parent.parent
+        / "nwb_models"
+        / "src"
+        / "nwb_models"
+        / "schema"
+        / "linkml",
     )
     parser.add_argument(
         "--pydantic",
         help="directory to export pydantic models",
         type=Path,
-        default=Path(__file__).parent.parent / "nwb_models" / "src" / "nwb_models" / "models",
+        default=Path(__file__).parent.parent
+        / "nwb_models"
+        / "src"
+        / "nwb_models"
+        / "models"
+        / "pydantic",
     )
     parser.add_argument("--hdmf", help="Only generate the HDMF namespaces", action="store_true")
     parser.add_argument(