diff --git a/Makefile b/Makefile
index 8cb3945..4412ef8 100644
--- a/Makefile
+++ b/Makefile
@@ -193,7 +193,7 @@ $(PYMODEL):
 	mkdir -p $@
 
 $(PYDANTIC): $(SOURCE_SCHEMA_PATH)
-	$(RUN) gen-pydantic --pydantic-version 2 $< > $@.tmp && mv $@.tmp $@
+	$(RUN) linkml generate pydantic $< > $@.tmp && mv $@.tmp $@
 
 $(DOCDIR):
 	mkdir -p $@
diff --git a/poetry.lock b/poetry.lock
index 458be53..282dab5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -42,22 +42,22 @@ test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock
 
 [[package]]
 name = "attrs"
-version = "23.2.0"
+version = "24.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 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.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[tests]", "pre-commit"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
-tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
-tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
+benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "beautifulsoup4"
@@ -82,13 +82,13 @@ lxml = ["lxml"]
 
 [[package]]
 name = "bioregistry"
-version = "0.11.10"
+version = "0.11.21"
 description = "Integrated registry of biological databases and nomenclatures"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "bioregistry-0.11.10-py3-none-any.whl", hash = "sha256:0af02ca586024f3791364dae2c04e03156e01df9b6d7eb7f3cb6be5682a40a2d"},
-    {file = "bioregistry-0.11.10.tar.gz", hash = "sha256:d3e155ba38d88f5e4a84a2d337c33109f3434f6b2e64a285eba14817ed5c4492"},
+    {file = "bioregistry-0.11.21-py3-none-any.whl", hash = "sha256:4e69bd9c68697eb9b45c9bd1827c52ecd0a324a581bc273207ff5f6f6a025aed"},
+    {file = "bioregistry-0.11.21.tar.gz", hash = "sha256:2ef97406581612be2a8a07ea99e846f2f9eea5eb773af81107068f1457f77655"},
 ]
 
 [package.dependencies]
@@ -103,33 +103,33 @@ tqdm = "*"
 [package.extras]
 align = ["beautifulsoup4", "class-resolver", "defusedxml", "fairsharing-client (>=0.1.0)", "pandas", "pyyaml", "tabulate"]
 charts = ["jinja2", "matplotlib", "matplotlib-venn", "pandas", "seaborn"]
-docs = ["autodoc-pydantic", "sphinx (<7.3)", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
+docs = ["autodoc-pydantic", "sphinx (>=8)", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme (>=3.0)"]
 export = ["ndex2", "pyyaml", "rdflib", "rdflib-jsonld"]
 gha = ["more-itertools"]
 health = ["click-default-group", "jinja2", "pandas", "pyyaml", "tabulate"]
 tests = ["coverage", "httpx", "more-itertools", "pytest"]
-web = ["bootstrap-flask (<=2.0.0)", "curies[fastapi]", "fastapi", "flask (<2.2.4)", "markdown", "pyyaml", "rdflib", "rdflib-endpoint", "rdflib-jsonld", "uvicorn", "werkzeug (<2.3.0)"]
+web = ["a2wsgi", "bootstrap-flask (<=2.0.0)", "curies[fastapi]", "fastapi", "flask (<2.2.4)", "markdown", "pyyaml", "rdflib", "rdflib-endpoint", "rdflib-jsonld", "uvicorn", "werkzeug (<2.3.0)"]
 
 [[package]]
 name = "cachetools"
-version = "5.3.3"
+version = "5.5.0"
 description = "Extensible memoizing collections and decorators"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "cachetools-5.3.3-py3-none-any.whl", hash = "sha256:0abad1021d3f8325b2fc1d2e9c8b9c9d57b04c3932657a72465447332c24d945"},
-    {file = "cachetools-5.3.3.tar.gz", hash = "sha256:ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105"},
+    {file = "cachetools-5.5.0-py3-none-any.whl", hash = "sha256:02134e8439cdc2ffb62023ce1debca2944c3f289d66bb17ead3ab3dede74b292"},
+    {file = "cachetools-5.5.0.tar.gz", hash = "sha256:2cc24fb4cbe39633fb7badd9db9ca6295d766d9c2995f245725a46715d050f2a"},
 ]
 
 [[package]]
 name = "certifi"
-version = "2024.6.2"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 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-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
 [[package]]
@@ -158,101 +158,116 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
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-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9063e24fdb1e498ab71cb7419e24622516c4a04476b17a2dab57e8baa30d6e03"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6897af51655e3691ff853668779c7bad41579facacf5fd7253b0133308cf000d"},
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+    {file = "charset_normalizer-3.4.0.tar.gz", hash = "sha256:223217c3d4f82c3ac5e29032b3f1c2eb0fb591b72161f86d93f5719079dae93e"},
 ]
 
 [[package]]
@@ -282,27 +297,26 @@ files = [
 
 [[package]]
 name = "curies"
-version = "0.7.9"
-description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
+version = "0.9.0"
+description = "Idiomatic conversion between URIs and compact URIs (CURIEs)"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "curies-0.7.9-py3-none-any.whl", hash = "sha256:e4c5beb91642376953c94db0ee2fb5d2b011c3b16749516436114ba61442f260"},
-    {file = "curies-0.7.9.tar.gz", hash = "sha256:3b63c5fea7b0e967629a3a384b1a8c59b56c503487c1dcbacddeab59e25db4d8"},
+    {file = "curies-0.9.0-py3-none-any.whl", hash = "sha256:a4b8d9fff89288190c658ac5941f3099196205cd805cc98fceba1ac5a96daa50"},
+    {file = "curies-0.9.0.tar.gz", hash = "sha256:f630fa05b31aff144da66ace18a2c25b30adfa859df36e5fbd8b633b43c80d3a"},
 ]
 
 [package.dependencies]
-pydantic = "*"
+pydantic = ">=2.0"
 pytrie = "*"
-requests = "*"
 
 [package.extras]
-docs = ["sphinx", "sphinx-automodapi", "sphinx-rtd-theme"]
+docs = ["sphinx (>=8)", "sphinx-automodapi", "sphinx-rtd-theme (>=3.0)"]
 fastapi = ["defusedxml", "fastapi", "httpx", "python-multipart", "uvicorn"]
 flask = ["defusedxml", "flask"]
 pandas = ["pandas"]
 rdflib = ["rdflib"]
-tests = ["coverage", "pytest"]
+tests = ["coverage", "pytest", "requests"]
 
 [[package]]
 name = "daff"
@@ -343,24 +357,24 @@ files = [
 
 [[package]]
 name = "et-xmlfile"
-version = "1.1.0"
+version = "2.0.0"
 description = "An implementation of lxml.xmlfile for the standard library"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "et_xmlfile-1.1.0-py3-none-any.whl", hash = "sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada"},
-    {file = "et_xmlfile-1.1.0.tar.gz", hash = "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c"},
+    {file = "et_xmlfile-2.0.0-py3-none-any.whl", hash = "sha256:7a91720bc756843502c3b7504c77b8fe44217c85c537d85037f0f536151b2caa"},
+    {file = "et_xmlfile-2.0.0.tar.gz", hash = "sha256:dab3f4764309081ce75662649be815c4c9081e88f0837825f90fd28317d4da54"},
 ]
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.1"
+version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.2.1-py3-none-any.whl", hash = "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad"},
-    {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"},
+    {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"},
+    {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"},
 ]
 
 [package.extras]
@@ -410,36 +424,40 @@ beautifulsoup4 = "*"
 
 [[package]]
 name = "google-api-core"
-version = "2.19.1"
+version = "2.22.0"
 description = "Google API client core library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-api-core-2.19.1.tar.gz", hash = "sha256:f4695f1e3650b316a795108a76a1c416e6afb036199d1c1f1f110916df479ffd"},
-    {file = "google_api_core-2.19.1-py3-none-any.whl", hash = "sha256:f12a9b8309b5e21d92483bbd47ce2c445861ec7d269ef6784ecc0ea8c1fa6125"},
+    {file = "google_api_core-2.22.0-py3-none-any.whl", hash = "sha256:a6652b6bd51303902494998626653671703c420f6f4c88cfd3f50ed723e9d021"},
+    {file = "google_api_core-2.22.0.tar.gz", hash = "sha256:26f8d76b96477db42b55fd02a33aae4a42ec8b86b98b94969b7333a2c828bf35"},
 ]
 
 [package.dependencies]
 google-auth = ">=2.14.1,<3.0.dev0"
 googleapis-common-protos = ">=1.56.2,<2.0.dev0"
-proto-plus = ">=1.22.3,<2.0.0dev"
+proto-plus = [
+    {version = ">=1.25.0,<2.0.0dev", markers = "python_version >= \"3.13\""},
+    {version = ">=1.22.3,<2.0.0dev", markers = "python_version < \"3.13\""},
+]
 protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<6.0.0.dev0"
 requests = ">=2.18.0,<3.0.0.dev0"
 
 [package.extras]
+async-rest = ["google-auth[aiohttp] (>=2.35.0,<3.0.dev0)"]
 grpc = ["grpcio (>=1.33.2,<2.0dev)", "grpcio (>=1.49.1,<2.0dev)", "grpcio-status (>=1.33.2,<2.0.dev0)", "grpcio-status (>=1.49.1,<2.0.dev0)"]
 grpcgcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
 grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
 
 [[package]]
 name = "google-api-python-client"
-version = "2.134.0"
+version = "2.151.0"
 description = "Google API Client Library for Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-api-python-client-2.134.0.tar.gz", hash = "sha256:4a8f0bea651a212997cc83c0f271fc86f80ef93d1cee9d84de7dfaeef2a858b6"},
-    {file = "google_api_python_client-2.134.0-py2.py3-none-any.whl", hash = "sha256:ba05d60f6239990b7994f6328f17bb154c602d31860fb553016dc9f8ce886945"},
+    {file = "google_api_python_client-2.151.0-py2.py3-none-any.whl", hash = "sha256:4427b2f47cd88b0355d540c2c52215f68c337f3bc9d6aae1ceeae4525977504c"},
+    {file = "google_api_python_client-2.151.0.tar.gz", hash = "sha256:a9d26d630810ed4631aea21d1de3e42072f98240aaf184a8a1a874a371115034"},
 ]
 
 [package.dependencies]
@@ -451,13 +469,13 @@ uritemplate = ">=3.0.1,<5"
 
 [[package]]
 name = "google-auth"
-version = "2.30.0"
+version = "2.35.0"
 description = "Google Authentication Library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-auth-2.30.0.tar.gz", hash = "sha256:ab630a1320f6720909ad76a7dbdb6841cdf5c66b328d690027e4867bdfb16688"},
-    {file = "google_auth-2.30.0-py2.py3-none-any.whl", hash = "sha256:8df7da660f62757388b8a7f249df13549b3373f24388cb5d2f1dd91cc18180b5"},
+    {file = "google_auth-2.35.0-py2.py3-none-any.whl", hash = "sha256:25df55f327ef021de8be50bad0dfd4a916ad0de96da86cd05661c9297723ad3f"},
+    {file = "google_auth-2.35.0.tar.gz", hash = "sha256:f4c64ed4e01e8e8b646ef34c018f8bf3338df0c8e37d8b3bba40e7f574a3278a"},
 ]
 
 [package.dependencies]
@@ -467,7 +485,7 @@ rsa = ">=3.1.4,<5"
 
 [package.extras]
 aiohttp = ["aiohttp (>=3.6.2,<4.0.0.dev0)", "requests (>=2.20.0,<3.0.0.dev0)"]
-enterprise-cert = ["cryptography (==36.0.2)", "pyopenssl (==22.0.0)"]
+enterprise-cert = ["cryptography", "pyopenssl"]
 pyopenssl = ["cryptography (>=38.0.3)", "pyopenssl (>=20.0.0)"]
 reauth = ["pyu2f (>=0.1.5)"]
 requests = ["requests (>=2.20.0,<3.0.0.dev0)"]
@@ -489,13 +507,13 @@ httplib2 = ">=0.19.0"
 
 [[package]]
 name = "google-auth-oauthlib"
-version = "1.2.0"
+version = "1.2.1"
 description = "Google Authentication Library"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "google-auth-oauthlib-1.2.0.tar.gz", hash = "sha256:292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8"},
-    {file = "google_auth_oauthlib-1.2.0-py2.py3-none-any.whl", hash = "sha256:297c1ce4cb13a99b5834c74a1fe03252e1e499716718b190f56bcb9c4abc4faf"},
+    {file = "google_auth_oauthlib-1.2.1-py2.py3-none-any.whl", hash = "sha256:2d58a27262d55aa1b87678c3ba7142a080098cbc2024f903c62355deb235d91f"},
+    {file = "google_auth_oauthlib-1.2.1.tar.gz", hash = "sha256:afd0cad092a2eaa53cd8e8298557d6de1034c6cb4a740500b5357b648af97263"},
 ]
 
 [package.dependencies]
@@ -507,13 +525,13 @@ tool = ["click (>=6.0.0)"]
 
 [[package]]
 name = "googleapis-common-protos"
-version = "1.63.2"
+version = "1.65.0"
 description = "Common protobufs used in Google APIs"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "googleapis-common-protos-1.63.2.tar.gz", hash = "sha256:27c5abdffc4911f28101e635de1533fb4cfd2c37fbaa9174587c799fac90aa87"},
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 [package.dependencies]
@@ -540,69 +558,84 @@ test = ["coverage", "pytest (>=7,<8.1)", "pytest-cov", "pytest-mock (>=3)"]
 
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+    {file = "greenlet-3.1.1.tar.gz", hash = "sha256:4ce3ac6cdb6adf7946475d7ef31777c26d94bccc377e070a7986bd2d5c515467"},
 ]
 
 [package.extras]
@@ -611,13 +644,13 @@ test = ["objgraph", "psutil"]
 
 [[package]]
 name = "gspread"
-version = "6.1.2"
+version = "6.1.4"
 description = "Google Spreadsheets Python API"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "gspread-6.1.2-py3-none-any.whl", hash = "sha256:345996fbb74051ee574e3d330a375ac625774f289459f73cb1f8b6fb3cf4cac5"},
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+    {file = "gspread-6.1.4-py3-none-any.whl", hash = "sha256:c34781c426031a243ad154952b16f21ac56a5af90687885fbee3d1fba5280dcd"},
+    {file = "gspread-6.1.4.tar.gz", hash = "sha256:b8eec27de7cadb338bb1b9f14a9be168372dee8965c0da32121816b5050ac1de"},
 ]
 
 [package.dependencies]
@@ -665,15 +698,18 @@ pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0
 
 [[package]]
 name = "idna"
-version = "3.7"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 files = [
-    {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"},
-    {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
+    {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"},
+    {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
 ]
 
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "ijson"
 version = "3.3.0"
@@ -779,22 +815,26 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "8.0.0"
+version = "8.5.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-8.0.0-py3-none-any.whl", hash = "sha256:15584cf2b1bf449d98ff8a6ff1abef57bf20f3ac6454f431736cd3e660921b2f"},
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+    {file = "importlib_metadata-8.5.0-py3-none-any.whl", hash = "sha256:45e54197d28b7a7f1559e60b95e7c567032b602131fbd588f1497f47880aa68b"},
+    {file = "importlib_metadata-8.5.0.tar.gz", hash = "sha256:71522656f0abace1d072b9e5481a48f07c138e00f079c38c8f883823f9c26bd7"},
 ]
 
 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
-test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
@@ -809,18 +849,15 @@ files = [
 
 [[package]]
 name = "isodate"
-version = "0.6.1"
+version = "0.7.2"
 description = "An ISO 8601 date/time/duration parser and formatter"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
 files = [
-    {file = "isodate-0.6.1-py2.py3-none-any.whl", hash = "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96"},
-    {file = "isodate-0.6.1.tar.gz", hash = "sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9"},
+    {file = "isodate-0.7.2-py3-none-any.whl", hash = "sha256:28009937d8031054830160fce6d409ed342816b543597cece116d966c6d99e15"},
+    {file = "isodate-0.7.2.tar.gz", hash = "sha256:4cd1aa0f43ca76f4a6c6c0292a85f40b35ec2e43e315b59f06e6d32171a953e6"},
 ]
 
-[package.dependencies]
-six = "*"
-
 [[package]]
 name = "isoduration"
 version = "20.11.0"
@@ -914,6 +951,7 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
     {file = "jsonpatch-1.33-py2.py3-none-any.whl", hash = "sha256:0ae28c0cd062bbd8b8ecc26d7d164fbbea9652a1a3693f3b956c1eae5145dade"},
+    {file = "jsonpatch-1.33.tar.gz", hash = "sha256:9fcd4009c41e6d12348b4a0ff2563ba56a2923a7dfee731d004e212e1ee5030c"},
 ]
 
 [package.dependencies]
@@ -921,13 +959,12 @@ jsonpointer = ">=1.9"
 
 [[package]]
 name = "jsonpath-ng"
-version = "1.6.1"
+version = "1.7.0"
 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-1.6.1.tar.gz", hash = "sha256:086c37ba4917304850bd837aeab806670224d3f038fe2833ff593a672ef0a5fa"},
-    {file = "jsonpath_ng-1.6.1-py3-none-any.whl", hash = "sha256:8f22cd8273d7772eea9aaa84d922e0841aa36fdb8a2c6b7f6c3791a16a9bc0be"},
+    {file = "jsonpath-ng-1.7.0.tar.gz", hash = "sha256:f6f5f7fd4e5ff79c785f1573b394043b39849fb2bb47bcead935d12b00beab3c"},
 ]
 
 [package.dependencies]
@@ -946,13 +983,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.22.0"
+version = "4.23.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.22.0-py3-none-any.whl", hash = "sha256:ff4cfd6b1367a40e7bc6411caec72effadd3db0bbe5017de188f2d6108335802"},
-    {file = "jsonschema-4.22.0.tar.gz", hash = "sha256:5b22d434a45935119af990552c862e5d6d564e8f6601206b305a61fdf661a2b7"},
+    {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"},
+    {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
 ]
 
 [package.dependencies]
@@ -971,17 +1008,17 @@ webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\"
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
-format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=24.6.0)"]
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.12.1"
+version = "2024.10.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "jsonschema_specifications-2023.12.1-py3-none-any.whl", hash = "sha256:87e4fdf3a94858b8a2ba2778d9ba57d8a9cafca7c7489c46ba0d30a8bc6a9c3c"},
-    {file = "jsonschema_specifications-2023.12.1.tar.gz", hash = "sha256:48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc"},
+    {file = "jsonschema_specifications-2024.10.1-py3-none-any.whl", hash = "sha256:a09a0680616357d9a0ecf05c12ad234479f549239d0f5b55f3deea67475da9bf"},
+    {file = "jsonschema_specifications-2024.10.1.tar.gz", hash = "sha256:0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272"},
 ]
 
 [package.dependencies]
@@ -989,13 +1026,13 @@ referencing = ">=0.31.0"
 
 [[package]]
 name = "linkml"
-version = "1.7.10"
+version = "1.8.5"
 description = "Linked Open Data Modeling Language"
 optional = false
 python-versions = "<4.0.0,>=3.8.1"
 files = [
-    {file = "linkml-1.7.10-py3-none-any.whl", hash = "sha256:bf21cce814e9d1509489f1e6e15a7e86e4f11d949490d9a7a5c3f6b5b412ec62"},
-    {file = "linkml-1.7.10.tar.gz", hash = "sha256:1c38601c3cd495e34490b8cf7277fd3674ec68dcbe9f5efcec2658093801ce91"},
+    {file = "linkml-1.8.5-py3-none-any.whl", hash = "sha256:5a45577a4bb380f3a128f45764545cb2da92dd3310a110de7dc5355796d5ac43"},
+    {file = "linkml-1.8.5.tar.gz", hash = "sha256:8f31834560ade4b7f1aebc973d22b31951d7061643d32bdcba258a650db9b140"},
 ]
 
 [package.dependencies]
@@ -1008,7 +1045,7 @@ jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = {version = ">=4.0.0", extras = ["format"]}
 linkml-dataops = "*"
-linkml-runtime = ">=1.7.4"
+linkml-runtime = ">=1.8.1,<2.0.0"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
@@ -1026,8 +1063,9 @@ watchdog = ">=0.9.0"
 
 [package.extras]
 black = ["black (>=24.0.0)"]
+numpydantic = ["numpydantic (>=1.6.1)"]
 shacl = ["pyshacl (>=0.25.0,<0.26.0)"]
-tests = ["black (>=24.0.0)", "pyshacl (>=0.25.0,<0.26.0)"]
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 [[package]]
 name = "linkml-dataops"
@@ -1049,13 +1087,13 @@ linkml-runtime = ">=1.1.6"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.7.7"
+version = "1.8.3"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
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 [package.dependencies]
@@ -1075,13 +1113,13 @@ requests = "*"
 
 [[package]]
 name = "markdown"
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+version = "3.7"
 description = "Python implementation of John Gruber's Markdown."
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
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 [package.dependencies]
@@ -1541,19 +1593,19 @@ files = [
 
 [[package]]
 name = "platformdirs"
-version = "4.2.2"
+version = "4.3.6"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
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-type = ["mypy (>=1.8)"]
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+type = ["mypy (>=1.11.2)"]
 
 [[package]]
 name = "pluggy"
@@ -1600,13 +1652,13 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.2.5"
+version = "0.2.6"
 description = "A python library for retrieving semantic prefix maps"
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 python-versions = "<4.0,>=3.8"
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 ]
 
 [package.dependencies]
@@ -1615,13 +1667,13 @@ pyyaml = ">=5.3.1"
 
 [[package]]
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+version = "1.25.0"
 description = "Beautiful, Pythonic protocol buffers."
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 python-versions = ">=3.7"
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 [package.dependencies]
@@ -1632,44 +1684,44 @@ testing = ["google-api-core (>=1.31.5)"]
 
 [[package]]
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 description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)"
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 python-versions = ">=3.8"
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 [[package]]
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 description = "A collection of ASN.1-based protocols modules"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -1677,18 +1729,18 @@ pyasn1 = ">=0.4.6,<0.7.0"
 
 [[package]]
 name = "pydantic"
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+version = "2.9.2"
 description = "Data validation using Python type hints"
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 [package.dependencies]
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 typing-extensions = [
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     {version = ">=4.6.1", markers = "python_version < \"3.13\""},
@@ -1696,103 +1748,104 @@ typing-extensions = [
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
+timezone = ["tzdata"]
 
 [[package]]
 name = "pydantic-core"
-version = "2.20.1"
+version = "2.23.4"
 description = "Core functionality for Pydantic validation and serialization"
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 python-versions = ">=3.8"
 files = [
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+    {file = "pystow-0.5.6.tar.gz", hash = "sha256:db567e82a5b7aea34cdcf4ae00ba822cd64a51ae2f465b1995599676e4cdbff2"},
 ]
 
 [package.dependencies]
@@ -1918,7 +1971,7 @@ tqdm = "*"
 
 [package.extras]
 aws = ["boto3"]
-docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
+docs = ["sphinx (<8.0)", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
 pandas = ["pandas"]
 rdf = ["rdflib"]
 tests = ["coverage", "pytest", "requests-file"]
@@ -1926,13 +1979,13 @@ xml = ["lxml"]
 
 [[package]]
 name = "pytest"
-version = "8.2.2"
+version = "8.3.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "pytest-8.3.3.tar.gz", hash = "sha256:70b98107bd648308a7952b06e6ca9a50bc660be218d53c257cc1fc94fda10181"},
 ]
 
 [package.dependencies]
@@ -1940,7 +1993,7 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
-pluggy = ">=1.5,<2.0"
+pluggy = ">=1.5,<2"
 tomli = {version = ">=1", markers = "python_version < \"3.11\""}
 
 [package.extras]
@@ -1980,6 +2033,7 @@ description = "A pure Python implementation of the trie data structure."
 optional = false
 python-versions = "*"
 files = [
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 ]
 
@@ -1988,62 +2042,75 @@ sortedcontainers = "*"
 
 [[package]]
 name = "pytz"
-version = "2024.1"
+version = "2024.2"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
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+    {file = "pytz-2024.2-py2.py3-none-any.whl", hash = "sha256:31c7c1817eb7fae7ca4b8c7ee50c72f93aa2dd863de768e1ef4245d426aa0725"},
+    {file = "pytz-2024.2.tar.gz", hash = "sha256:2aa355083c50a0f93fa581709deac0c9ad65cca8a9e9beac660adcbd493c798a"},
 ]
 
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 name = "pyyaml"
-version = "6.0.1"
+version = "6.0.2"
 description = "YAML parser and emitter for Python"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
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 [[package]]
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-lxml = ["lxml (>=4.3.0,<5.0.0)"]
-networkx = ["networkx (>=2.0.0,<3.0.0)"]
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+networkx = ["networkx (>=2,<4)"]
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 [[package]]
 name = "rdflib-jsonld"
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 [[package]]
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-version = "70.1.1"
+version = "75.3.0"
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 [[package]]
 name = "shexjsg"
@@ -2497,13 +2585,13 @@ files = [
 
 [[package]]
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+version = "2.6"
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 [[package]]
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 [package.dependencies]
@@ -2610,7 +2706,7 @@ aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
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 mssql = ["pyodbc"]
 mssql-pymssql = ["pymssql"]
 mssql-pyodbc = ["pyodbc"]
@@ -2645,13 +2741,13 @@ widechars = ["wcwidth"]
 
 [[package]]
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+version = "2.5.0"
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 [package.extras]
@@ -2659,24 +2755,24 @@ tests = ["pytest", "pytest-cov"]
 
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 [package.dependencies]
@@ -2690,13 +2786,13 @@ telegram = ["requests"]
 
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 [[package]]
@@ -2712,13 +2808,13 @@ files = [
 
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 description = "Provider of IANA time zone data"
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 python-versions = ">=2"
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 ]
 
 [[package]]
@@ -2748,13 +2844,13 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "2.2.2"
+version = "2.2.3"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -2765,43 +2861,41 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "watchdog"
-version = "4.0.1"
+version = "5.0.3"
 description = "Filesystem events monitoring"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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-    {file = "watchdog-4.0.1.tar.gz", hash = "sha256:eebaacf674fa25511e8867028d281e602ee6500045b57f43b08778082f7f8b44"},
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+    {file = "watchdog-5.0.3-pp39-pypy39_pp73-macosx_10_15_x86_64.whl", hash = "sha256:223160bb359281bb8e31c8f1068bf71a6b16a8ad3d9524ca6f523ac666bb6a1e"},
+    {file = "watchdog-5.0.3-pp39-pypy39_pp73-macosx_11_0_arm64.whl", hash = "sha256:560135542c91eaa74247a2e8430cf83c4342b29e8ad4f520ae14f0c8a19cfb5b"},
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+    {file = "watchdog-5.0.3-py3-none-manylinux2014_armv7l.whl", hash = "sha256:78864cc8f23dbee55be34cc1494632a7ba30263951b5b2e8fc8286b95845f82c"},
+    {file = "watchdog-5.0.3-py3-none-manylinux2014_i686.whl", hash = "sha256:1e9679245e3ea6498494b3028b90c7b25dbb2abe65c7d07423ecfc2d6218ff7c"},
+    {file = "watchdog-5.0.3-py3-none-manylinux2014_ppc64.whl", hash = "sha256:9413384f26b5d050b6978e6fcd0c1e7f0539be7a4f1a885061473c5deaa57221"},
+    {file = "watchdog-5.0.3-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:294b7a598974b8e2c6123d19ef15de9abcd282b0fbbdbc4d23dfa812959a9e05"},
+    {file = "watchdog-5.0.3-py3-none-manylinux2014_s390x.whl", hash = "sha256:26dd201857d702bdf9d78c273cafcab5871dd29343748524695cecffa44a8d97"},
+    {file = "watchdog-5.0.3-py3-none-manylinux2014_x86_64.whl", hash = "sha256:0f9332243355643d567697c3e3fa07330a1d1abf981611654a1f2bf2175612b7"},
+    {file = "watchdog-5.0.3-py3-none-win32.whl", hash = "sha256:c66f80ee5b602a9c7ab66e3c9f36026590a0902db3aea414d59a2f55188c1f49"},
+    {file = "watchdog-5.0.3-py3-none-win_amd64.whl", hash = "sha256:f00b4cf737f568be9665563347a910f8bdc76f88c2970121c86243c8cfdf90e9"},
+    {file = "watchdog-5.0.3-py3-none-win_ia64.whl", hash = "sha256:49f4d36cb315c25ea0d946e018c01bb028048023b9e103d3d3943f58e109dd45"},
+    {file = "watchdog-5.0.3.tar.gz", hash = "sha256:108f42a7f0345042a854d4d0ad0834b741d421330d5f575b81cb27b883500176"},
 ]
 
 [package.extras]
@@ -2809,13 +2903,13 @@ watchmedo = ["PyYAML (>=3.10)"]
 
 [[package]]
 name = "webcolors"
-version = "24.6.0"
+version = "24.8.0"
 description = "A library for working with the color formats defined by HTML and CSS."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "webcolors-24.6.0-py3-none-any.whl", hash = "sha256:8cf5bc7e28defd1d48b9e83d5fc30741328305a8195c29a8e668fa45586568a1"},
-    {file = "webcolors-24.6.0.tar.gz", hash = "sha256:1d160d1de46b3e81e58d0a280d0c78b467dc80f47294b91b1ad8029d2cedb55b"},
+    {file = "webcolors-24.8.0-py3-none-any.whl", hash = "sha256:fc4c3b59358ada164552084a8ebee637c221e4059267d0f8325b3b560f6c7f0a"},
+    {file = "webcolors-24.8.0.tar.gz", hash = "sha256:08b07af286a01bcd30d583a7acadf629583d1f79bfef27dd2c2c5c263817277d"},
 ]
 
 [package.extras]
@@ -2903,18 +2997,22 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.19.2"
+version = "3.20.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 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-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
+    {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
 ]
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [metadata]
 lock-version = "2.0"
diff --git a/src/gocam/datamodel/gocam.py b/src/gocam/datamodel/gocam.py
index 95cbadc..f6afc5e 100644
--- a/src/gocam/datamodel/gocam.py
+++ b/src/gocam/datamodel/gocam.py
@@ -1,34 +1,32 @@
 from __future__ import annotations 
+
+import re
+import sys
 from datetime import (
+    date,
     datetime,
-    date
+    time
 )
 from decimal import Decimal 
 from enum import Enum 
-import re
-import sys
 from typing import (
     Any,
+    ClassVar,
+    Dict,
     List,
     Literal,
-    Dict,
     Optional,
     Union
 )
-from pydantic.version import VERSION  as PYDANTIC_VERSION 
-if int(PYDANTIC_VERSION[0])>=2:
-    from pydantic import (
-        BaseModel,
-        ConfigDict,
-        Field,
-        field_validator
-    )
-else:
-    from pydantic import (
-        BaseModel,
-        Field,
-        validator
-    )
+
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator
+)
+
 
 metamodel_version = "None"
 version = "None"
@@ -46,6 +44,77 @@ class ConfiguredBaseModel(BaseModel):
     pass
 
 
+
+
+class LinkMLMeta(RootModel):
+    root: Dict[str, Any] = {}
+    model_config = ConfigDict(frozen=True)
+
+    def __getattr__(self, key:str):
+        return getattr(self.root, key)
+
+    def __getitem__(self, key:str):
+        return self.root[key]
+
+    def __setitem__(self, key:str, value):
+        self.root[key] = value
+
+    def __contains__(self, key:str) -> bool:
+        return key in self.root
+
+
+linkml_meta = LinkMLMeta({'default_prefix': 'gocam',
+     'default_range': 'string',
+     'description': 'GO CAM LinkML schema (experimental)\n'
+                    '\n'
+                    'The central class in this datamodel is a [Model](Model.md). A '
+                    'model consists of a set of\n'
+                    '[Activity](Activity.md) objects.',
+     'id': 'https://w3id.org/gocam',
+     'imports': ['linkml:types'],
+     'name': 'gocam',
+     'prefixes': {'BFO': {'prefix_prefix': 'BFO',
+                          'prefix_reference': 'http://purl.obolibrary.org/obo/BFO_'},
+                  'ECO': {'prefix_prefix': 'ECO',
+                          'prefix_reference': 'http://purl.obolibrary.org/obo/ECO_'},
+                  'GO': {'prefix_prefix': 'GO',
+                         'prefix_reference': 'http://purl.obolibrary.org/obo/GO_'},
+                  'NCBITaxon': {'prefix_prefix': 'NCBITaxon',
+                                'prefix_reference': 'http://purl.obolibrary.org/obo/NCBITaxon_'},
+                  'OBAN': {'prefix_prefix': 'OBAN',
+                           'prefix_reference': 'http://purl.org/oban/'},
+                  'PMID': {'prefix_prefix': 'PMID',
+                           'prefix_reference': 'http://identifiers.org/pmid/'},
+                  'RO': {'prefix_prefix': 'RO',
+                         'prefix_reference': 'http://purl.obolibrary.org/obo/RO_'},
+                  'UniProtKB': {'prefix_prefix': 'UniProtKB',
+                                'prefix_reference': 'http://identifiers.org/uniprot/'},
+                  'biolink': {'prefix_prefix': 'biolink',
+                              'prefix_reference': 'https://w3id.org/biolink/vocab/'},
+                  'dce': {'prefix_prefix': 'dce',
+                          'prefix_reference': 'http://purl.org/dc/elements/1.1/'},
+                  'dcterms': {'prefix_prefix': 'dcterms',
+                              'prefix_reference': 'http://purl.org/dc/terms/'},
+                  'gocam': {'prefix_prefix': 'gocam',
+                            'prefix_reference': 'https://w3id.org/gocam/'},
+                  'gomodel': {'prefix_prefix': 'gomodel',
+                              'prefix_reference': 'http://model.geneontology.org/'},
+                  'goshapes': {'prefix_prefix': 'goshapes',
+                               'prefix_reference': 'http://purl.obolibrary.org/obo/go/shapes/'},
+                  'lego': {'prefix_prefix': 'lego',
+                           'prefix_reference': 'http://geneontology.org/lego/'},
+                  'linkml': {'prefix_prefix': 'linkml',
+                             'prefix_reference': 'https://w3id.org/linkml/'},
+                  'oio': {'prefix_prefix': 'oio',
+                          'prefix_reference': 'http://www.geneontology.org/formats/oboInOwl#'},
+                  'orcid': {'prefix_prefix': 'orcid',
+                            'prefix_reference': 'https://orcid.org/'},
+                  'pav': {'prefix_prefix': 'pav',
+                          'prefix_reference': 'http://purl.org/pav/'}},
+     'see_also': ['https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012280/',
+                  'https://docs.google.com/presentation/d/1ja0Vkw0AoENJ58emM77dGnqPtY1nfIJMeyVnObBxIxI/edit#slide=id.p8'],
+     'source_file': 'src/gocam/schema/gocam.yaml'} )
+
 class ModelStateEnum(str, Enum):
     """
     Status of a model
@@ -74,338 +143,548 @@ class CausalPredicateEnum(str, Enum):
     positively_regulates = "positively regulates"
 
 
+
 class Model(ConfiguredBaseModel):
     """
     A model of a biological program consisting of a set of causally connected activities
     """
-    id: str = Field(..., description="""The identifier of the model. Should be in gocam namespace.""")
-    title: Optional[str] = Field(None, description="""The human-readable descriptive title of the model""")
-    taxon: Optional[str] = Field(None, description="""The primary taxon that the model is about""")
-    status: Optional[ModelStateEnum] = Field(None, description="""The status of the model""")
-    comments: Optional[List[str]] = Field(default_factory=list, description="""Comments about the model""")
-    activities: Optional[List[Activity]] = Field(default_factory=list, description="""All of the activities that are part of the model""")
-    objects: Optional[List[Union[Object,TermObject,PublicationObject,EvidenceTermObject,MolecularFunctionTermObject,BiologicalProcessTermObject,CellularAnatomicalEntityTermObject,MoleculeTermObject,CellTypeTermObject,GrossAnatomicalStructureTermObject,PhaseTermObject,InformationBiomacromoleculeTermObject,TaxonTermObject,PredicateTermObject,GeneProductTermObject,ProteinComplexTermObject]]] = Field(default_factory=list, description="""All of the objects that are part of the model. This includes terms as well as publications and database objects like gene. This is not strictly part of the data managed by the model, it is for convenience, and should be refreshed from outside.""")
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list, description="""Model-level provenance information""")
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam'})
+
+    id: str = Field(..., description="""The identifier of the model. Should be in gocam namespace.""", json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    title: Optional[str] = Field(None, description="""The human-readable descriptive title of the model""", json_schema_extra = { "linkml_meta": {'alias': 'title', 'domain_of': ['Model'], 'slot_uri': 'dct:title'} })
+    taxon: Optional[str] = Field(None, description="""The primary taxon that the model is about""", json_schema_extra = { "linkml_meta": {'alias': 'taxon', 'domain_of': ['Model']} })
+    status: Optional[ModelStateEnum] = Field(None, description="""The status of the model""", json_schema_extra = { "linkml_meta": {'alias': 'status',
+         'aliases': ['model state'],
+         'domain_of': ['Model'],
+         'slot_uri': 'pav:status'} })
+    comments: Optional[List[str]] = Field(None, description="""Comments about the model""", json_schema_extra = { "linkml_meta": {'alias': 'comments', 'domain_of': ['Model'], 'slot_uri': 'rdfs:comment'} })
+    activities: Optional[List[Activity]] = Field(None, description="""All of the activities that are part of the model""", json_schema_extra = { "linkml_meta": {'alias': 'activities', 'domain_of': ['Model']} })
+    objects: Optional[List[Union[Object,TermObject,PublicationObject,EvidenceTermObject,MolecularFunctionTermObject,BiologicalProcessTermObject,CellularAnatomicalEntityTermObject,MoleculeTermObject,CellTypeTermObject,GrossAnatomicalStructureTermObject,PhaseTermObject,InformationBiomacromoleculeTermObject,TaxonTermObject,PredicateTermObject,GeneProductTermObject,ProteinComplexTermObject]]] = Field(None, description="""All of the objects that are part of the model. This includes terms as well as publications and database objects like gene. This is not strictly part of the data managed by the model, it is for convenience, and should be refreshed from outside.""", json_schema_extra = { "linkml_meta": {'alias': 'objects', 'domain_of': ['Model']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, description="""Model-level provenance information""", json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class Activity(ConfiguredBaseModel):
     """
     An individual activity in a causal model, representing the individual molecular activity of a single gene product or complex in the context of a particular model
     """
-    id: str = Field(..., description="""Identifier of the activity unit. Should be in gocam namespace.""")
-    enabled_by: Optional[Union[EnabledByAssociation,EnabledByGeneProductAssociation,EnabledByProteinComplexAssociation]] = Field(None, description="""The gene product or complex that carries out the activity""")
-    molecular_function: Optional[MolecularFunctionAssociation] = Field(None, description="""The molecular function that is carried out by the gene product or complex""")
-    occurs_in: Optional[CellularAnatomicalEntityAssociation] = Field(None, description="""The cellular location in which the activity occurs""")
-    part_of: Optional[BiologicalProcessAssociation] = Field(None, description="""The larger biological process in which the activity is a part""")
-    has_input: Optional[List[MoleculeAssociation]] = Field(default_factory=list, description="""The input molecules that are directly consumed by the activity""")
-    has_primary_input: Optional[MoleculeAssociation] = Field(None, description="""The primary input molecule that is directly consumed by the activity""")
-    has_output: Optional[List[MoleculeAssociation]] = Field(default_factory=list, description="""The output molecules that are directly produced by the activity""")
-    has_primary_output: Optional[MoleculeAssociation] = Field(None, description="""The primary output molecule that is directly produced by the activity""")
-    causal_associations: Optional[List[CausalAssociation]] = Field(default_factory=list, description="""The causal associations that connect this activity to other activities""")
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list, description="""Provenance information for the activity""")
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'aliases': ['annoton'], 'from_schema': 'https://w3id.org/gocam'})
+
+    id: str = Field(..., description="""Identifier of the activity unit. Should be in gocam namespace.""", json_schema_extra = { "linkml_meta": {'alias': 'id',
+         'comments': ['Typically does not need to be exposed to end-user, this exists '
+                      'to allow activity flows'],
+         'domain_of': ['Model', 'Activity', 'Object']} })
+    enabled_by: Optional[Union[EnabledByAssociation,EnabledByGeneProductAssociation,EnabledByProteinComplexAssociation]] = Field(None, description="""The gene product or complex that carries out the activity""", json_schema_extra = { "linkml_meta": {'alias': 'enabled_by', 'domain_of': ['Activity']} })
+    molecular_function: Optional[MolecularFunctionAssociation] = Field(None, description="""The molecular function that is carried out by the gene product or complex""", json_schema_extra = { "linkml_meta": {'alias': 'molecular_function',
+         'domain_of': ['Activity'],
+         'todos': ['currently BP, CC etc are at the level of the activity, not the '
+                   'MolecularFunctionAssociation']} })
+    occurs_in: Optional[CellularAnatomicalEntityAssociation] = Field(None, description="""The cellular location in which the activity occurs""", json_schema_extra = { "linkml_meta": {'alias': 'occurs_in', 'domain_of': ['Activity']} })
+    part_of: Optional[BiologicalProcessAssociation] = Field(None, description="""The larger biological process in which the activity is a part""", json_schema_extra = { "linkml_meta": {'alias': 'part_of',
+         'domain_of': ['Activity',
+                       'BiologicalProcessAssociation',
+                       'CellularAnatomicalEntityAssociation',
+                       'CellTypeAssociation',
+                       'GrossAnatomyAssociation']} })
+    has_input: Optional[List[MoleculeAssociation]] = Field(None, description="""The input molecules that are directly consumed by the activity""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', 'domain_of': ['Activity']} })
+    has_primary_input: Optional[MoleculeAssociation] = Field(None, description="""The primary input molecule that is directly consumed by the activity""", json_schema_extra = { "linkml_meta": {'alias': 'has_primary_input', 'domain_of': ['Activity']} })
+    has_output: Optional[List[MoleculeAssociation]] = Field(None, description="""The output molecules that are directly produced by the activity""", json_schema_extra = { "linkml_meta": {'alias': 'has_output', 'domain_of': ['Activity']} })
+    has_primary_output: Optional[MoleculeAssociation] = Field(None, description="""The primary output molecule that is directly produced by the activity""", json_schema_extra = { "linkml_meta": {'alias': 'has_primary_output', 'domain_of': ['Activity']} })
+    causal_associations: Optional[List[CausalAssociation]] = Field(None, description="""The causal associations that connect this activity to other activities""", json_schema_extra = { "linkml_meta": {'alias': 'causal_associations', 'domain_of': ['Activity']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, description="""Provenance information for the activity""", json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class EvidenceItem(ConfiguredBaseModel):
     """
     An individual piece of evidence that is associated with an assertion in a model
     """
-    term: Optional[str] = Field(None, description="""The ECO term representing the type of evidence""")
-    reference: Optional[str] = Field(None, description="""The publication of reference that describes the evidence""")
-    with_objects: Optional[List[str]] = Field(default_factory=list, description="""Supporting database entities or terms""")
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list, description="""Provenance about the assertion, e.g. who made it""")
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam'})
+
+    term: Optional[str] = Field(None, description="""The ECO term representing the type of evidence""", json_schema_extra = { "linkml_meta": {'alias': 'term',
+         'domain_of': ['EvidenceItem', 'EnabledByAssociation', 'TermAssociation']} })
+    reference: Optional[str] = Field(None, description="""The publication of reference that describes the evidence""", json_schema_extra = { "linkml_meta": {'alias': 'reference', 'domain_of': ['EvidenceItem']} })
+    with_objects: Optional[List[str]] = Field(None, description="""Supporting database entities or terms""", json_schema_extra = { "linkml_meta": {'alias': 'with_objects',
+         'aliases': ['with', 'with/from'],
+         'domain_of': ['EvidenceItem']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, description="""Provenance about the assertion, e.g. who made it""", json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class Association(ConfiguredBaseModel):
     """
     An abstract grouping for different kinds of evidence-associated provenance
     """
-    type: Literal["Association"] = Field("Association")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/gocam'})
+
+    type: Literal["Association"] = Field("Association", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class EnabledByAssociation(Association):
     """
     An association between an activity and the gene product or complex that carries it out
     """
-    term: Optional[str] = Field(None, description="""The gene product or complex that carries out the activity""")
-    type: Literal["EnabledByAssociation"] = Field("EnabledByAssociation")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/gocam'})
+
+    term: Optional[str] = Field(None, description="""The gene product or complex that carries out the activity""", json_schema_extra = { "linkml_meta": {'alias': 'term',
+         'domain_of': ['EvidenceItem', 'EnabledByAssociation', 'TermAssociation']} })
+    type: Literal["EnabledByAssociation"] = Field("EnabledByAssociation", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class EnabledByGeneProductAssociation(EnabledByAssociation):
     """
     An association between an activity and a gene product
     """
-    term: Optional[str] = Field(None, description="""The gene product or complex that carries out the activity""")
-    type: Literal["EnabledByGeneProductAssociation"] = Field("EnabledByGeneProductAssociation")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam',
+         'slot_usage': {'term': {'name': 'term', 'range': 'GeneProductTermObject'}}})
+
+    term: Optional[str] = Field(None, description="""The gene product or complex that carries out the activity""", json_schema_extra = { "linkml_meta": {'alias': 'term',
+         'domain_of': ['EvidenceItem', 'EnabledByAssociation', 'TermAssociation']} })
+    type: Literal["EnabledByGeneProductAssociation"] = Field("EnabledByGeneProductAssociation", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class EnabledByProteinComplexAssociation(EnabledByAssociation):
     """
     An association between an activity and a protein complex
     """
-    members: Optional[List[str]] = Field(default_factory=list, description="""The gene products that are part of the complex""")
-    term: Optional[str] = Field(None, description="""The gene product or complex that carries out the activity""")
-    type: Literal["EnabledByProteinComplexAssociation"] = Field("EnabledByProteinComplexAssociation")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam',
+         'slot_usage': {'term': {'name': 'term', 'range': 'ProteinComplexTermObject'}}})
+
+    members: Optional[List[str]] = Field(None, description="""The gene products that are part of the complex""", json_schema_extra = { "linkml_meta": {'alias': 'members', 'domain_of': ['EnabledByProteinComplexAssociation']} })
+    term: Optional[str] = Field(None, description="""The gene product or complex that carries out the activity""", json_schema_extra = { "linkml_meta": {'alias': 'term',
+         'domain_of': ['EvidenceItem', 'EnabledByAssociation', 'TermAssociation']} })
+    type: Literal["EnabledByProteinComplexAssociation"] = Field("EnabledByProteinComplexAssociation", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class CausalAssociation(Association):
     """
     A causal association between two activities
     """
-    predicate: Optional[str] = Field(None, description="""The RO relation that represents the type of relationship""")
-    downstream_activity: Optional[str] = Field(None, description="""The activity unit that is downstream of this one""")
-    type: Literal["CausalAssociation"] = Field("CausalAssociation")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam'})
+
+    predicate: Optional[str] = Field(None, description="""The RO relation that represents the type of relationship""", json_schema_extra = { "linkml_meta": {'alias': 'predicate', 'domain_of': ['CausalAssociation']} })
+    downstream_activity: Optional[str] = Field(None, description="""The activity unit that is downstream of this one""", json_schema_extra = { "linkml_meta": {'alias': 'downstream_activity',
+         'aliases': ['object'],
+         'domain_of': ['CausalAssociation']} })
+    type: Literal["CausalAssociation"] = Field("CausalAssociation", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class TermAssociation(Association):
     """
     An association between an activity and a term, potentially with extensions
     """
-    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""")
-    type: Literal["TermAssociation"] = Field("TermAssociation")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/gocam'})
+
+    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""", json_schema_extra = { "linkml_meta": {'alias': 'term',
+         'domain_of': ['EvidenceItem', 'EnabledByAssociation', 'TermAssociation']} })
+    type: Literal["TermAssociation"] = Field("TermAssociation", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class MolecularFunctionAssociation(TermAssociation):
     """
     An association between an activity and a molecular function term
     """
-    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""")
-    type: Literal["MolecularFunctionAssociation"] = Field("MolecularFunctionAssociation")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam',
+         'slot_usage': {'term': {'name': 'term',
+                                 'range': 'MolecularFunctionTermObject'}},
+         'todos': ['account for non-MF activity types in Reactome']})
+
+    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""", json_schema_extra = { "linkml_meta": {'alias': 'term',
+         'domain_of': ['EvidenceItem', 'EnabledByAssociation', 'TermAssociation']} })
+    type: Literal["MolecularFunctionAssociation"] = Field("MolecularFunctionAssociation", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class BiologicalProcessAssociation(TermAssociation):
     """
     An association between an activity and a biological process term
     """
-    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""")
-    type: Literal["BiologicalProcessAssociation"] = Field("BiologicalProcessAssociation")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam',
+         'slot_usage': {'term': {'name': 'term',
+                                 'range': 'BiologicalProcessTermObject'}}})
+
+    happens_during: Optional[str] = Field(None, description="""Optional extension describing where the BP takes place""", json_schema_extra = { "linkml_meta": {'alias': 'happens_during', 'domain_of': ['BiologicalProcessAssociation']} })
+    part_of: Optional[str] = Field(None, description="""Optional extension allowing hierarchical nesting of BPs""", json_schema_extra = { "linkml_meta": {'alias': 'part_of',
+         'domain_of': ['Activity',
+                       'BiologicalProcessAssociation',
+                       'CellularAnatomicalEntityAssociation',
+                       'CellTypeAssociation',
+                       'GrossAnatomyAssociation']} })
+    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""", json_schema_extra = { "linkml_meta": {'alias': 'term',
+         'domain_of': ['EvidenceItem', 'EnabledByAssociation', 'TermAssociation']} })
+    type: Literal["BiologicalProcessAssociation"] = Field("BiologicalProcessAssociation", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class CellularAnatomicalEntityAssociation(TermAssociation):
     """
     An association between an activity and a cellular anatomical entity term
     """
-    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""")
-    type: Literal["CellularAnatomicalEntityAssociation"] = Field("CellularAnatomicalEntityAssociation")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam',
+         'slot_usage': {'term': {'name': 'term',
+                                 'range': 'CellularAnatomicalEntityTermObject'}}})
+
+    part_of: Optional[CellTypeAssociation] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'part_of',
+         'domain_of': ['Activity',
+                       'BiologicalProcessAssociation',
+                       'CellularAnatomicalEntityAssociation',
+                       'CellTypeAssociation',
+                       'GrossAnatomyAssociation']} })
+    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""", json_schema_extra = { "linkml_meta": {'alias': 'term',
+         'domain_of': ['EvidenceItem', 'EnabledByAssociation', 'TermAssociation']} })
+    type: Literal["CellularAnatomicalEntityAssociation"] = Field("CellularAnatomicalEntityAssociation", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class CellTypeAssociation(TermAssociation):
     """
     An association between an activity and a cell type term
     """
-    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""")
-    type: Literal["CellTypeAssociation"] = Field("CellTypeAssociation")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam',
+         'slot_usage': {'term': {'name': 'term', 'range': 'CellTypeTermObject'}}})
+
+    part_of: Optional[GrossAnatomyAssociation] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'part_of',
+         'domain_of': ['Activity',
+                       'BiologicalProcessAssociation',
+                       'CellularAnatomicalEntityAssociation',
+                       'CellTypeAssociation',
+                       'GrossAnatomyAssociation']} })
+    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""", json_schema_extra = { "linkml_meta": {'alias': 'term',
+         'domain_of': ['EvidenceItem', 'EnabledByAssociation', 'TermAssociation']} })
+    type: Literal["CellTypeAssociation"] = Field("CellTypeAssociation", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class GrossAnatomyAssociation(TermAssociation):
     """
     An association between an activity and a gross anatomical structure term
     """
-    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""")
-    type: Literal["GrossAnatomyAssociation"] = Field("GrossAnatomyAssociation")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam',
+         'slot_usage': {'term': {'name': 'term',
+                                 'range': 'GrossAnatomicalStructureTermObject'}}})
+
+    part_of: Optional[GrossAnatomyAssociation] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'part_of',
+         'domain_of': ['Activity',
+                       'BiologicalProcessAssociation',
+                       'CellularAnatomicalEntityAssociation',
+                       'CellTypeAssociation',
+                       'GrossAnatomyAssociation']} })
+    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""", json_schema_extra = { "linkml_meta": {'alias': 'term',
+         'domain_of': ['EvidenceItem', 'EnabledByAssociation', 'TermAssociation']} })
+    type: Literal["GrossAnatomyAssociation"] = Field("GrossAnatomyAssociation", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class MoleculeAssociation(TermAssociation):
     """
     An association between an activity and a molecule term
     """
-    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""")
-    type: Literal["MoleculeAssociation"] = Field("MoleculeAssociation")
-    evidence: Optional[List[EvidenceItem]] = Field(default_factory=list)
-    provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam',
+         'slot_usage': {'term': {'name': 'term', 'range': 'MoleculeTermObject'}}})
+
+    term: Optional[str] = Field(None, description="""The ontology term that describes the nature of the association""", json_schema_extra = { "linkml_meta": {'alias': 'term',
+         'domain_of': ['EvidenceItem', 'EnabledByAssociation', 'TermAssociation']} })
+    type: Literal["MoleculeAssociation"] = Field("MoleculeAssociation", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    evidence: Optional[List[EvidenceItem]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'evidence', 'domain_of': ['Association']} })
+    provenances: Optional[List[ProvenanceInfo]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provenances',
+         'domain_of': ['Model', 'Activity', 'EvidenceItem', 'Association']} })
 
 
 class Object(ConfiguredBaseModel):
     """
     An abstract class for all identified objects in a model
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/Object","gocam:Object"] = Field("gocam:Object")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam'})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/Object","gocam:Object"] = Field("gocam:Object", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class TermObject(Object):
     """
     An abstract class for all ontology term objects
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/TermObject","gocam:TermObject"] = Field("gocam:TermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/gocam'})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/TermObject","gocam:TermObject"] = Field("gocam:TermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class PublicationObject(Object):
     """
     An object that represents a publication or other kind of reference
     """
-    abstract_text: Optional[str] = Field(None)
-    full_text: Optional[str] = Field(None)
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/PublicationObject","gocam:PublicationObject"] = Field("gocam:PublicationObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam',
+         'id_prefixes': ['PMID', 'GOREF', 'DOI']})
+
+    abstract_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'abstract_text', 'domain_of': ['PublicationObject']} })
+    full_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'full_text', 'domain_of': ['PublicationObject']} })
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/PublicationObject","gocam:PublicationObject"] = Field("gocam:PublicationObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class EvidenceTermObject(TermObject):
     """
     A term object that represents an evidence term from ECO
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/EvidenceTermObject","gocam:EvidenceTermObject"] = Field("gocam:EvidenceTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam', 'id_prefixes': ['ECO']})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/EvidenceTermObject","gocam:EvidenceTermObject"] = Field("gocam:EvidenceTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class MolecularFunctionTermObject(TermObject):
     """
     A term object that represents a molecular function term from GO
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/MolecularFunctionTermObject","gocam:MolecularFunctionTermObject"] = Field("gocam:MolecularFunctionTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam', 'id_prefixes': ['GO']})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/MolecularFunctionTermObject","gocam:MolecularFunctionTermObject"] = Field("gocam:MolecularFunctionTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class BiologicalProcessTermObject(TermObject):
     """
     A term object that represents a biological process term from GO
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/BiologicalProcessTermObject","gocam:BiologicalProcessTermObject"] = Field("gocam:BiologicalProcessTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam', 'id_prefixes': ['GO']})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/BiologicalProcessTermObject","gocam:BiologicalProcessTermObject"] = Field("gocam:BiologicalProcessTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class CellularAnatomicalEntityTermObject(TermObject):
     """
     A term object that represents a cellular anatomical entity term from GO
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/CellularAnatomicalEntityTermObject","gocam:CellularAnatomicalEntityTermObject"] = Field("gocam:CellularAnatomicalEntityTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam', 'id_prefixes': ['GO']})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/CellularAnatomicalEntityTermObject","gocam:CellularAnatomicalEntityTermObject"] = Field("gocam:CellularAnatomicalEntityTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class MoleculeTermObject(TermObject):
     """
     A term object that represents a molecule term from CHEBI or UniProtKB
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/MoleculeTermObject","gocam:MoleculeTermObject"] = Field("gocam:MoleculeTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam', 'id_prefixes': ['CHEBI', 'UniProtKB']})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/MoleculeTermObject","gocam:MoleculeTermObject"] = Field("gocam:MoleculeTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class CellTypeTermObject(TermObject):
     """
     A term object that represents a cell type term from CL
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/CellTypeTermObject","gocam:CellTypeTermObject"] = Field("gocam:CellTypeTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam',
+         'id_prefixes': ['CL', 'PO', 'FAO', 'DDANAT']})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/CellTypeTermObject","gocam:CellTypeTermObject"] = Field("gocam:CellTypeTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class GrossAnatomicalStructureTermObject(TermObject):
     """
     A term object that represents a gross anatomical structure term from UBERON
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/GrossAnatomicalStructureTermObject","gocam:GrossAnatomicalStructureTermObject"] = Field("gocam:GrossAnatomicalStructureTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam',
+         'id_prefixes': ['UBERON', 'PO', 'FAO', 'DDANAT']})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/GrossAnatomicalStructureTermObject","gocam:GrossAnatomicalStructureTermObject"] = Field("gocam:GrossAnatomicalStructureTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class PhaseTermObject(TermObject):
     """
     A term object that represents a phase term from GO or UBERON
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/PhaseTermObject","gocam:PhaseTermObject"] = Field("gocam:PhaseTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam', 'id_prefixes': ['GO', 'UBERON', 'PO']})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/PhaseTermObject","gocam:PhaseTermObject"] = Field("gocam:PhaseTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class InformationBiomacromoleculeTermObject(TermObject):
     """
     An abstract class for all information biomacromolecule term objects
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/InformationBiomacromoleculeTermObject","gocam:InformationBiomacromoleculeTermObject"] = Field("gocam:InformationBiomacromoleculeTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/gocam'})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/InformationBiomacromoleculeTermObject","gocam:InformationBiomacromoleculeTermObject"] = Field("gocam:InformationBiomacromoleculeTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class GeneProductTermObject(InformationBiomacromoleculeTermObject):
     """
     A term object that represents a gene product term from GO or UniProtKB
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/GeneProductTermObject","gocam:GeneProductTermObject"] = Field("gocam:GeneProductTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam'})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/GeneProductTermObject","gocam:GeneProductTermObject"] = Field("gocam:GeneProductTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class ProteinComplexTermObject(InformationBiomacromoleculeTermObject):
     """
     A term object that represents a protein complex term from GO
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/ProteinComplexTermObject","gocam:ProteinComplexTermObject"] = Field("gocam:ProteinComplexTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam'})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/ProteinComplexTermObject","gocam:ProteinComplexTermObject"] = Field("gocam:ProteinComplexTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class TaxonTermObject(TermObject):
     """
     A term object that represents a taxon term from NCBITaxon
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/TaxonTermObject","gocam:TaxonTermObject"] = Field("gocam:TaxonTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam', 'id_prefixes': ['NCBITaxon']})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/TaxonTermObject","gocam:TaxonTermObject"] = Field("gocam:TaxonTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class PredicateTermObject(TermObject):
     """
     A term object that represents a taxon term from NCBITaxon
     """
-    id: str = Field(...)
-    label: Optional[str] = Field(None)
-    type: Literal["https://w3id.org/gocam/PredicateTermObject","gocam:PredicateTermObject"] = Field("gocam:PredicateTermObject")
-    obsolete: Optional[bool] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam', 'id_prefixes': ['RO']})
+
+    id: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['Model', 'Activity', 'Object']} })
+    label: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Object'], 'slot_uri': 'rdfs:label'} })
+    type: Literal["https://w3id.org/gocam/PredicateTermObject","gocam:PredicateTermObject"] = Field("gocam:PredicateTermObject", json_schema_extra = { "linkml_meta": {'alias': 'type',
+         'designates_type': True,
+         'domain_of': ['Association', 'Object']} })
+    obsolete: Optional[bool] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'obsolete', 'domain_of': ['Object']} })
 
 
 class ProvenanceInfo(ConfiguredBaseModel):
     """
     Provenance information for an object
     """
-    contributor: Optional[str] = Field(None)
-    created: Optional[str] = Field(None)
-    date: Optional[str] = Field(None)
-    provided_by: Optional[str] = Field(None)
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://w3id.org/gocam'})
+
+    contributor: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'contributor',
+         'domain_of': ['ProvenanceInfo'],
+         'slot_uri': 'dct:contributor'} })
+    created: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'created', 'domain_of': ['ProvenanceInfo'], 'slot_uri': 'dct:created'} })
+    date: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'date', 'domain_of': ['ProvenanceInfo'], 'slot_uri': 'dct:date'} })
+    provided_by: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'provided_by',
+         'domain_of': ['ProvenanceInfo'],
+         'slot_uri': 'pav:providedBy'} })
 
 
 # Model rebuild
diff --git a/src/gocam/schema/gocam.yaml b/src/gocam/schema/gocam.yaml
index ba4d1cf..c0cd3b7 100644
--- a/src/gocam/schema/gocam.yaml
+++ b/src/gocam/schema/gocam.yaml
@@ -238,42 +238,46 @@ classes:
   BiologicalProcessAssociation:
     description: An association between an activity and a biological process term
     is_a: TermAssociation
-    slot_usage:
-      term:
-        range: BiologicalProcessTermObject
+    attributes:
       happens_during:
         description: Optional extension describing where the BP takes place
         range: PhaseTermObject
       part_of:
         description: Optional extension allowing hierarchical nesting of BPs
         range: BiologicalProcessTermObject
+    slot_usage:
+      term:
+        range: BiologicalProcessTermObject
 
   CellularAnatomicalEntityAssociation:
     description: An association between an activity and a cellular anatomical entity term
     is_a: TermAssociation
+    attributes:
+      part_of:
+        range: CellTypeAssociation
     slot_usage:
       term:
         range: CellularAnatomicalEntityTermObject
-      part_of:
-        range: CellTypeAssociation
 
   CellTypeAssociation:
     description: An association between an activity and a cell type term
     is_a: TermAssociation
+    attributes:
+      part_of:
+        range: GrossAnatomyAssociation
     slot_usage:
       term:
         range: CellTypeTermObject
-      part_of:
-        range: GrossAnatomyAssociation
 
   GrossAnatomyAssociation:
     description: An association between an activity and a gross anatomical structure term
     is_a: TermAssociation
+    attributes:
+      part_of:
+        range: GrossAnatomyAssociation
     slot_usage:
       term:
         range: GrossAnatomicalStructureTermObject
-      part_of:
-        range: GrossAnatomyAssociation
 
   MoleculeAssociation:
     description: An association between an activity and a molecule term
diff --git a/src/gocam/translation/cx2/main.py b/src/gocam/translation/cx2/main.py
index f329099..06dc710 100644
--- a/src/gocam/translation/cx2/main.py
+++ b/src/gocam/translation/cx2/main.py
@@ -201,6 +201,9 @@ def _add_input_output_nodes(
 
     # Add edges for causal associations between activity nodes
     for activity in gocam.activities:
+        if activity.causal_associations is None:
+            continue
+
         for association in activity.causal_associations:
             if association.downstream_activity in activity_nodes_by_activity_id:
                 relation_style = RELATIONS.get(association.predicate, None)
diff --git a/src/gocam/translation/minerva_wrapper.py b/src/gocam/translation/minerva_wrapper.py
index 6a99fb9..25136cd 100644
--- a/src/gocam/translation/minerva_wrapper.py
+++ b/src/gocam/translation/minerva_wrapper.py
@@ -322,6 +322,8 @@ def _iter_activities_by_fact_subject(
         for activity, term, evs in _iter_activities_by_fact_subject(
             fact_property=HAS_INPUT
         ):
+            if activity.has_input is None:
+                activity.has_input = []
             activity.has_input.append(MoleculeAssociation(term=term, evidence=evs))
 
         for activity, term, evs in _iter_activities_by_fact_subject(
@@ -333,6 +335,8 @@ def _iter_activities_by_fact_subject(
         for activity, term, evs in _iter_activities_by_fact_subject(
             fact_property=HAS_OUTPUT
         ):
+            if activity.has_output is None:
+                activity.has_output = []
             activity.has_output.append(MoleculeAssociation(term=term, evidence=evs))
 
         for activity, term, evs in _iter_activities_by_fact_subject(
@@ -366,6 +370,8 @@ def _iter_activities_by_fact_subject(
                     downstream_activity=object_activity.id,
                     evidence=evs,
                 )
+                if subject_activity.causal_associations is None:
+                    subject_activity.causal_associations = []
                 subject_activity.causal_associations.append(rel)
 
         annotations = _annotations(obj)