diff --git a/.github/workflows/build-deploy-documentation.yaml b/.github/workflows/build-deploy-documentation.yaml
deleted file mode 100644
index 4056c7c..0000000
--- a/.github/workflows/build-deploy-documentation.yaml
+++ /dev/null
@@ -1,35 +0,0 @@
-name: Build and Deploy Static Mkdocs Documentation
-
-# Controls when the action will run. Triggers the workflow on pull request
-on:
-  push:
-    branches:
-      - main
-    paths:
-      - 'mkdocs.yml'
-      - 'src/schema/*.yaml'
-      - 'src/docs/*'
-
-  repository_dispatch:
-    types: trigger-build-deploy-documentation
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
-jobs:
-  github-pages:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-        with:
-          python-version: 3.x
-          
-      # install dependencies
-      - run: pip install --upgrade pip
-      - run: pip install mkdocs
-      - run: pip install linkml
-        
-      # generate markdown files
-      - run: make stage-docs
-
-      # deploy documentation (note: requires documentation is in docs dir)
-      - run: make gh-deploy
diff --git a/poetry.lock b/poetry.lock
index 26b1c2b..1dabcad 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand.
 
 [[package]]
 name = "airium"
@@ -49,25 +49,25 @@ files = [
 
 [[package]]
 name = "anyio"
-version = "4.4.0"
+version = "4.8.0"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"},
-    {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"},
+    {file = "anyio-4.8.0-py3-none-any.whl", hash = "sha256:b5011f270ab5eb0abf13385f851315585cc37ef330dd88e27ec3d34d651fd47a"},
+    {file = "anyio-4.8.0.tar.gz", hash = "sha256:1d9fe889df5212298c0c0723fa20479d1b94883a2df44bd3897aa91083316f7a"},
 ]
 
 [package.dependencies]
 exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
 idna = ">=2.8"
 sniffio = ">=1.1"
-typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""}
+typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""}
 
 [package.extras]
-doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
-test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
-trio = ["trio (>=0.23)"]
+doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21)"]
+trio = ["trio (>=0.26.1)"]
 
 [[package]]
 name = "appdirs"
@@ -169,21 +169,18 @@ test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock
 
 [[package]]
 name = "asttokens"
-version = "2.4.1"
+version = "3.0.0"
 description = "Annotate AST trees with source code positions"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
-    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
-    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
+    {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"},
+    {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"},
 ]
 
-[package.dependencies]
-six = ">=1.12.0"
-
 [package.extras]
-astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
-test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
+astroid = ["astroid (>=2,<4)"]
+test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "async-lru"
@@ -201,19 +198,19 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "attrs"
-version = "24.2.0"
+version = "25.1.0"
 description = "Classes Without Boilerplate"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
-    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
+    {file = "attrs-25.1.0-py3-none-any.whl", hash = "sha256:c75a69e28a550a7e93789579c22aa26b0f5b83b75dc4e08fe092980051e1090a"},
+    {file = "attrs-25.1.0.tar.gz", hash = "sha256:1c97078a80c814273a76b2a298a932eb681c87415c11dee0a6921de7f1b02c3e"},
 ]
 
 [package.extras]
 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]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "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"]
@@ -266,19 +263,19 @@ lxml = ["lxml"]
 
 [[package]]
 name = "bioregistry"
-version = "0.11.10"
+version = "0.11.35"
 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-0.11.35-py3-none-any.whl", hash = "sha256:64713a6595190175d506f2053b1599707a8cf266a2ba44cff3c2e29b71063f90"},
+    {file = "bioregistry-0.11.35.tar.gz", hash = "sha256:f3c57638c193161674f3569312dd6c3a3f99ace862a5c8e0c7986c06e30815d0"},
 ]
 
 [package.dependencies]
 click = "*"
 curies = ">=0.7.0"
-more-click = ">=0.1.2"
+more_click = ">=0.1.2"
 pydantic = "*"
 pystow = ">=0.1.13"
 requests = "*"
@@ -286,52 +283,53 @@ 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"]
+charts = ["jinja2", "matplotlib", "matplotlib_venn", "pandas", "seaborn"]
+docs = ["autodoc_pydantic", "sphinx (>=8)", "sphinx-click", "sphinx-rtd-theme (>=3.0)", "sphinx_automodapi"]
 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)"]
+gha = ["more_itertools"]
+health = ["click_default_group", "jinja2", "pandas", "pyyaml", "tabulate"]
+paper-ranking = ["indra", "more_itertools", "pandas", "scikit-learn", "tabulate"]
+tests = ["coverage", "httpx", "indra", "more_itertools", "pytest", "scikit-learn"]
+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 = "bleach"
-version = "6.1.0"
+version = "6.2.0"
 description = "An easy safelist-based HTML-sanitizing tool."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "bleach-6.1.0-py3-none-any.whl", hash = "sha256:3225f354cfc436b9789c66c4ee030194bee0568fbf9cbdad3bc8b5c26c5f12b6"},
-    {file = "bleach-6.1.0.tar.gz", hash = "sha256:0a31f1837963c41d46bbf1331b8778e1308ea0791db03cc4e7357b97cf42a8fe"},
+    {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"},
+    {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"},
 ]
 
 [package.dependencies]
-six = ">=1.9.0"
+tinycss2 = {version = ">=1.1.0,<1.5", optional = true, markers = "extra == \"css\""}
 webencodings = "*"
 
 [package.extras]
-css = ["tinycss2 (>=1.1.0,<1.3)"]
+css = ["tinycss2 (>=1.1.0,<1.5)"]
 
 [[package]]
 name = "cachetools"
-version = "5.4.0"
+version = "5.5.1"
 description = "Extensible memoizing collections and decorators"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "cachetools-5.4.0-py3-none-any.whl", hash = "sha256:3ae3b49a3d5e28a77a0be2b37dbcb89005058959cb2323858c2657c4a8cab474"},
-    {file = "cachetools-5.4.0.tar.gz", hash = "sha256:b8adc2e7c07f105ced7bc56dbb6dfbe7c4a00acce20e2227b3f355be89bc6827"},
+    {file = "cachetools-5.5.1-py3-none-any.whl", hash = "sha256:b76651fdc3b24ead3c648bbdeeb940c1b04d365b38b4af66788f9ec4a81d42bb"},
+    {file = "cachetools-5.5.1.tar.gz", hash = "sha256:70f238fbba50383ef62e55c6aff6d9673175fe59f7c6782c7a0b9e38f4a9df95"},
 ]
 
 [[package]]
 name = "cattrs"
-version = "23.2.3"
+version = "24.1.2"
 description = "Composable complex class support for attrs and dataclasses."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "cattrs-23.2.3-py3-none-any.whl", hash = "sha256:0341994d94971052e9ee70662542699a3162ea1e0c62f7ce1b4a57f563685108"},
-    {file = "cattrs-23.2.3.tar.gz", hash = "sha256:a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f"},
+    {file = "cattrs-24.1.2-py3-none-any.whl", hash = "sha256:67c7495b760168d931a10233f979b28dc04daf853b30752246f4f8471c6d68d0"},
+    {file = "cattrs-24.1.2.tar.gz", hash = "sha256:8028cfe1ff5382df59dd36474a86e02d817b06eaf8af84555441bac915d2ef85"},
 ]
 
 [package.dependencies]
@@ -343,6 +341,7 @@ typing-extensions = {version = ">=4.1.0,<4.6.3 || >4.6.3", markers = "python_ver
 bson = ["pymongo (>=4.4.0)"]
 cbor2 = ["cbor2 (>=5.4.6)"]
 msgpack = ["msgpack (>=1.0.5)"]
+msgspec = ["msgspec (>=0.18.5)"]
 orjson = ["orjson (>=3.9.2)"]
 pyyaml = ["pyyaml (>=6.0)"]
 tomlkit = ["tomlkit (>=0.11.8)"]
@@ -350,89 +349,89 @@ ujson = ["ujson (>=5.7.0)"]
 
 [[package]]
 name = "certifi"
-version = "2024.7.4"
+version = "2025.1.31"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
-    {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
+    {file = "certifi-2025.1.31-py3-none-any.whl", hash = "sha256:ca78db4565a652026a4db2bcdf68f2fb589ea80d0be70e03929ed730746b84fe"},
+    {file = "certifi-2025.1.31.tar.gz", hash = "sha256:3d5da6925056f6f18f119200434a4780a94263f10d1c21d032a6f6b2baa20651"},
 ]
 
 [[package]]
 name = "cffi"
-version = "1.17.0"
+version = "1.17.1"
 description = "Foreign Function Interface for Python calling C code."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
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 ]
 
 [[package]]
 name = "class-resolver"
-version = "0.4.3"
+version = "0.5.4"
 description = "Lookup and instantiate classes with style."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
 files = [
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-    {file = "class_resolver-0.4.3.tar.gz", hash = "sha256:18bb9983cb377f669e5900979de4aa65449d95ead61838fa12862958998c71a2"},
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 ]
 
 [package.dependencies]
@@ -577,25 +578,25 @@ importlib-metadata = {version = ">3.6", markers = "python_version < \"3.10\""}
 
 [package.extras]
 click = ["click"]
-docdata = ["docdata"]
-docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-theme"]
+docs = ["sphinx (<8)", "sphinx-automodapi", "sphinx-rtd-theme"]
 numpy = ["numpy"]
 optuna = ["optuna"]
 ray = ["ray[tune] (<2.0.0)"]
 sklearn = ["scikit-learn"]
+tabulate = ["tabulate"]
 tests = ["coverage", "docdata", "pytest"]
 torch = ["torch"]
 torch-geometric = ["torch", "torch-geometric", "torch-sparse"]
 
 [[package]]
 name = "click"
-version = "8.1.7"
+version = "8.1.8"
 description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -662,27 +663,28 @@ test = ["pytest"]
 
 [[package]]
 name = "curies"
-version = "0.7.10"
-description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
+version = "0.10.3"
+description = "Idiomatic conversion between URIs and compact URIs (CURIEs)"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
-pydantic = "*"
+eval-type-backport = {version = "*", markers = "python_version < \"3.10\""}
+pydantic = ">=2.0"
 pytrie = "*"
-requests = "*"
+typing-extensions = "*"
 
 [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[toml]", "pytest", "requests"]
 
 [[package]]
 name = "daff"
@@ -696,33 +698,37 @@ files = [
 
 [[package]]
 name = "debugpy"
-version = "1.8.5"
+version = "1.8.12"
 description = "An implementation of the Debug Adapter Protocol for Python"
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 python-versions = ">=3.8"
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 ]
 
 [[package]]
@@ -749,20 +755,20 @@ files = [
 
 [[package]]
 name = "deprecated"
-version = "1.2.14"
+version = "1.2.18"
 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
 files = [
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-    {file = "Deprecated-1.2.14.tar.gz", hash = "sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3"},
+    {file = "Deprecated-1.2.18-py2.py3-none-any.whl", hash = "sha256:bd5011788200372a32418f888e326a09ff80d0214bd961147cfed01b5c018eec"},
+    {file = "deprecated-1.2.18.tar.gz", hash = "sha256:422b6f6d859da6f2ef57857761bfb392480502a64c3028ca9bbe86085d72115d"},
 ]
 
 [package.dependencies]
 wrapt = ">=1.10,<2"
 
 [package.extras]
-dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
+dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "setuptools", "tox"]
 
 [[package]]
 name = "deprecation"
@@ -814,7 +820,7 @@ files = [
 name = "duckdb"
 version = "0.10.3"
 description = "DuckDB in-process database"
-optional = false
+optional = true
 python-versions = ">=3.7.0"
 files = [
     {file = "duckdb-0.10.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:cd25cc8d001c09a19340739ba59d33e12a81ab285b7a6bed37169655e1cefb31"},
@@ -868,13 +874,13 @@ 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]]
@@ -896,6 +902,20 @@ requests = "*"
 [package.extras]
 dev = ["flake8", "ipython", "mock", "pytest", "pytest-cov", "restview", "setuptools", "sphinx", "sphinx-rtd-theme", "tox", "vcrpy", "yapf"]
 
+[[package]]
+name = "eval-type-backport"
+version = "0.2.2"
+description = "Like `typing._eval_type`, but lets older Python versions use newer typing features."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "eval_type_backport-0.2.2-py3-none-any.whl", hash = "sha256:cb6ad7c393517f476f96d456d0412ea80f0a8cf96f6892834cd9340149111b0a"},
+    {file = "eval_type_backport-0.2.2.tar.gz", hash = "sha256:f0576b4cf01ebb5bd358d02314d31846af5e07678387486e2c798af0e7d849c1"},
+]
+
+[package.extras]
+tests = ["pytest"]
+
 [[package]]
 name = "exceptiongroup"
 version = "1.2.2"
@@ -912,13 +932,13 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "executing"
-version = "2.0.1"
+version = "2.2.0"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
 files = [
-    {file = "executing-2.0.1-py2.py3-none-any.whl", hash = "sha256:eac49ca94516ccc753f9fb5ce82603156e590b27525a8bc32cce8ae302eb61bc"},
-    {file = "executing-2.0.1.tar.gz", hash = "sha256:35afe2ce3affba8ee97f2d69927fa823b08b472b7b994e36a52a964b93d16147"},
+    {file = "executing-2.2.0-py2.py3-none-any.whl", hash = "sha256:11387150cad388d62750327a53d3339fad4888b39a6fe233c3afbb54ecffd3aa"},
+    {file = "executing-2.2.0.tar.gz", hash = "sha256:5d108c028108fe2551d1a7b2e8b713341e2cb4fc0aa7dcf966fa4327a5226755"},
 ]
 
 [package.extras]
@@ -926,13 +946,13 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
 name = "fastjsonschema"
-version = "2.20.0"
+version = "2.21.1"
 description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
 files = [
-    {file = "fastjsonschema-2.20.0-py3-none-any.whl", hash = "sha256:5875f0b0fa7a0043a91e93a9b8f793bcbbba9691e7fd83dca95c28ba26d21f0a"},
-    {file = "fastjsonschema-2.20.0.tar.gz", hash = "sha256:3d48fc5300ee96f5d116f10fe6f28d938e6008f59a6a025c2649475b87f76a23"},
+    {file = "fastjsonschema-2.21.1-py3-none-any.whl", hash = "sha256:c9e5b7e908310918cf494a434eeb31384dd84a98b57a30bcb1f535015b554667"},
+    {file = "fastjsonschema-2.21.1.tar.gz", hash = "sha256:794d4f0a58f848961ba16af7b9c85a3e88cd360df008c59aac6fc5ae9323b5d4"},
 ]
 
 [package.extras]
@@ -1023,23 +1043,6 @@ rdflib = ">=6.2.0,<8"
 rdflib-shim = "*"
 rfc3987 = "*"
 
-[[package]]
-name = "ghp-import"
-version = "2.1.0"
-description = "Copy your docs directly to the gh-pages branch."
-optional = false
-python-versions = "*"
-files = [
-    {file = "ghp-import-2.1.0.tar.gz", hash = "sha256:9c535c4c61193c2df8871222567d7fd7e5014d835f97dc7b7439069e2413d343"},
-    {file = "ghp_import-2.1.0-py3-none-any.whl", hash = "sha256:8337dd7b50877f163d4c0289bc1f1c7f127550241988d568c1db512c4324a619"},
-]
-
-[package.dependencies]
-python-dateutil = ">=2.8.1"
-
-[package.extras]
-dev = ["flake8", "markdown", "twine", "wheel"]
-
 [[package]]
 name = "google"
 version = "3.0.0"
@@ -1056,36 +1059,40 @@ beautifulsoup4 = "*"
 
 [[package]]
 name = "google-api-core"
-version = "2.19.1"
+version = "2.24.1"
 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"},
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+    {file = "google_api_core-2.24.1-py3-none-any.whl", hash = "sha256:bc78d608f5a5bf853b80bd70a795f703294de656c096c0968320830a4bc280f1"},
+    {file = "google_api_core-2.24.1.tar.gz", hash = "sha256:f8b36f5456ab0dd99a1b693a40a31d1e7757beea380ad1b38faaf8941eae9d8a"},
 ]
 
 [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 = ">=1.22.3,<2.0.0dev", markers = "python_version < \"3.13\""},
+    {version = ">=1.25.0,<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 = "2.140.0"
+version = "2.160.0"
 description = "Google API Client Library for Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google_api_python_client-2.140.0-py2.py3-none-any.whl", hash = "sha256:aeb4bb99e9fdd241473da5ff35464a0658fea0db76fe89c0f8c77ecfc3813404"},
-    {file = "google_api_python_client-2.140.0.tar.gz", hash = "sha256:0bb973adccbe66a3d0a70abe4e49b3f2f004d849416bfec38d22b75649d389d8"},
+    {file = "google_api_python_client-2.160.0-py2.py3-none-any.whl", hash = "sha256:63d61fb3e4cf3fb31a70a87f45567c22f6dfe87bbfa27252317e3e2c42900db4"},
+    {file = "google_api_python_client-2.160.0.tar.gz", hash = "sha256:a8ccafaecfa42d15d5b5c3134ced8de08380019717fc9fb1ed510ca58eca3b7e"},
 ]
 
 [package.dependencies]
@@ -1097,13 +1104,13 @@ uritemplate = ">=3.0.1,<5"
 
 [[package]]
 name = "google-auth"
-version = "2.33.0"
+version = "2.38.0"
 description = "Google Authentication Library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google_auth-2.33.0-py2.py3-none-any.whl", hash = "sha256:8eff47d0d4a34ab6265c50a106a3362de6a9975bb08998700e389f857e4d39df"},
-    {file = "google_auth-2.33.0.tar.gz", hash = "sha256:d6a52342160d7290e334b4d47ba390767e4438ad0d45b7630774533e82655b95"},
+    {file = "google_auth-2.38.0-py2.py3-none-any.whl", hash = "sha256:e7dae6694313f434a2727bf2906f27ad259bae090d7aa896590d86feec3d9d4a"},
+    {file = "google_auth-2.38.0.tar.gz", hash = "sha256:8285113607d3b80a3f1543b75962447ba8a09fe85783432a784fdeef6ac094c4"},
 ]
 
 [package.dependencies]
@@ -1113,7 +1120,8 @@ 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"]
+pyjwt = ["cryptography (>=38.0.3)", "pyjwt (>=2.0)"]
 pyopenssl = ["cryptography (>=38.0.3)", "pyopenssl (>=20.0.0)"]
 reauth = ["pyu2f (>=0.1.5)"]
 requests = ["requests (>=2.20.0,<3.0.0.dev0)"]
@@ -1153,13 +1161,13 @@ tool = ["click (>=6.0.0)"]
 
 [[package]]
 name = "googleapis-common-protos"
-version = "1.63.2"
+version = "1.66.0"
 description = "Common protobufs used in Google APIs"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "googleapis_common_protos-1.66.0-py2.py3-none-any.whl", hash = "sha256:d7abcd75fabb2e0ec9f74466401f6c119a0b498e27370e9be4c94cb7e382b8ed"},
+    {file = "googleapis_common_protos-1.66.0.tar.gz", hash = "sha256:c3e7b33d15fdca5374cc0a7346dd92ffa847425cc4ea941d970f13680052ec8c"},
 ]
 
 [package.dependencies]
@@ -1186,69 +1194,84 @@ test = ["coverage", "pytest (>=7,<8.1)", "pytest-cov", "pytest-mock (>=3)"]
 
 [[package]]
 name = "greenlet"
-version = "3.0.3"
+version = "3.1.1"
 description = "Lightweight in-process concurrent programming"
 optional = false
 python-versions = ">=3.7"
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+    {file = "greenlet-3.1.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:d0028e725ee18175c6e422797c407874da24381ce0690d6b9396c204c7f7276e"},
+    {file = "greenlet-3.1.1-cp39-cp39-win32.whl", hash = "sha256:5e06afd14cbaf9e00899fae69b24a32f2196c19de08fcb9f4779dd4f004e5e7c"},
+    {file = "greenlet-3.1.1-cp39-cp39-win_amd64.whl", hash = "sha256:3319aa75e0e0639bc15ff54ca327e8dc7a6fe404003496e3c6925cd3142e0e22"},
+    {file = "greenlet-3.1.1.tar.gz", hash = "sha256:4ce3ac6cdb6adf7946475d7ef31777c26d94bccc377e070a7986bd2d5c515467"},
 ]
 
 [package.extras]
@@ -1257,13 +1280,13 @@ 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"},
-    {file = "gspread-6.1.2.tar.gz", hash = "sha256:b147688b8c7a18c9835d5f998997ec17c97c0470babcab17f65ac2b3a32402b7"},
+    {file = "gspread-6.1.4-py3-none-any.whl", hash = "sha256:c34781c426031a243ad154952b16f21ac56a5af90687885fbee3d1fba5280dcd"},
+    {file = "gspread-6.1.4.tar.gz", hash = "sha256:b8eec27de7cadb338bb1b9f14a9be168372dee8965c0da32121816b5050ac1de"},
 ]
 
 [package.dependencies]
@@ -1308,13 +1331,13 @@ files = [
 
 [[package]]
 name = "httpcore"
-version = "1.0.5"
+version = "1.0.7"
 description = "A minimal low-level HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpcore-1.0.5-py3-none-any.whl", hash = "sha256:421f18bac248b25d310f3cacd198d55b8e6125c107797b609ff9b7a6ba7991b5"},
-    {file = "httpcore-1.0.5.tar.gz", hash = "sha256:34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61"},
+    {file = "httpcore-1.0.7-py3-none-any.whl", hash = "sha256:a3fff8f43dc260d5bd363d9f9cf1830fa3a458b332856f34282de498ed420edd"},
+    {file = "httpcore-1.0.7.tar.gz", hash = "sha256:8551cb62a169ec7162ac7be8d4817d561f60e08eaa485234898414bb5a8a0b4c"},
 ]
 
 [package.dependencies]
@@ -1325,7 +1348,7 @@ h11 = ">=0.13,<0.15"
 asyncio = ["anyio (>=4.0,<5.0)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
-trio = ["trio (>=0.22.0,<0.26.0)"]
+trio = ["trio (>=0.22.0,<1.0)"]
 
 [[package]]
 name = "httplib2"
@@ -1343,13 +1366,13 @@ pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0
 
 [[package]]
 name = "httpx"
-version = "0.27.0"
+version = "0.28.1"
 description = "The next generation HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpx-0.27.0-py3-none-any.whl", hash = "sha256:71d5465162c13681bff01ad59b2cc68dd838ea1f10e51574bac27103f00c91a5"},
-    {file = "httpx-0.27.0.tar.gz", hash = "sha256:a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5"},
+    {file = "httpx-0.28.1-py3-none-any.whl", hash = "sha256:d909fcccc110f8c7faf814ca82a9a4d816bc5a6dbfea25d6591d6985b8ba59ad"},
+    {file = "httpx-0.28.1.tar.gz", hash = "sha256:75e98c5f16b0f35b567856f597f06ff2270a374470a5c2392242528e3e3e42fc"},
 ]
 
 [package.dependencies]
@@ -1357,25 +1380,28 @@ anyio = "*"
 certifi = "*"
 httpcore = "==1.*"
 idna = "*"
-sniffio = "*"
 
 [package.extras]
 brotli = ["brotli", "brotlicffi"]
 cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[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"
@@ -1492,59 +1518,71 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "8.2.0"
+version = "8.6.1"
 description = "Read metadata from Python packages"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "importlib_metadata-8.2.0-py3-none-any.whl", hash = "sha256:11901fa0c2f97919b288679932bb64febaeacf289d18ac84dd68cb2e74213369"},
-    {file = "importlib_metadata-8.2.0.tar.gz", hash = "sha256:72e8d4399996132204f9a16dcc751af254a48f8d1b20b9ff0f98d4a8f901e73d"},
+    {file = "importlib_metadata-8.6.1-py3-none-any.whl", hash = "sha256:02a89390c1e15fdfdc0d7c6b25cb3e62650d0494005c97d6f148bf5b9787525e"},
+    {file = "importlib_metadata-8.6.1.tar.gz", hash = "sha256:310b41d755445d74569f993ccfc22838295d9fe005425094fad953d7f15c8580"},
 ]
 
 [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 = "importlib-resources"
-version = "6.4.0"
+version = "6.5.2"
 description = "Read resources from Python packages"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "importlib_resources-6.4.0-py3-none-any.whl", hash = "sha256:50d10f043df931902d4194ea07ec57960f66a80449ff867bfe782b4c486ba78c"},
-    {file = "importlib_resources-6.4.0.tar.gz", hash = "sha256:cdb2b453b8046ca4e3798eb1d84f3cce1446a0e8e7b5ef4efb600f19fc398145"},
+    {file = "importlib_resources-6.5.2-py3-none-any.whl", hash = "sha256:789cfdc3ed28c78b67a06acb8126751ced69a3d5f79c095a98298cd8a760ccec"},
+    {file = "importlib_resources-6.5.2.tar.gz", hash = "sha256:185f87adef5bcc288449d98fb4fba07cea78bc036455dd44c5fc4a2fe78fed2c"},
 ]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
+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)"]
+test = ["jaraco.test (>=5.4)", "pytest (>=6,!=8.1.*)", "zipp (>=3.17)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "inflect"
-version = "7.3.1"
+version = "7.5.0"
 description = "Correctly generate plurals, singular nouns, ordinals, indefinite articles"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "inflect-7.3.1-py3-none-any.whl", hash = "sha256:bedbae76877b054ecf0597153725677ab618fdd69abf189cc82e0f7a6720669d"},
-    {file = "inflect-7.3.1.tar.gz", hash = "sha256:edd785148a673b0c6dfef1a7d80cc1bcb2dd6d041cdb313b60032e464fd4e808"},
+    {file = "inflect-7.5.0-py3-none-any.whl", hash = "sha256:2aea70e5e70c35d8350b8097396ec155ffd68def678c7ff97f51aa69c1d92344"},
+    {file = "inflect-7.5.0.tar.gz", hash = "sha256:faf19801c3742ed5a05a8ce388e0d8fe1a07f8d095c82201eb904f5d27ad571f"},
 ]
 
 [package.dependencies]
-more-itertools = ">=8.5.0"
+more_itertools = ">=8.5.0"
 typeguard = ">=4.0.1"
 
 [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 = ["pygments", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["pygments", "pytest (>=6,!=8.1.*)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
@@ -1629,39 +1667,36 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pa
 
 [[package]]
 name = "ipywidgets"
-version = "8.1.3"
+version = "8.1.5"
 description = "Jupyter interactive widgets"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ipywidgets-8.1.3-py3-none-any.whl", hash = "sha256:efafd18f7a142248f7cb0ba890a68b96abd4d6e88ddbda483c9130d12667eaf2"},
-    {file = "ipywidgets-8.1.3.tar.gz", hash = "sha256:f5f9eeaae082b1823ce9eac2575272952f40d748893972956dc09700a6392d9c"},
+    {file = "ipywidgets-8.1.5-py3-none-any.whl", hash = "sha256:3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245"},
+    {file = "ipywidgets-8.1.5.tar.gz", hash = "sha256:870e43b1a35656a80c18c9503bbf2d16802db1cb487eec6fab27d683381dde17"},
 ]
 
 [package.dependencies]
 comm = ">=0.1.3"
 ipython = ">=6.1.0"
-jupyterlab-widgets = ">=3.0.11,<3.1.0"
+jupyterlab-widgets = ">=3.0.12,<3.1.0"
 traitlets = ">=4.3.1"
-widgetsnbextension = ">=4.0.11,<4.1.0"
+widgetsnbextension = ">=4.0.12,<4.1.0"
 
 [package.extras]
 test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
 
 [[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"
@@ -1678,32 +1713,32 @@ arrow = ">=0.15.0"
 
 [[package]]
 name = "jedi"
-version = "0.19.1"
+version = "0.19.2"
 description = "An autocompletion tool for Python that can be used for text editors."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "jedi-0.19.1-py2.py3-none-any.whl", hash = "sha256:e983c654fe5c02867aef4cdfce5a2fbb4a50adc0af145f70504238f18ef5e7e0"},
-    {file = "jedi-0.19.1.tar.gz", hash = "sha256:cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd"},
+    {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"},
+    {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"},
 ]
 
 [package.dependencies]
-parso = ">=0.8.3,<0.9.0"
+parso = ">=0.8.4,<0.9.0"
 
 [package.extras]
 docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
 qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
-testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
 
 [[package]]
 name = "jinja2"
-version = "3.1.4"
+version = "3.1.5"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"},
-    {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"},
+    {file = "jinja2-3.1.5-py3-none-any.whl", hash = "sha256:aba0f4dc9ed8013c424088f68a5c226f7d6097ed89b246d7749c2ec4175c6adb"},
+    {file = "jinja2-3.1.5.tar.gz", hash = "sha256:8fefff8dc3034e27bb80d67c671eb8a9bc424c0ef4c0826edbff304cceff43bb"},
 ]
 
 [package.dependencies]
@@ -1714,72 +1749,87 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jiter"
-version = "0.5.0"
+version = "0.8.2"
 description = "Fast iterable JSON parser."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jiter-0.5.0-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:b599f4e89b3def9a94091e6ee52e1d7ad7bc33e238ebb9c4c63f211d74822c3f"},
-    {file = "jiter-0.5.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2a063f71c4b06225543dddadbe09d203dc0c95ba352d8b85f1221173480a71d5"},
-    {file = "jiter-0.5.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:acc0d5b8b3dd12e91dd184b87273f864b363dfabc90ef29a1092d269f18c7e28"},
-    {file = "jiter-0.5.0-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:c22541f0b672f4d741382a97c65609332a783501551445ab2df137ada01e019e"},
-    {file = "jiter-0.5.0-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:63314832e302cc10d8dfbda0333a384bf4bcfce80d65fe99b0f3c0da8945a91a"},
-    {file = "jiter-0.5.0-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:a25fbd8a5a58061e433d6fae6d5298777c0814a8bcefa1e5ecfff20c594bd749"},
-    {file = "jiter-0.5.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:503b2c27d87dfff5ab717a8200fbbcf4714516c9d85558048b1fc14d2de7d8dc"},
-    {file = "jiter-0.5.0-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:6d1f3d27cce923713933a844872d213d244e09b53ec99b7a7fdf73d543529d6d"},
-    {file = "jiter-0.5.0-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:c95980207b3998f2c3b3098f357994d3fd7661121f30669ca7cb945f09510a87"},
-    {file = "jiter-0.5.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:afa66939d834b0ce063f57d9895e8036ffc41c4bd90e4a99631e5f261d9b518e"},
-    {file = "jiter-0.5.0-cp310-none-win32.whl", hash = "sha256:f16ca8f10e62f25fd81d5310e852df6649af17824146ca74647a018424ddeccf"},
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 ]
 
 [[package]]
@@ -1799,15 +1849,18 @@ pyyaml = "*"
 
 [[package]]
 name = "json5"
-version = "0.9.25"
+version = "0.10.0"
 description = "A Python implementation of the JSON5 data format."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.8.0"
 files = [
-    {file = "json5-0.9.25-py3-none-any.whl", hash = "sha256:34ed7d834b1341a86987ed52f3f76cd8ee184394906b6e22a1e0deb9ab294e8f"},
-    {file = "json5-0.9.25.tar.gz", hash = "sha256:548e41b9be043f9426776f05df8635a00fe06104ea51ed24b67f908856e151ae"},
+    {file = "json5-0.10.0-py3-none-any.whl", hash = "sha256:19b23410220a7271e8377f81ba8aacba2fdd56947fbb137ee5977cbe1f5e8dfa"},
+    {file = "json5-0.10.0.tar.gz", hash = "sha256:e66941c8f0a02026943c52c2eb34ebeb2a6f819a0be05920a6f5243cd30fd559"},
 ]
 
+[package.extras]
+dev = ["build (==1.2.2.post1)", "coverage (==7.5.3)", "mypy (==1.13.0)", "pip (==24.3.1)", "pylint (==3.2.3)", "ruff (==0.7.3)", "twine (==5.1.1)", "uv (==0.5.1)"]
+
 [[package]]
 name = "jsonasobj"
 version = "1.3.1"
@@ -1863,13 +1916,14 @@ 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 = [
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-    {file = "jsonpath_ng-1.6.1-py3-none-any.whl", hash = "sha256:8f22cd8273d7772eea9aaa84d922e0841aa36fdb8a2c6b7f6c3791a16a9bc0be"},
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 ]
 
 [package.dependencies]
@@ -1921,13 +1975,13 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[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"},
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+    {file = "jsonschema_specifications-2024.10.1.tar.gz", hash = "sha256:0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272"},
 ]
 
 [package.dependencies]
@@ -1935,33 +1989,32 @@ referencing = ">=0.31.0"
 
 [[package]]
 name = "jupyter"
-version = "1.0.0"
+version = "1.1.1"
 description = "Jupyter metapackage. Install all the Jupyter components in one go."
 optional = false
 python-versions = "*"
 files = [
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+    {file = "jupyter-1.1.1.tar.gz", hash = "sha256:d55467bceabdea49d7e3624af7e33d59c37fff53ed3a350e1ac957bed731de7a"},
 ]
 
 [package.dependencies]
 ipykernel = "*"
 ipywidgets = "*"
 jupyter-console = "*"
+jupyterlab = "*"
 nbconvert = "*"
 notebook = "*"
-qtconsole = "*"
 
 [[package]]
 name = "jupyter-client"
-version = "8.6.2"
+version = "8.6.3"
 description = "Jupyter protocol implementation and client libraries"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"},
+    {file = "jupyter_client-8.6.3.tar.gz", hash = "sha256:35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419"},
 ]
 
 [package.dependencies]
@@ -2022,13 +2075,13 @@ test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"
 
 [[package]]
 name = "jupyter-events"
-version = "0.10.0"
+version = "0.11.0"
 description = "Jupyter Event System library"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "jupyter_events-0.10.0-py3-none-any.whl", hash = "sha256:4b72130875e59d57716d327ea70d3ebc3af1944d3717e5a498b8a06c6c159960"},
-    {file = "jupyter_events-0.10.0.tar.gz", hash = "sha256:670b8229d3cc882ec782144ed22e0d29e1c2d639263f92ca8383e66682845e22"},
+    {file = "jupyter_events-0.11.0-py3-none-any.whl", hash = "sha256:36399b41ce1ca45fe8b8271067d6a140ffa54cec4028e95491c93b78a855cacf"},
+    {file = "jupyter_events-0.11.0.tar.gz", hash = "sha256:c0bc56a37aac29c1fbc3bcfbddb8c8c49533f9cf11f1c4e6adadba936574ab90"},
 ]
 
 [package.dependencies]
@@ -2042,7 +2095,7 @@ traitlets = ">=5.3"
 
 [package.extras]
 cli = ["click", "rich"]
-docs = ["jupyterlite-sphinx", "myst-parser", "pydata-sphinx-theme", "sphinxcontrib-spelling"]
+docs = ["jupyterlite-sphinx", "myst-parser", "pydata-sphinx-theme (>=0.16)", "sphinx (>=8)", "sphinxcontrib-spelling"]
 test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "pytest-console-scripts", "rich"]
 
 [[package]]
@@ -2062,13 +2115,13 @@ jupyter-server = ">=1.1.2"
 
 [[package]]
 name = "jupyter-server"
-version = "2.14.2"
+version = "2.15.0"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "jupyter_server-2.14.2-py3-none-any.whl", hash = "sha256:47ff506127c2f7851a17bf4713434208fc490955d0e8632e95014a9a9afbeefd"},
-    {file = "jupyter_server-2.14.2.tar.gz", hash = "sha256:66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b"},
+    {file = "jupyter_server-2.15.0-py3-none-any.whl", hash = "sha256:872d989becf83517012ee669f09604aa4a28097c0bd90b2f424310156c2cdae3"},
+    {file = "jupyter_server-2.15.0.tar.gz", hash = "sha256:9d446b8697b4f7337a1b7cdcac40778babdd93ba614b6d68ab1c0c918f1c4084"},
 ]
 
 [package.dependencies]
@@ -2077,7 +2130,7 @@ argon2-cffi = ">=21.1"
 jinja2 = ">=3.0.3"
 jupyter-client = ">=7.4.4"
 jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
-jupyter-events = ">=0.9.0"
+jupyter-events = ">=0.11.0"
 jupyter-server-terminals = ">=0.4.4"
 nbconvert = ">=6.4.4"
 nbformat = ">=5.3.0"
@@ -2117,13 +2170,13 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 
 [[package]]
 name = "jupyterlab"
-version = "4.2.4"
+version = "4.3.5"
 description = "JupyterLab computational environment"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyterlab-4.2.4-py3-none-any.whl", hash = "sha256:807a7ec73637744f879e112060d4b9d9ebe028033b7a429b2d1f4fc523d00245"},
-    {file = "jupyterlab-4.2.4.tar.gz", hash = "sha256:343a979fb9582fd08c8511823e320703281cd072a0049bcdafdc7afeda7f2537"},
+    {file = "jupyterlab-4.3.5-py3-none-any.whl", hash = "sha256:571bbdee20e4c5321ab5195bc41cf92a75a5cff886be5e57ce78dfa37a5e9fdb"},
+    {file = "jupyterlab-4.3.5.tar.gz", hash = "sha256:c779bf72ced007d7d29d5bcef128e7fdda96ea69299e19b04a43635a7d641f9d"},
 ]
 
 [package.dependencies]
@@ -2138,15 +2191,15 @@ jupyter-server = ">=2.4.0,<3"
 jupyterlab-server = ">=2.27.1,<3"
 notebook-shim = ">=0.2"
 packaging = "*"
-setuptools = ">=40.1.0"
+setuptools = ">=40.8.0"
 tomli = {version = ">=1.2.2", markers = "python_version < \"3.11\""}
 tornado = ">=6.2.0"
 traitlets = "*"
 
 [package.extras]
-dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.3.5)"]
-docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-jupyter", "sphinx (>=1.8,<7.3.0)", "sphinx-copybutton"]
-docs-screenshots = ["altair (==5.3.0)", "ipython (==8.16.1)", "ipywidgets (==8.1.2)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.1.post2)", "matplotlib (==3.8.3)", "nbconvert (>=7.0.0)", "pandas (==2.2.1)", "scipy (==1.12.0)", "vega-datasets (==0.9.0)"]
+dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.6.9)"]
+docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-jupyter", "sphinx (>=1.8,<8.1.0)", "sphinx-copybutton"]
+docs-screenshots = ["altair (==5.4.1)", "ipython (==8.16.1)", "ipywidgets (==8.1.5)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.2.post3)", "matplotlib (==3.9.2)", "nbconvert (>=7.0.0)", "pandas (==2.2.3)", "scipy (==1.14.1)", "vega-datasets (==0.9.0)"]
 test = ["coverage", "pytest (>=7.0)", "pytest-check-links (>=0.7)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter (>=0.5.3)", "pytest-timeout", "pytest-tornasync", "requests", "requests-cache", "virtualenv"]
 upgrade-extension = ["copier (>=9,<10)", "jinja2-time (<0.3)", "pydantic (<3.0)", "pyyaml-include (<3.0)", "tomli-w (<2.0)"]
 
@@ -2189,13 +2242,13 @@ test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-v
 
 [[package]]
 name = "jupyterlab-widgets"
-version = "3.0.11"
+version = "3.0.13"
 description = "Jupyter interactive widgets for JupyterLab"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "jupyterlab_widgets-3.0.11-py3-none-any.whl", hash = "sha256:78287fd86d20744ace330a61625024cf5521e1c012a352ddc0a3cdc2348becd0"},
-    {file = "jupyterlab_widgets-3.0.11.tar.gz", hash = "sha256:dd5ac679593c969af29c9bed054c24f26842baa51352114736756bc035deee27"},
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 ]
 
 [[package]]
@@ -2215,13 +2268,13 @@ linkml-runtime = ">=1.1.24"
 
 [[package]]
 name = "kgcl-schema"
-version = "0.6.8"
+version = "0.6.9"
 description = "Schema for the KGCL project."
 optional = false
 python-versions = "<4.0,>=3.9"
 files = [
-    {file = "kgcl_schema-0.6.8-py3-none-any.whl", hash = "sha256:84deb921203c5b94c9fa6386e7fec24593162abbccdadeb78a5f7231c0c75803"},
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 ]
 
 [package.dependencies]
@@ -2232,13 +2285,13 @@ prefixmaps = ">=0.2.0,<0.3.0"
 
 [[package]]
 name = "lark"
-version = "1.1.9"
+version = "1.2.2"
 description = "a modern parsing library"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -2249,13 +2302,13 @@ regex = ["regex"]
 
 [[package]]
 name = "linkml"
-version = "1.8.1"
+version = "1.8.6"
 description = "Linked Open Data Modeling Language"
 optional = false
 python-versions = "<4.0.0,>=3.8.1"
 files = [
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+    {file = "linkml-1.8.6.tar.gz", hash = "sha256:81da9eb75a1cdbe050eaa421fbe4c1e035be9f5f05c154ec667a2ec711839bc5"},
 ]
 
 [package.dependencies]
@@ -2268,7 +2321,7 @@ jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = {version = ">=4.0.0", extras = ["format"]}
 linkml-dataops = "*"
-linkml-runtime = "1.8.0"
+linkml-runtime = ">=1.8.1,<2.0.0"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
@@ -2282,12 +2335,14 @@ pyyaml = "*"
 rdflib = ">=6.0.0"
 requests = ">=2.22"
 sqlalchemy = ">=1.4.31"
+typing-extensions = {version = ">=4.6.0", markers = "python_version < \"3.12\""}
 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)"]
+tests = ["black (>=24.0.0)", "numpydantic (>=1.6.1)", "pyshacl (>=0.25.0,<0.26.0)"]
 
 [[package]]
 name = "linkml-dataops"
@@ -2326,13 +2381,13 @@ pydantic = "*"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.8.0"
+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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+    {file = "linkml_runtime-1.8.3.tar.gz", hash = "sha256:5b7f682eef54aaf0a59c50eeacdb11463b43b124a044caf496cde59936ac05c8"},
 ]
 
 [package.dependencies]
@@ -2352,21 +2407,22 @@ requests = "*"
 
 [[package]]
 name = "llm"
-version = "0.15"
+version = "0.20"
 description = "A CLI utility and Python library for interacting with Large Language Models, including OpenAI, PaLM and local models installed on your own machine."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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+    {file = "llm-0.20.tar.gz", hash = "sha256:7f185db83d9e433923fe78fdd4ce4923952fb2c642273e3c099c03b0b48c1ad5"},
 ]
 
 [package.dependencies]
 click = "*"
 click-default-group = ">=1.2.3"
-openai = ">=1.0"
+openai = ">=1.55.3"
 pip = "*"
 pluggy = "*"
+puremagic = "*"
 pydantic = ">=1.10.2"
 pyreadline3 = {version = "*", markers = "sys_platform == \"win32\""}
 python-ulid = "*"
@@ -2376,153 +2432,153 @@ sqlite-migrate = ">=0.1a2"
 sqlite-utils = ">=3.37"
 
 [package.extras]
-test = ["black (>=24.1.0)", "cogapp", "mypy (>=1.10.0)", "numpy", "pytest", "pytest-httpx", "ruff", "types-PyYAML", "types-click", "types-setuptools"]
+test = ["black (>=24.1.0)", "cogapp", "mypy (>=1.10.0)", "numpy", "pytest", "pytest-asyncio", "pytest-httpx (>=0.33.0)", "ruff", "types-PyYAML", "types-click", "types-setuptools"]
 
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 name = "lxml"
-version = "5.2.2"
+version = "5.3.0"
 description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
 optional = false
 python-versions = ">=3.6"
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 htmlsoup = ["BeautifulSoup4"]
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 [[package]]
 name = "markdown-it-py"
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 [[package]]
@@ -2659,13 +2721,13 @@ traitlets = "*"
 
 [[package]]
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+version = "0.4.2"
 description = "Collection of plugins for markdown-it-py"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2687,75 +2749,19 @@ files = [
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-optional = false
-python-versions = ">=3.6"
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-]
-
 [[package]]
 name = "mistune"
-version = "3.0.2"
+version = "3.1.1"
 description = "A sane and fast Markdown parser with useful plugins and renderers"
 optional = false
-python-versions = ">=3.7"
-files = [
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-    {file = "mistune-3.0.2.tar.gz", hash = "sha256:fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8"},
-]
-
-[[package]]
-name = "mkdocs"
-version = "1.6.0"
-description = "Project documentation with Markdown."
-optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "mkdocs-1.6.0-py3-none-any.whl", hash = "sha256:1eb5cb7676b7d89323e62b56235010216319217d4af5ddc543a91beb8d125ea7"},
-    {file = "mkdocs-1.6.0.tar.gz", hash = "sha256:a73f735824ef83a4f3bcb7a231dcab23f5a838f88b7efc54a0eef5fbdbc3c512"},
+    {file = "mistune-3.1.1-py3-none-any.whl", hash = "sha256:02106ac2aa4f66e769debbfa028509a275069dcffce0dfa578edd7b991ee700a"},
+    {file = "mistune-3.1.1.tar.gz", hash = "sha256:e0740d635f515119f7d1feb6f9b192ee60f0cc649f80a8f944f905706a21654c"},
 ]
 
 [package.dependencies]
-click = ">=7.0"
-colorama = {version = ">=0.4", markers = "platform_system == \"Windows\""}
-ghp-import = ">=1.0"
-importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
-jinja2 = ">=2.11.1"
-markdown = ">=3.3.6"
-markupsafe = ">=2.0.1"
-mergedeep = ">=1.3.4"
-mkdocs-get-deps = ">=0.2.0"
-packaging = ">=20.5"
-pathspec = ">=0.11.1"
-pyyaml = ">=5.1"
-pyyaml-env-tag = ">=0.1"
-watchdog = ">=2.0"
-
-[package.extras]
-i18n = ["babel (>=2.9.0)"]
-min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.4)", "jinja2 (==2.11.1)", "markdown (==3.3.6)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "mkdocs-get-deps (==0.2.0)", "packaging (==20.5)", "pathspec (==0.11.1)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "watchdog (==2.0)"]
-
-[[package]]
-name = "mkdocs-get-deps"
-version = "0.2.0"
-description = "MkDocs extension that lists all dependencies according to a mkdocs.yml file"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "mkdocs_get_deps-0.2.0-py3-none-any.whl", hash = "sha256:2bf11d0b133e77a0dd036abeeb06dec8775e46efa526dc70667d8863eefc6134"},
-    {file = "mkdocs_get_deps-0.2.0.tar.gz", hash = "sha256:162b3d129c7fad9b19abfdcb9c1458a651628e4b1dea628ac68790fb3061c60c"},
-]
-
-[package.dependencies]
-importlib-metadata = {version = ">=4.3", markers = "python_version < \"3.10\""}
-mergedeep = ">=1.3.4"
-platformdirs = ">=2.2.0"
-pyyaml = ">=5.1"
+typing-extensions = {version = "*", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "more-click"
@@ -2776,24 +2782,13 @@ tests = ["coverage", "pytest"]
 
 [[package]]
 name = "more-itertools"
-version = "10.4.0"
+version = "10.6.0"
 description = "More routines for operating on iterables, beyond itertools"
 optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "more-itertools-10.4.0.tar.gz", hash = "sha256:fe0e63c4ab068eac62410ab05cccca2dc71ec44ba8ef29916a0090df061cf923"},
-    {file = "more_itertools-10.4.0-py3-none-any.whl", hash = "sha256:0f7d9f83a0a8dcfa8a2694a770590d98a67ea943e3d9f5298309a484758c4e27"},
-]
-
-[[package]]
-name = "multimethod"
-version = "1.10"
-description = "Multiple argument dispatching."
-optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "multimethod-1.10-py3-none-any.whl", hash = "sha256:afd84da9c3d0445c84f827e4d63ad42d17c6d29b122427c6dee9032ac2d2a0d4"},
-    {file = "multimethod-1.10.tar.gz", hash = "sha256:daa45af3fe257f73abb69673fd54ddeaf31df0eb7363ad6e1251b7c9b192d8c5"},
+    {file = "more-itertools-10.6.0.tar.gz", hash = "sha256:2cd7fad1009c31cc9fb6a035108509e6547547a7a738374f10bd49a09eb3ee3b"},
+    {file = "more_itertools-10.6.0-py3-none-any.whl", hash = "sha256:6eb054cb4b6db1473f6e15fcc676a08e4732548acd47c708f0e179c2c7c01e89"},
 ]
 
 [[package]]
@@ -2835,13 +2830,13 @@ testing-docutils = ["pygments", "pytest (>=8,<9)", "pytest-param-files (>=0.6.0,
 
 [[package]]
 name = "nbclient"
-version = "0.10.0"
+version = "0.10.2"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
 optional = false
-python-versions = ">=3.8.0"
+python-versions = ">=3.9.0"
 files = [
-    {file = "nbclient-0.10.0-py3-none-any.whl", hash = "sha256:f13e3529332a1f1f81d82a53210322476a168bb7090a0289c795fe9cc11c9d3f"},
-    {file = "nbclient-0.10.0.tar.gz", hash = "sha256:4b3f1b7dba531e498449c4db4f53da339c91d449dc11e9af3a43b4eb5c5abb09"},
+    {file = "nbclient-0.10.2-py3-none-any.whl", hash = "sha256:4ffee11e788b4a27fabeb7955547e4318a5298f34342a4bfd01f2e1faaeadc3d"},
+    {file = "nbclient-0.10.2.tar.gz", hash = "sha256:90b7fc6b810630db87a6d0c2250b1f0ab4cf4d3c27a299b0cde78a4ed3fd9193"},
 ]
 
 [package.dependencies]
@@ -2852,23 +2847,23 @@ traitlets = ">=5.4"
 
 [package.extras]
 dev = ["pre-commit"]
-docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling"]
-test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
+docs = ["autodoc-traits", "flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "mock", "moto", "myst-parser", "nbconvert (>=7.1.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling", "testpath", "xmltodict"]
+test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.1.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
 
 [[package]]
 name = "nbconvert"
-version = "7.16.4"
+version = "7.16.6"
 description = "Converting Jupyter Notebooks (.ipynb files) to other formats.  Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script.  nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "nbconvert-7.16.4-py3-none-any.whl", hash = "sha256:05873c620fe520b6322bf8a5ad562692343fe3452abda5765c7a34b7d1aa3eb3"},
-    {file = "nbconvert-7.16.4.tar.gz", hash = "sha256:86ca91ba266b0a448dc96fa6c5b9d98affabde2867b363258703536807f9f7f4"},
+    {file = "nbconvert-7.16.6-py3-none-any.whl", hash = "sha256:1375a7b67e0c2883678c48e506dc320febb57685e5ee67faa51b18a90f3a712b"},
+    {file = "nbconvert-7.16.6.tar.gz", hash = "sha256:576a7e37c6480da7b8465eefa66c17844243816ce1ccc372633c6b71c3c0f582"},
 ]
 
 [package.dependencies]
 beautifulsoup4 = "*"
-bleach = "!=5.0.0"
+bleach = {version = "!=5.0.0", extras = ["css"]}
 defusedxml = "*"
 importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
 jinja2 = ">=3.0"
@@ -2881,7 +2876,6 @@ nbformat = ">=5.7"
 packaging = "*"
 pandocfilters = ">=1.4.1"
 pygments = ">=2.4.1"
-tinycss2 = "*"
 traitlets = ">=5.1"
 
 [package.extras]
@@ -2916,13 +2910,13 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
 
 [[package]]
 name = "ndex2"
-version = "3.9.0"
+version = "3.10.0"
 description = "Nice CX Python includes a client and a data model."
 optional = false
 python-versions = "*"
 files = [
-    {file = "ndex2-3.9.0-py2.py3-none-any.whl", hash = "sha256:168a6ed3209f2c9596752897fe535599b11f87305c10d55446bf8ffef4762283"},
-    {file = "ndex2-3.9.0.tar.gz", hash = "sha256:388b2f110b2eb1ba787298bc4210ca0cea821c462ec71a4ec4cb6eb0e1b74f70"},
+    {file = "ndex2-3.10.0-py2.py3-none-any.whl", hash = "sha256:fdb8307ccdbdf49044c9119373852242ca24a4926df1c5566e94965e59b70b67"},
+    {file = "ndex2-3.10.0.tar.gz", hash = "sha256:7e8cfc3fc940cddfd612810fc8c913ab61e01a43e4f482608e86c6548b81b7e1"},
 ]
 
 [package.dependencies]
@@ -2966,18 +2960,18 @@ test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "notebook"
-version = "7.2.1"
+version = "7.3.2"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "notebook-7.2.1-py3-none-any.whl", hash = "sha256:f45489a3995746f2195a137e0773e2130960b51c9ac3ce257dbc2705aab3a6ca"},
-    {file = "notebook-7.2.1.tar.gz", hash = "sha256:4287b6da59740b32173d01d641f763d292f49c30e7a51b89c46ba8473126341e"},
+    {file = "notebook-7.3.2-py3-none-any.whl", hash = "sha256:e5f85fc59b69d3618d73cf27544418193ff8e8058d5bf61d315ce4f473556288"},
+    {file = "notebook-7.3.2.tar.gz", hash = "sha256:705e83a1785f45b383bf3ee13cb76680b92d24f56fb0c7d2136fe1d850cd3ca8"},
 ]
 
 [package.dependencies]
 jupyter-server = ">=2.4.0,<3"
-jupyterlab = ">=4.2.0,<4.3"
+jupyterlab = ">=4.3.4,<4.4"
 jupyterlab-server = ">=2.27.1,<3"
 notebook-shim = ">=0.2,<0.3"
 tornado = ">=6.2.0"
@@ -3006,13 +3000,13 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync"
 
 [[package]]
 name = "num2words"
-version = "0.5.13"
+version = "0.5.14"
 description = "Modules to convert numbers to words. Easily extensible."
 optional = false
 python-versions = "*"
 files = [
-    {file = "num2words-0.5.13-py3-none-any.whl", hash = "sha256:39e662c663f0a7e15415431ea68eb3dc711b49e3b776d93403e1da0a219ca4ee"},
-    {file = "num2words-0.5.13.tar.gz", hash = "sha256:a3064716fbbf90d75c449450cebfbc73a6a13e63b2531d09bdecc3ab1a2209cf"},
+    {file = "num2words-0.5.14-py3-none-any.whl", hash = "sha256:1c8e5b00142fc2966fd8d685001e36c4a9911e070d1b120e1beb721fa1edb33d"},
+    {file = "num2words-0.5.14.tar.gz", hash = "sha256:b066ec18e56b6616a3b38086b5747daafbaa8868b226a36127e0451c0cf379c6"},
 ]
 
 [package.dependencies]
@@ -3065,13 +3059,13 @@ files = [
 
 [[package]]
 name = "oaklib"
-version = "0.6.14"
+version = "0.6.19"
 description = "Ontology Access Kit: Python library for common ontology operations over a variety of backends"
 optional = false
 python-versions = "<4.0.0,>=3.9"
 files = [
-    {file = "oaklib-0.6.14-py3-none-any.whl", hash = "sha256:addd99b50d8123867d09c1012b4c6a82096bec8b2d584567b70f02b000b32977"},
-    {file = "oaklib-0.6.14.tar.gz", hash = "sha256:53e53551a1ae63d8df3323627b17ef54b975640422a0a9234f34effebf5c47d4"},
+    {file = "oaklib-0.6.19-py3-none-any.whl", hash = "sha256:8b31cacfc525d00b66bf5953a7b3dfbae000b3d115ec9c4e4aad51b49a577840"},
+    {file = "oaklib-0.6.19.tar.gz", hash = "sha256:6ce85ddc5076e1a5f5e2a56a80e85eb712817052d61eb174cabc2bffe05561a2"},
 ]
 
 [package.dependencies]
@@ -3085,7 +3079,7 @@ eutils = ">=0.6.0"
 funowl = ">=0.2.0"
 jsonlines = "*"
 kgcl-rdflib = "0.5.0"
-kgcl-schema = ">=0.6.8,<0.7.0"
+kgcl-schema = ">=0.6.9,<0.7.0"
 linkml-renderer = ">=0.3.0"
 linkml-runtime = ">=1.5.3"
 ndex2 = ">=3.5.0"
@@ -3108,7 +3102,7 @@ tenacity = ">=8.2.3"
 [package.extras]
 gilda = ["gilda (>=1.0.0)", "urllib3 (<2)"]
 llm = ["aiohttp", "html2text", "llm (>=0.14,<0.15)"]
-semsimian = ["semsimian (>=0.2.16)"]
+semsimian = ["semsimian (>=0.2.18)"]
 
 [[package]]
 name = "oauthlib"
@@ -3190,13 +3184,13 @@ tests = ["coverage", "pytest", "unittest-templates"]
 
 [[package]]
 name = "openai"
-version = "1.40.2"
+version = "1.60.2"
 description = "The official Python library for the openai API"
 optional = false
-python-versions = ">=3.7.1"
+python-versions = ">=3.8"
 files = [
-    {file = "openai-1.40.2-py3-none-any.whl", hash = "sha256:38068f858f310b4fd4b0ea8734c3efcfde3c15a2978311e1453bd84817231b96"},
-    {file = "openai-1.40.2.tar.gz", hash = "sha256:2180e9070bd36084328248b3ce668964e8ddd2e9019e1d426e31dc54cc117bb5"},
+    {file = "openai-1.60.2-py3-none-any.whl", hash = "sha256:993bd11b96900b9098179c728026f016b4982ded7ee30dfcf4555eab1171fff9"},
+    {file = "openai-1.60.2.tar.gz", hash = "sha256:a8f843e10f2855713007f491d96afb2694b11b5e02cb97c7d01a0be60bc5bb51"},
 ]
 
 [package.dependencies]
@@ -3211,6 +3205,7 @@ typing-extensions = ">=4.11,<5"
 
 [package.extras]
 datalib = ["numpy (>=1)", "pandas (>=1.2.3)", "pandas-stubs (>=1.1.0.11)"]
+realtime = ["websockets (>=13,<15)"]
 
 [[package]]
 name = "openpyxl"
@@ -3239,51 +3234,64 @@ files = [
 
 [[package]]
 name = "packaging"
-version = "24.1"
+version = "24.2"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"},
+    {file = "packaging-24.2-py3-none-any.whl", hash = "sha256:09abb1bccd265c01f4a3aa3f7a7db064b36514d2cba19a2f694fe6150451a759"},
+    {file = "packaging-24.2.tar.gz", hash = "sha256:c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f"},
 ]
 
 [[package]]
 name = "pandas"
-version = "2.2.2"
+version = "2.2.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.9"
 files = [
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+    {file = "pandas-2.2.3.tar.gz", hash = "sha256:4f18ba62b61d7e192368b84517265a99b4d7ee8912f8708660fb4a366cc82667"},
 ]
 
 [package.dependencies]
@@ -3323,27 +3331,25 @@ xml = ["lxml (>=4.9.2)"]
 
 [[package]]
 name = "pandera"
-version = "0.20.3"
+version = "0.22.1"
 description = "A light-weight and flexible data validation and testing tool for statistical data objects."
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "pandera-0.22.1.tar.gz", hash = "sha256:091ebc353383ba642e5a20ee0df763ed2059ab99cb4b2ac3e83f482de8493645"},
 ]
 
 [package.dependencies]
-multimethod = "<=1.10.0"
 numpy = ">=1.19.0"
 packaging = ">=20.0"
 pandas = ">=1.2.0"
 pydantic = "*"
 typeguard = "*"
-typing-inspect = ">=0.6.0"
-wrapt = "*"
+typing_inspect = ">=0.6.0"
 
 [package.extras]
-all = ["black", "dask[dataframe]", "fastapi", "frictionless (<=4.40.8)", "geopandas", "hypothesis (>=6.92.7)", "modin", "pandas-stubs", "polars (>=0.20.0)", "pyspark (>=3.2.0)", "pyyaml (>=5.1)", "ray", "scipy", "shapely"]
+all = ["black", "dask[dataframe]", "fastapi", "frictionless (<=4.40.8)", "geopandas", "hypothesis (>=6.92.7)", "modin", "pandas-stubs", "polars (>=0.20.0)", "pyspark[connect] (>=3.2.0)", "pyyaml (>=5.1)", "ray", "scipy", "shapely"]
 dask = ["dask[dataframe]"]
 fastapi = ["fastapi"]
 geopandas = ["geopandas", "shapely"]
@@ -3354,7 +3360,7 @@ modin-dask = ["dask[dataframe]", "modin"]
 modin-ray = ["modin", "ray"]
 mypy = ["pandas-stubs"]
 polars = ["polars (>=0.20.0)"]
-pyspark = ["pyspark (>=3.2.0)"]
+pyspark = ["pyspark[connect] (>=3.2.0)"]
 strategies = ["hypothesis (>=6.92.7)"]
 
 [[package]]
@@ -3410,17 +3416,6 @@ files = [
 qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
 testing = ["docopt", "pytest"]
 
-[[package]]
-name = "pathspec"
-version = "0.12.1"
-description = "Utility library for gitignore style pattern matching of file paths."
-optional = false
-python-versions = ">=3.8"
-files = [
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-]
-
 [[package]]
 name = "pexpect"
 version = "4.9.0"
@@ -3437,30 +3432,30 @@ ptyprocess = ">=0.5"
 
 [[package]]
 name = "pip"
-version = "24.2"
+version = "25.0"
 description = "The PyPA recommended tool for installing Python packages."
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "pip-24.2.tar.gz", hash = "sha256:5b5e490b5e9cb275c879595064adce9ebd31b854e3e803740b72f9ccf34a45b8"},
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 ]
 
 [[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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+    {file = "platformdirs-4.3.6.tar.gz", hash = "sha256:357fb2acbc885b0419afd3ce3ed34564c13c9b95c89360cd9563f73aa5e2b907"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
-type = ["mypy (>=1.8)"]
+docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)"]
+type = ["mypy (>=1.11.2)"]
 
 [[package]]
 name = "pluggy"
@@ -3507,13 +3502,13 @@ 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"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
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-    {file = "prefixmaps-0.2.5.tar.gz", hash = "sha256:aaccd2425ade2ea97a502c58be49fe8f3536e3d5e919712ae0358a39fc800799"},
+    {file = "prefixmaps-0.2.6-py3-none-any.whl", hash = "sha256:f6cef28a7320fc6337cf411be212948ce570333a0ce958940ef684c7fb192a62"},
+    {file = "prefixmaps-0.2.6.tar.gz", hash = "sha256:7421e1244eea610217fa1ba96c9aebd64e8162a930dc0626207cd8bf62ecf4b9"},
 ]
 
 [package.dependencies]
@@ -3522,13 +3517,13 @@ pyyaml = ">=5.3.1"
 
 [[package]]
 name = "prometheus-client"
-version = "0.20.0"
+version = "0.21.1"
 description = "Python client for the Prometheus monitoring system."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "prometheus_client-0.20.0-py3-none-any.whl", hash = "sha256:cde524a85bce83ca359cc837f28b8c0db5cac7aa653a588fd7e84ba061c329e7"},
-    {file = "prometheus_client-0.20.0.tar.gz", hash = "sha256:287629d00b147a32dcb2be0b9df905da599b2d82f80377083ec8463309a4bb89"},
+    {file = "prometheus_client-0.21.1-py3-none-any.whl", hash = "sha256:594b45c410d6f4f8888940fe80b5cc2521b305a1fafe1c58609ef715a001f301"},
+    {file = "prometheus_client-0.21.1.tar.gz", hash = "sha256:252505a722ac04b0456be05c05f75f45d760c2911ffc45f2a06bcaed9f3ae3fb"},
 ]
 
 [package.extras]
@@ -3536,13 +3531,13 @@ twisted = ["twisted"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.47"
+version = "3.0.50"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
-python-versions = ">=3.7.0"
+python-versions = ">=3.8.0"
 files = [
-    {file = "prompt_toolkit-3.0.47-py3-none-any.whl", hash = "sha256:0d7bfa67001d5e39d02c224b663abc33687405033a8c422d0d675a5a13361d10"},
-    {file = "prompt_toolkit-3.0.47.tar.gz", hash = "sha256:1e1b29cb58080b1e69f207c893a1a7bf16d127a5c30c9d17a25a5d77792e5360"},
+    {file = "prompt_toolkit-3.0.50-py3-none-any.whl", hash = "sha256:9b6427eb19e479d98acff65196a307c555eb567989e6d88ebbb1b509d9779198"},
+    {file = "prompt_toolkit-3.0.50.tar.gz", hash = "sha256:544748f3860a2623ca5cd6d2795e7a14f3d0e1c3c9728359013f79877fc89bab"},
 ]
 
 [package.dependencies]
@@ -3550,13 +3545,13 @@ wcwidth = "*"
 
 [[package]]
 name = "pronto"
-version = "2.5.7"
+version = "2.5.8"
 description = "Python frontend to ontologies."
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.extras]
 tests = ["pytest"]
 
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 ]
 
 [package.dependencies]
@@ -3898,13 +3909,13 @@ typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
 
 [[package]]
 name = "pydbml"
-version = "1.1.2"
+version = "1.1.3"
 description = "Python parser and builder for DBML"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -3912,13 +3923,13 @@ pyparsing = ">=3.0.0"
 
 [[package]]
 name = "pygments"
-version = "2.18.0"
+version = "2.19.1"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -3941,13 +3952,13 @@ jsonasobj = ">=1.2.1"
 
 [[package]]
 name = "pyparsing"
-version = "3.1.2"
+version = "3.2.1"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
-python-versions = ">=3.6.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
@@ -3955,15 +3966,18 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyreadline3"
-version = "3.4.1"
+version = "3.5.4"
 description = "A python implementation of GNU readline."
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
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 ]
 
+[package.extras]
+dev = ["build", "flake8", "mypy", "pytest", "twine"]
+
 [[package]]
 name = "pyshex"
 version = "0.8.1"
@@ -4007,53 +4021,55 @@ shexjsg = ">=0.8.1"
 
 [[package]]
 name = "pysolr"
-version = "3.9.0"
+version = "3.10.0"
 description = "Lightweight Python client for Apache Solr"
 optional = false
 python-versions = "*"
 files = [
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+    {file = "pysolr-3.10.0.tar.gz", hash = "sha256:127b4a2dd169234acb1586643a6cd1e3e94b917921e69bf569d7b2a2aa0ef409"},
 ]
 
 [package.dependencies]
 requests = ">=2.9.1"
+setuptools = "*"
 
 [package.extras]
 solrcloud = ["kazoo (>=2.5.0)"]
 
 [[package]]
 name = "pystow"
-version = "0.5.4"
-description = "Easily pick a place to store data for your python package."
+version = "0.7.0"
+description = "Easily pick a place to store data for your Python code"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
 click = "*"
 requests = "*"
 tqdm = "*"
+typing-extensions = "*"
 
 [package.extras]
 aws = ["boto3"]
-docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
+docs = ["sphinx (>=8)", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme (>=3.0)"]
 pandas = ["pandas"]
 rdf = ["rdflib"]
-tests = ["coverage", "pytest", "requests-file"]
+tests = ["coverage[toml]", "pytest", "requests-file"]
 xml = ["lxml"]
 
 [[package]]
 name = "pytest"
-version = "8.3.2"
+version = "8.3.4"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "pytest-8.3.2.tar.gz", hash = "sha256:c132345d12ce551242c87269de812483f5bcc87cdbb4722e48487ba194f9fdce"},
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+    {file = "pytest-8.3.4.tar.gz", hash = "sha256:965370d062bce11e73868e0335abac31b4d3de0e82f4007408d242b4f8610761"},
 ]
 
 [package.dependencies]
@@ -4096,24 +4112,30 @@ six = ">=1.5"
 
 [[package]]
 name = "python-json-logger"
-version = "2.0.7"
-description = "A python library adding a json log formatter"
+version = "3.2.1"
+description = "JSON Log Formatter for the Python Logging Package"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "python-json-logger-2.0.7.tar.gz", hash = "sha256:23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c"},
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 ]
 
 [[package]]
@@ -4930,19 +4898,23 @@ win32 = ["pywin32"]
 
 [[package]]
 name = "setuptools"
-version = "72.1.0"
+version = "75.8.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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-    {file = "setuptools-72.1.0.tar.gz", hash = "sha256:8d243eff56d095e5817f796ede6ae32941278f542e0f941867cc05ae52b162ec"},
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 ]
 
 [package.extras]
-core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "ordered-set (>=3.1.1)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
-doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.8.0)"]
+core = ["importlib_metadata (>=6)", "jaraco.collections", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more_itertools", "more_itertools (>=8.8)", "packaging", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.7.2)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"]
+type = ["importlib_metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.14.*)", "pytest-mypy"]
 
 [[package]]
 name = "shexjsg"
@@ -4960,13 +4932,13 @@ pyjsg = ">=0.11.10"
 
 [[package]]
 name = "six"
-version = "1.16.0"
+version = "1.17.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
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+    {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
 ]
 
 [[package]]
@@ -5004,13 +4976,13 @@ files = [
 
 [[package]]
 name = "soupsieve"
-version = "2.5"
+version = "2.6"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "soupsieve-2.5-py3-none-any.whl", hash = "sha256:eaa337ff55a1579b6549dc679565eac1e3d000563bcb1c8ab0d0fefbc0c2cdc7"},
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+    {file = "soupsieve-2.6-py3-none-any.whl", hash = "sha256:e72c4ff06e4fb6e4b5a9f0f55fe6e81514581fca1515028625d0f299c602ccc9"},
+    {file = "soupsieve-2.6.tar.gz", hash = "sha256:e2e68417777af359ec65daac1057404a3c8a5455bb8abc36f1a9866ab1a51abb"},
 ]
 
 [[package]]
@@ -5103,12 +5075,12 @@ sphinx = ">=4.0"
 
 [[package]]
 name = "sphinx-pdj-theme"
-version = "0.4.0"
+version = "0.5.0"
 description = "A cool theme for sphinx documentation"
 optional = false
 python-versions = "*"
 files = [
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+[package.dependencies]
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+sphinx = "*"
+
+[package.extras]
+test = ["defusedxml", "myst-parser", "pytest", "ruff", "sphinx"]
+
 [[package]]
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 version = "2.0.0"
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+]
+
+[package.dependencies]
+greenlet = {version = "!=0.4.17", markers = "python_version < \"3.14\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"}
 typing-extensions = ">=4.6.0"
 
 [package.extras]
@@ -5284,7 +5271,7 @@ aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
 aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
 asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
-mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5,!=1.1.10)"]
 mssql = ["pyodbc"]
 mssql-pymssql = ["pymssql"]
 mssql-pyodbc = ["pyodbc"]
@@ -5364,13 +5351,13 @@ test = ["black", "mypy", "pytest", "ruff"]
 
 [[package]]
 name = "sqlite-utils"
-version = "3.37"
+version = "3.38"
 description = "CLI tool and Python library for manipulating SQLite databases"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -5390,13 +5377,13 @@ tui = ["trogon"]
 
 [[package]]
 name = "sssom"
-version = "0.4.11"
+version = "0.4.15"
 description = "Operations on SSSOM mapping tables"
 optional = false
-python-versions = "<4.0,>=3.8"
+python-versions = "<4.0.0,>=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -5404,6 +5391,7 @@ click = ">=8.1.6"
 curies = ">=0.7.3"
 deprecation = ">=2.1.0,<3.0.0"
 importlib-resources = ">=6.1.1,<7.0.0"
+linkml = ">1.7.10"
 linkml-runtime = ">=1.7.5,<2.0.0"
 networkx = {version = ">=3.1", extras = ["networkx"]}
 pandas = ">1.0.3"
@@ -5412,18 +5400,18 @@ pyyaml = ">=6.0.1,<7.0.0"
 rdflib = ">=6.0.0"
 scipy = {version = "*", extras = ["scipy"]}
 sparqlwrapper = ">=2.0.0"
-sssom-schema = ">=0.15.2,<0.16.0"
+sssom-schema = ">=1.0.0,<2.0.0"
 validators = ">=0.20.0"
 
 [[package]]
 name = "sssom-schema"
-version = "0.15.2"
+version = "1.0.0"
 description = "SSSOM is a Simple Standard for Sharing Ontology Mappings."
 optional = false
-python-versions = "<4.0,>=3.8"
+python-versions = "<4.0.0,>=3.8.1"
 files = [
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 ]
 
 [package.dependencies]
@@ -5490,13 +5478,13 @@ test = ["pytest", "tornado (>=4.5)", "typeguard"]
 
 [[package]]
 name = "termcolor"
-version = "2.4.0"
+version = "2.5.0"
 description = "ANSI color formatting for output in terminal"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
@@ -5525,13 +5513,13 @@ typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"]
 
 [[package]]
 name = "tinycss2"
-version = "1.3.0"
+version = "1.4.0"
 description = "A tiny CSS parser"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -5543,62 +5531,93 @@ test = ["pytest", "ruff"]
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.2.1"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "tomlkit"
-version = "0.13.0"
+version = "0.13.2"
 description = "Style preserving TOML library"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "tornado"
-version = "6.4.1"
+version = "6.4.2"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 optional = false
 python-versions = ">=3.8"
 files = [
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 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+dev = ["nbval", "pytest (>=6)", "pytest-asyncio (>=0.24)", "pytest-cov", "pytest-timeout"]
+discord = ["requests"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
@@ -5620,13 +5639,13 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 
 [[package]]
 name = "typeguard"
-version = "4.3.0"
+version = "4.4.1"
 description = "Run-time type checker for Python"
 optional = false
-python-versions = ">=3.8"
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 files = [
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 [package.dependencies]
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 [[package]]
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 [[package]]
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 [[package]]
 name = "tzdata"
-version = "2024.1"
+version = "2025.1"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
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 ]
 
 [[package]]
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 [[package]]
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+version = "2.3.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
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 [package.extras]
@@ -5743,13 +5762,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "validators"
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+version = "0.34.0"
 description = "Python Data Validation for Humans™"
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 python-versions = ">=3.8"
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 [package.extras]
@@ -5757,43 +5776,41 @@ crypto-eth-addresses = ["eth-hash[pycryptodome] (>=0.7.0)"]
 
 [[package]]
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 description = "Filesystem events monitoring"
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+    {file = "wrapt-1.17.2.tar.gz", hash = "sha256:41388e9d4d1522446fe79d3213196bd9e3b301a336965b9e27ca2788ebd122f3"},
 ]
 
 [[package]]
 name = "zipp"
-version = "3.19.2"
+version = "3.21.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 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-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"},
+    {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"},
 ]
 
 [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"]
 
 [extras]
 docs = []
-mariadb = []
+mariadb = ["mariadb"]
+postgres = ["psycopg2-binary"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "bf523e82bb08caf05eb970b29b6a68e01a536a14ac38257d27756b869d38f4fe"
+content-hash = "19ed43bf987b6bf44ed6117dd8ffbd77dd1749812f6bf4de6513d1a0969308a5"
diff --git a/pyproject.toml b/pyproject.toml
index 745879f..2abfc12 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,14 +33,12 @@ packages = [
 [tool.poetry.dependencies]
 python = "^3.9"
 linkml = "^1.7.4"
-mkdocs = ">=1.2.3"
 pandas = ">=1.3.5"
 python-dateutil = ">=2.8.2"
-jsonpatch = ">=1.32"
 quantulum3 = ">=0.7.9"
 funowl = ">=0.2.3"
 click-log = ">=0.4.0"
-psycopg2-binary = "^2.9.2"
+psycopg2-binary = { version = "^2.9.2", optional = true }
 strsimpy = ">=0.2.1"
 requests = ">=2.26.0"
 oaklib = ">=0.5.25"
@@ -48,10 +46,16 @@ pandera = ">=0.12.0"
 tomlkit = ">=0.11.4"
 inflect = ">=6.0.0"
 schemasheets = ">=0.1.24"
-xmltodict = "^0.13.0"
-click-default-group = "^1.2.4"
 linkml-runtime = "^1.7.2"
-duckdb = "^0.10.1"
+duckdb = { version = "^0.10.1", optional = true }
+click = "^8.1.7"
+deprecated = "^1.2.15"
+mariadb = {version = "^1.1.11", optional = true}
+sqlalchemy = "^2.0.36"
+ruamel-yaml = "^0.18.6"
+rdflib = "^7.1.1"
+jsonasobj2 = "^1.0.4"
+deprecation = "^2.1.0"
 numpy = "<2.0"
 pydbml = "^1.1.2"
 
@@ -84,6 +88,7 @@ extract-schema = "schema_automator.utils.schema_extractor:cli"
 [tool.poetry.extras]
 docs = ["Sphinx", "sphinx-pdj-theme", "sphinxcontrib-mermaid"]
 mariadb = ["mariadb"]
+postgres = ["psycopg2-binary"]
 
 [tool.codespell]
 # Ref: https://github.com/codespell-project/codespell#using-a-config-file
diff --git a/schema_automator/cli.py b/schema_automator/cli.py
index bd76320..780d0b3 100644
--- a/schema_automator/cli.py
+++ b/schema_automator/cli.py
@@ -473,7 +473,7 @@ def import_owl(owlfile, output, **args):
 @click.argument('rdfsfile')
 @output_option
 @schema_name_option
-@click.option('--input-type', '-I',
+@click.option('--format', '-f',
               default='turtle',
               help="Input format, eg. turtle")
 @click.option('--identifier', '-I', help="Slot to use as identifier")
@@ -481,7 +481,7 @@ def import_owl(owlfile, output, **args):
 @click.option('--metamodel-mappings',
               help="Path to metamodel mappings YAML dictionary")
 @click.option('--output', '-o', help="Path to saved yaml schema")
-def import_rdfs(rdfsfile, output, metamodel_mappings, **args):
+def import_rdfs(rdfsfile: str, output: str, metamodel_mappings: str, schema_name: str, **args):
     """
     Import an RDFS schema to LinkML
 
@@ -494,7 +494,7 @@ def import_rdfs(rdfsfile, output, metamodel_mappings, **args):
         with open(metamodel_mappings) as f:
             mappings_obj = yaml.safe_load(f)
     sie = RdfsImportEngine(initial_metamodel_mappings=mappings_obj)
-    schema = sie.convert(rdfsfile, **args)
+    schema = sie.convert(rdfsfile, name=schema_name, **args)
     write_schema(schema, output)
 
 @main.command()
diff --git a/schema_automator/importers/rdfs_import_engine.py b/schema_automator/importers/rdfs_import_engine.py
index 3abc4cb..b2e17c9 100644
--- a/schema_automator/importers/rdfs_import_engine.py
+++ b/schema_automator/importers/rdfs_import_engine.py
@@ -1,32 +1,35 @@
 import logging
-from typing import Dict, List, Any
-from collections import defaultdict
+from pathlib import Path
+from typing import Dict, Iterable, List, Any, Mapping, TextIO
+import typing
+from collections import defaultdict, Counter
 
+from jsonasobj2 import JsonObj
 from linkml.utils.schema_builder import SchemaBuilder
 from linkml_runtime import SchemaView
 from linkml_runtime.linkml_model import (
     SchemaDefinition,
     SlotDefinition,
     ClassDefinition,
+    Prefix,
 )
-from funowl.converters.functional_converter import to_python
-from funowl import *
 
 from dataclasses import dataclass, field
 
 from linkml_runtime.utils.formatutils import underscore
 from linkml_runtime.utils.introspection import package_schemaview
-from rdflib import Graph, RDF, OWL, URIRef, RDFS, SKOS, SDO, Namespace
+from rdflib import Graph, RDF, OWL, URIRef, RDFS, SKOS, SDO, Namespace, Literal
 from schema_automator.importers.import_engine import ImportEngine
-from schema_automator.utils.schemautils import write_schema
 
 
 HTTP_SDO = Namespace("http://schema.org/")
 
-DEFAULT_METAMODEL_MAPPINGS = {
+DEFAULT_METAMODEL_MAPPINGS: Dict[str, List[URIRef]] = {
+    # See https://github.com/linkml/linkml/issues/2507
+    "description": [RDFS.comment],
     "is_a": [RDFS.subClassOf, SKOS.broader],
-    "domain_of": [HTTP_SDO.domainIncludes, SDO.domainIncludes],
-    "rangeIncludes": [HTTP_SDO.rangeIncludes, SDO.rangeIncludes],
+    "domain_of": [HTTP_SDO.domainIncludes, SDO.domainIncludes, RDFS.domain],
+    "range": [HTTP_SDO.rangeIncludes, SDO.rangeIncludes, RDFS.range],
     "exact_mappings": [OWL.sameAs, HTTP_SDO.sameAs],
     ClassDefinition.__name__: [RDFS.Class, OWL.Class, SKOS.Concept],
     SlotDefinition.__name__: [
@@ -43,22 +46,30 @@ class RdfsImportEngine(ImportEngine):
     """
     An ImportEngine that takes RDFS and converts it to a LinkML schema
     """
-
-    mappings: dict = None
-    initial_metamodel_mappings: Dict[str, List[URIRef]] = None
-    metamodel_mappings: Dict[str, List[URIRef]] = None
-    reverse_metamodel_mappings: Dict[URIRef, List[str]] = None
-    include_unmapped_annotations = False
-    metamodel = None
-    metamodel_schemaview: SchemaView = None
-    classdef_slots: List[str] = None
+    #: View over the LinkML metamodel
+    metamodel: SchemaView = field(init=False)
+    #: Mapping from field names in this RDF schema (e.g. `price`) to IRIs (e.g. `http://schema.org/price`)
+    mappings: Dict[str, URIRef] = field(default_factory=dict)
+    #: User-defined mapping from LinkML metamodel slots (such as `domain_of`) to RDFS IRIs (such as http://schema.org/domainIncludes)
+    initial_metamodel_mappings: Dict[str, URIRef | List[URIRef]] = field(default_factory=dict)
+    #: Combined mapping from LinkML metamodel slots to RDFS IRIs
+    metamodel_mappings: Dict[str, List[URIRef]] = field(default_factory=lambda: defaultdict(list))
+    #: Reverse of `metamodel_mappings`, but supports multiple terms mapping to the same IRI
+    reverse_metamodel_mappings: Dict[URIRef, List[str]] = field(default_factory=lambda: defaultdict(list))
+    #: The names of LinkML ClassDefinition slots
+    classdef_slots: set[str] = field(init=False)
+    #: The names of LinkML SlotDefinition slots
+    slotdef_slots: set[str] = field(init=False)
+    #: Every prefix seen in the graph
+    seen_prefixes: set[str] = field(default_factory=set)
+    #: The counts of each prefix, used to infer the default prefix
+    prefix_counts: Counter[str] = field(default_factory=Counter)
 
     def __post_init__(self):
         sv = package_schemaview("linkml_runtime.linkml_model.meta")
-        self.metamodel_schemaview = sv
         self.metamodel = sv
-        self.metamodel_mappings = defaultdict(list)
-        self.reverse_metamodel_mappings = defaultdict(list)
+
+        # Populate the combined metamodel mappings
         for k, vs in DEFAULT_METAMODEL_MAPPINGS.items():
             self.metamodel_mappings[k].extend(vs)
             for v in vs:
@@ -71,6 +82,8 @@ def __post_init__(self):
                 for v in vs:
                     self.reverse_metamodel_mappings[URIRef(v)].append(k)
                     logging.info(f"Adding mapping {k} -> {v}")
+
+        # LinkML fields have some built-in mappings to other ontologies, such as https://w3id.org/linkml/Any -> AnyValue
         for e in sv.all_elements().values():
             mappings = []
             for ms in sv.get_mappings(e.name, expand=True).values():
@@ -79,116 +92,207 @@ def __post_init__(self):
                     mappings.append(uri)
                     self.reverse_metamodel_mappings[uri].append(e.name)
             self.metamodel_mappings[e.name] = mappings
-        self.defclass_slots = [s.name for s in sv.class_induced_slots(ClassDefinition.class_name)]
+        self.classdef_slots = {s.name for s in sv.class_induced_slots(ClassDefinition.class_name)}
+        self.slotdef_slots = {s.name for s in sv.class_induced_slots(SlotDefinition.class_name)}
 
     def convert(
         self,
-        file: str,
-        name: str = None,
-        format="turtle",
-        default_prefix: str = None,
-        model_uri: str = None,
-        identifier: str = None,
-        **kwargs,
+        file: str | Path | TextIO,
+        name: str | None = None,
+        format: str | None="turtle",
+        default_prefix: str | None = None,
+        model_uri: str | None = None,
+        identifier: str | None = None,
+        **kwargs: Any,
     ) -> SchemaDefinition:
         """
         Converts an OWL schema-style ontology
-
-        :param file:
-        :param name:
-        :param model_uri:
-        :param identifier:
-        :param kwargs:
-        :return:
         """
-        self.mappings = {}
-        g = Graph()
+        g = Graph(bind_namespaces="none")
         g.parse(file, format=format)
-        if name is not None and default_prefix is None:
-            default_prefix = name
-        if name is None:
-            name = default_prefix
-        if name is None:
-            name = "example"
-        sb = SchemaBuilder(name=name)
+        sb = SchemaBuilder()
         sb.add_defaults()
         schema = sb.schema
         for k, v in g.namespaces():
-            if k == "schema" and v != "http://schema.org/":
+            if str(v) == "https://schema.org/":
+                # Normalise schema.org to HTTP
+                v = "http://schema.org/"
+            if k == "schema" and str(v) != "http://schema.org/":
                 continue
             sb.add_prefix(k, v, replace_if_present=True)
-        if default_prefix is not None:
+        if default_prefix is not None and isinstance(schema.prefixes, dict):
             schema.default_prefix = default_prefix
-            if default_prefix not in schema.prefixes:
+            if model_uri is not None and default_prefix not in schema.prefixes:
                 sb.add_prefix(default_prefix, model_uri, replace_if_present=True)
-            schema.id = schema.prefixes[default_prefix].prefix_reference
+            prefix = schema.prefixes[default_prefix]
+            if isinstance(prefix, Prefix):
+                schema.id = prefix.prefix_reference
         cls_slots = defaultdict(list)
-        props = []
-        for rdfs_property_metaclass in self._rdfs_metamodel_iri(
-            SlotDefinition.__name__
-        ):
-            for p in g.subjects(RDF.type, rdfs_property_metaclass):
-                props.append(p)
-        # implicit properties
-        for metap in (
-            self.reverse_metamodel_mappings["domain_of"]
-            + self.reverse_metamodel_mappings["rangeIncludes"]
-        ):
-            for p, _, _o in g.triples((None, metap, None)):
-                props.append(p)
-        for p in set(props):
-            sn = self.iri_to_name(p)
-            init_dict = self._dict_for_subject(g, p)
-            if "domain_of" in init_dict:
-                for x in init_dict["domain_of"]:
-                    cls_slots[x].append(sn)
-                del init_dict["domain_of"]
-            if "rangeIncludes" in init_dict:
-                init_dict["any_of"] = [{"range": x} for x in init_dict["rangeIncludes"]]
-                del init_dict["rangeIncludes"]
-            slot = SlotDefinition(sn, **init_dict)
-            slot.slot_uri = str(p.n3(g.namespace_manager))
+
+        for slot in self.generate_rdfs_properties(g, cls_slots):
             sb.add_slot(slot)
-        rdfs_classes = []
+        for cls in self.process_rdfs_classes(g, cls_slots):
+            sb.add_class(cls)
+
+        if identifier is not None and isinstance(schema.slots, dict) and isinstance(schema.classes, dict):
+            id_slot = SlotDefinition(identifier, identifier=True, range="uriorcurie")
+            schema.slots[identifier] = id_slot
+            for c in schema.classes.values():
+                if isinstance(c, ClassDefinition) and isinstance(c.slots, list):
+                    if not c.is_a and not c.mixins:
+                        if identifier not in c.slots:
+                            c.slots.append(identifier)
+
+        # Remove prefixes that aren't used
+        if isinstance(schema.imports, list):
+            for imp in schema.imports:
+                prefix, _suffix = imp.split(":", 1)
+                self.seen_prefixes.add(prefix)
+        schema.prefixes = {key: value for key, value in schema.prefixes.items() if key in self.seen_prefixes}
+        self.infer_metadata(schema, name, default_prefix, model_uri)
+        self.fix_missing(schema)
+        return schema
+
+    def infer_metadata(self, schema: SchemaDefinition, name: str | None, default_prefix: str | None = None, model_uri: str | None = None):
+        top_count = self.prefix_counts.most_common(1)
+        if len(top_count) == 0:
+            raise ValueError("No prefixes found in the graph")
+        inferred_prefix = top_count[0][0]
+
+        schema.name = name or inferred_prefix
+        schema.default_prefix = default_prefix or inferred_prefix
+        prefix_uri = None
+        if isinstance(schema.prefixes, Mapping):
+            prefix_uri = schema.prefixes.get(inferred_prefix)
+        elif isinstance(schema.prefixes, JsonObj):
+            prefix_uri = schema.prefixes._get(inferred_prefix)
+        if isinstance(prefix_uri, Prefix):
+            schema.id = model_uri or prefix_uri.prefix_reference
+
+    def fix_missing(self, schema: SchemaDefinition) -> None:
+        """
+        For some properties we have a `subproperty_of` that references a slot that doesn't exist.
+        This removes such links.
+        For example with `schema:name`, we have a `subPropertyOf` that references `rdfs:label`, which is from
+        the RDFS metamodel that we don't currently import.
+        """
+        if not isinstance(schema.slots, dict):
+            raise ValueError("SchemaBuilder schema must have slots as a dict")
+        slot_names: set[str] = set(schema.slots.keys())
+        for slot in schema.slots.values():
+            if not isinstance(slot, SlotDefinition):
+                raise ValueError(f"Slot {slot} is not a SlotDefinition")
+            if slot.subproperty_of is not None and slot.subproperty_of not in slot_names:
+                logging.warning(f"Slot {slot.name} has subproperty_of {slot.subproperty_of}, but that slot is missing")
+                slot.subproperty_of = None
+
+    def track_uri(self, uri: str, g: Graph) -> None:
+        """
+        Updates the set of prefixes seen in the graph
+        """
+        prefix, _namespace, _name = g.namespace_manager.compute_qname(uri)
+        self.seen_prefixes.add(prefix)
+        self.prefix_counts.update([prefix])
+
+    def process_rdfs_classes(
+        self,
+        g: Graph, 
+        cls_slots: Dict[str, List[str]], 
+    ) -> Iterable[ClassDefinition]:
+        """
+        Converts the RDFS classes in the graph to LinkML SlotDefinitions
+        """
+        rdfs_classes: List[URIRef] = []
+        
         for rdfs_class_metaclass in self._rdfs_metamodel_iri(ClassDefinition.__name__):
             for s in g.subjects(RDF.type, rdfs_class_metaclass):
-                rdfs_classes.append(s)
+                if isinstance(s, URIRef):
+                    rdfs_classes.append(s)
+        
         # implicit classes
         for metap in [RDFS.subClassOf]:
             for s, _, o in g.triples((None, metap, None)):
-                rdfs_classes.append(s)
-                rdfs_classes.append(o)
+                if isinstance(s, URIRef):
+                    rdfs_classes.append(s)
+                if isinstance(o, URIRef):
+                    rdfs_classes.append(o)
+
         for s in set(rdfs_classes):
+            self.track_uri(s, g)
             cn = self.iri_to_name(s)
-            init_dict = self._dict_for_subject(g, s)
+            init_dict = self._dict_for_subject(g, s, "class")
             c = ClassDefinition(cn, **init_dict)
             c.slots = cls_slots.get(cn, [])
             c.class_uri = str(s.n3(g.namespace_manager))
-            sb.add_class(c)
-        if identifier is not None:
-            id_slot = SlotDefinition(identifier, identifier=True, range="uriorcurie")
-            schema.slots[identifier] = id_slot
-            for c in schema.classes.values():
-                if not c.is_a and not c.mixins:
-                    if identifier not in c.slots:
-                        c.slots.append(identifier)
-        return schema
+            yield c
+
+    def generate_rdfs_properties(
+        self,
+        g: Graph, 
+        cls_slots: Dict[str, List[str]]
+    ) -> Iterable[SlotDefinition]:
+        """
+        Converts the RDFS properties in the graph to LinkML SlotDefinitions
+        """
+        # All property IDs
+        props: set[URIRef] = set()
+
+        # Add explicit properties, ie those with a RDF.type mapping
+        for rdfs_property_metaclass in self._rdfs_metamodel_iri(SlotDefinition.__name__):
+            for p in g.subjects(RDF.type, rdfs_property_metaclass):
+                if isinstance(p, URIRef):
+                    props.add(p)
+
+        # Add implicit properties, ie those that are the domain or range of a property
+        for metap in (
+            self.metamodel_mappings["domain_of"]
+            + self.metamodel_mappings["rangeIncludes"]
+        ):
+            for p, _, _o in g.triples((None, metap, None)):
+                if isinstance(p, URIRef):
+                    props.add(p)
+
+        for p in props:
+            self.track_uri(p, g)
+            sn = self.iri_to_name(p)
+            #: kwargs for SlotDefinition
+            init_dict = self._dict_for_subject(g, p, "slot")
 
-    def _dict_for_subject(self, g: Graph, s: URIRef) -> Dict[str, Any]:
+            # Special case for domains and ranges: add them directly as class slots
+            if "domain_of" in init_dict:
+                for x in init_dict["domain_of"]:
+                    cls_slots[x].append(sn)
+                del init_dict["domain_of"]
+            if "range" in init_dict:
+                range = init_dict["range"]
+                # Handle a range of multiple types
+                if isinstance(range, list):
+                    init_dict["any_of"] = [{"range": x} for x in init_dict["rangeIncludes"]]
+                    del init_dict["range"]
+            slot = SlotDefinition(sn, **init_dict)
+            slot.slot_uri = str(p.n3(g.namespace_manager))
+            yield slot
+
+    def _dict_for_subject(self, g: Graph, s: URIRef, subject_type: typing.Literal["slot", "class"]) -> Dict[str, Any]:
         """
         Looks up triples for a subject and converts to dict using linkml keys.
 
-        :param g:
-        :param p:
-        :return:
+        :param g: RDFS graph
+        :param s: property URI in that graph
+        :return: Dictionary mapping linkml metamodel keys to values
         """
         init_dict = {}
+        # Each RDFS predicate/object pair corresponds to a LinkML key value pair for the slot
         for pp, obj in g.predicate_objects(s):
             if pp == RDF.type:
                 continue
             metaslot_name = self._element_from_iri(pp)
             logging.debug(f"Mapping {pp} -> {metaslot_name}")
-            if metaslot_name not in self.defclass_slots:
+            # Filter out slots that don't belong in a class definition
+            if subject_type == "class" and metaslot_name not in self.classdef_slots:
+                continue
+            # Filter out slots that don't belong in a slot definition
+            if subject_type == "slot" and metaslot_name not in self.slotdef_slots:
                 continue
             if metaslot_name is None:
                 logging.warning(f"Not mapping {pp}")
@@ -209,14 +313,14 @@ def _dict_for_subject(self, g: Graph, s: URIRef) -> Dict[str, Any]:
     def _rdfs_metamodel_iri(self, name: str) -> List[URIRef]:
         return self.metamodel_mappings.get(name, [])
 
-    def _element_from_iri(self, iri: URIRef) -> str:
+    def _element_from_iri(self, iri: URIRef) -> str | None:
         r = self.reverse_metamodel_mappings.get(iri, [])
         if len(r) > 0:
             if len(r) > 1:
                 logging.debug(f"Multiple mappings for {iri}: {r}")
             return r[0]
 
-    def _object_to_value(self, obj: Any, metaslot: SlotDefinition = None) -> Any:
+    def _object_to_value(self, obj: Any, metaslot: SlotDefinition) -> Any:
         if isinstance(obj, URIRef):
             if metaslot.range == "uriorcurie" or metaslot.range == "uri":
                 return str(obj)
@@ -231,9 +335,9 @@ def iri_to_name(self, v: URIRef) -> str:
             self.mappings[n] = v
         return n
 
-    def _as_name(self, v: URIRef):
-        v = str(v)
+    def _as_name(self, v: URIRef) -> str:
+        v_str = str(v)
         for sep in ["#", "/", ":"]:
-            if sep in v:
-                return v.split(sep)[-1]
-        return v
+            if sep in v_str:
+                return v_str.split(sep)[-1]
+        return v_str
diff --git a/tests/resources/foaf_snippet.ttl b/tests/resources/foaf_snippet.ttl
new file mode 100644
index 0000000..ac9ab9d
--- /dev/null
+++ b/tests/resources/foaf_snippet.ttl
@@ -0,0 +1,19 @@
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+
+foaf:knows rdf:type owl:ObjectProperty ;
+           rdfs:domain foaf:Person ;
+           rdfs:range foaf:Person ;
+           rdfs:comment "A person known by this person (indicating some level of reciprocated interaction between the parties)." ;
+           rdfs:isDefinedBy <http://xmlns.com/foaf/0.1/> ;
+           rdfs:label "knows" .
+
+foaf:Person rdf:type owl:Class ;
+            rdfs:subClassOf <http://www.w3.org/2003/01/geo/wgs84_pos#SpatialThing> ,
+                            foaf:Agent ;
+            owl:disjointWith foaf:Project ;
+            rdfs:comment "A person." ;
+            rdfs:isDefinedBy <http://xmlns.com/foaf/0.1/> ;
+            rdfs:label "Person" .
diff --git a/tests/test_importers/test_rdfs_importer.py b/tests/test_importers/test_rdfs_importer.py
index 98b44ca..e539ce9 100644
--- a/tests/test_importers/test_rdfs_importer.py
+++ b/tests/test_importers/test_rdfs_importer.py
@@ -2,6 +2,7 @@
 
 """Test the module can be imported."""
 
+from io import StringIO
 import unittest
 import os
 import yaml
@@ -16,8 +17,55 @@
 
 REPRO = os.path.join(INPUT_DIR, 'reproschema.ttl')
 OUTSCHEMA = os.path.join(OUTPUT_DIR, 'reproschema-from-ttl.yaml')
+FOAF = os.path.join(INPUT_DIR, 'foaf_snippet.ttl')
 
 
+def test_import_foaf():
+    engine = RdfsImportEngine()
+    schema = engine.convert(FOAF)
+    sv = SchemaView(schema)
+    assert len(sv.all_classes()) == 3
+    assert len(sv.all_slots()) == 1
+    assert sv.get_slot("knows").range == "Person"
+    assert sv.schema.default_prefix == "foaf"
+    assert "foaf" in sv.schema.prefixes
+
+def test_comment_description():
+    """
+    rdfs:comment should be converted to description
+    """
+    rdf = StringIO("""
+    @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+    <http://example.org/Class> a rdfs:Class ;
+        rdfs:comment "A class." .
+    """)
+    engine = RdfsImportEngine()
+    schema = engine.convert(rdf)
+    sv = SchemaView(schema)
+    cls = sv.get_class("Class")
+    assert cls.description == "A class."
+
+def test_infer_prefix():
+    """
+    If the schema has no name, id or default prefix, the importer should infer them from prefix usage in the schema.
+    """
+    rdf = StringIO("""
+    @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+    @prefix foo: <https://foo.com> .
+
+    foo:Class a rdfs:Class ;
+        rdfs:comment "A class." .
+
+    foo:prop a rdfs:Property ;
+        rdfs:comment "A property." .
+    """)
+    engine = RdfsImportEngine()
+    schema = engine.convert(rdf)
+    # Although not explicitly provided, the importer should realise that the prefix is "foo"
+    assert schema.default_prefix == "foo"
+    assert schema.id == "https://foo.com"
+    assert schema.name == "foo"
 
 def test_from_rdfs():
     """Test OWL conversion."""
@@ -26,7 +74,6 @@ def test_from_rdfs():
     write_schema(schema, OUTSCHEMA)
     # roundtrip
     s = YAMLGenerator(OUTSCHEMA).serialize()
-    print(s[0:100])
     sv = SchemaView(OUTSCHEMA)
     activity = sv.get_class("Activity")
     assert activity
@@ -36,7 +83,3 @@ def test_from_rdfs():
     assert len(slots) == 1
     slot = slots[0]
     assert slot.name == "id"
-
-
-
-