diff --git a/poetry.lock b/poetry.lock
index 0edde3b..d5b8689 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,19 +1,19 @@
-# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand.
 
 [[package]]
 name = "airium"
-version = "0.2.6"
+version = "0.2.7"
 description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. Serves pure pythonic library with no dependencies."
 optional = false
 python-versions = "*"
 groups = ["main"]
 files = [
-    {file = "airium-0.2.6-py3-none-any.whl", hash = "sha256:50af5cf491e084f27909e29a93550b4170e587cde01334d58c6249644ee8c6c2"},
-    {file = "airium-0.2.6.tar.gz", hash = "sha256:ccab36b798b6cce3d0c5074e52ce8059f6e82991caae4985f42cadfad80b1de4"},
+    {file = "airium-0.2.7-py3-none-any.whl", hash = "sha256:35e3ae334327b17b7c2fc39bb57ab2c48171ca849f8cf3dff11437d1e054952e"},
+    {file = "airium-0.2.7.tar.gz", hash = "sha256:6b4dd8b69838b7766179ab90078a049dc337b1da4fc0f7754f30f74d6eed706e"},
 ]
 
 [package.extras]
-dev = ["pytest (>=6.2,<7.0)", "pytest-cov (>=3.0,<4.0)", "pytest-mock (>=3.6,<4.0)"]
+dev = ["check-manifest", "flake8 (>=7.1,<8.0)", "mypy (>=1.10,<2.0)", "pytest (>=6.2,<7.0)", "pytest-cov (>=3.0,<4.0)", "pytest-mock (>=3.6,<4.0)", "types-beautifulsoup4 (>=4.12,<5.0)", "types-requests (>=2.32,<3.0)"]
 parse = ["beautifulsoup4 (>=4.10.0,<5.0)", "requests (>=2.12.0,<3)"]
 
 [[package]]
@@ -48,7 +48,7 @@ version = "0.7.0"
 description = "Reusable constraint types to use with typing.Annotated"
 optional = false
 python-versions = ">=3.8"
-groups = ["main"]
+groups = ["main", "llm"]
 files = [
     {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
     {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
@@ -67,16 +67,15 @@ files = [
 
 [[package]]
 name = "anyio"
-version = "4.9.0"
-description = "High level compatibility layer for multiple asynchronous event loop implementations"
+version = "4.11.0"
+description = "High-level concurrency and networking framework on top of asyncio or Trio"
 optional = false
 python-versions = ">=3.9"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 files = [
-    {file = "anyio-4.9.0-py3-none-any.whl", hash = "sha256:9f76d541cad6e36af7beb62e978876f3b41e3e04f2c1fbf0884604c0a9c4d93c"},
-    {file = "anyio-4.9.0.tar.gz", hash = "sha256:673c0c244e15788651a4ff38710fea9675823028a6f08a5eda409e0c9840a028"},
+    {file = "anyio-4.11.0-py3-none-any.whl", hash = "sha256:0287e96f4d26d4149305414d4e3bc32f0dcd0862365a4bddea19d7a1ec38c4fc"},
+    {file = "anyio-4.11.0.tar.gz", hash = "sha256:82a8d0b81e318cc5ce71a5f1f8b5c4e63619620b63141ef8c995fa0db95a57c4"},
 ]
-markers = {main = "extra == \"llm\""}
 
 [package.dependencies]
 exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
@@ -85,9 +84,7 @@ sniffio = ">=1.1"
 typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""}
 
 [package.extras]
-doc = ["Sphinx (>=8.2,<9.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"]
-test = ["anyio[trio]", "blockbuster (>=1.5.23)", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1) ; python_version >= \"3.10\"", "uvloop (>=0.21) ; platform_python_implementation == \"CPython\" and platform_system != \"Windows\" and python_version < \"3.14\""]
-trio = ["trio (>=0.26.1)"]
+trio = ["trio (>=0.31.0)"]
 
 [[package]]
 name = "appdirs"
@@ -116,98 +113,96 @@ files = [
 
 [[package]]
 name = "argon2-cffi"
-version = "23.1.0"
+version = "25.1.0"
 description = "Argon2 for Python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "argon2_cffi-23.1.0-py3-none-any.whl", hash = "sha256:c670642b78ba29641818ab2e68bd4e6a78ba53b7eff7b4c3815ae16abf91c7ea"},
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+    {file = "argon2_cffi-25.1.0.tar.gz", hash = "sha256:694ae5cc8a42f4c4e2bf2ca0e64e51e23a040c6a517a85074683d3959e1346c1"},
 ]
 
 [package.dependencies]
 argon2-cffi-bindings = "*"
 
-[package.extras]
-dev = ["argon2-cffi[tests,typing]", "tox (>4)"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-copybutton", "sphinx-notfound-page"]
-tests = ["hypothesis", "pytest"]
-typing = ["mypy"]
-
 [[package]]
 name = "argon2-cffi-bindings"
-version = "21.2.0"
+version = "25.1.0"
 description = "Low-level CFFI bindings for Argon2"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.9"
 groups = ["dev"]
 files = [
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-]
-
-[package.dependencies]
-cffi = ">=1.0.1"
-
-[package.extras]
-dev = ["cogapp", "pre-commit", "pytest", "wheel"]
-tests = ["pytest"]
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+]
+
+[package.dependencies]
+cffi = [
+    {version = ">=1.0.1", markers = "python_version < \"3.14\""},
+    {version = ">=2.0.0b1", markers = "python_version >= \"3.14\""},
+]
 
 [[package]]
 name = "arrow"
-version = "1.3.0"
+version = "1.4.0"
 description = "Better dates & times for Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["main", "dev"]
 files = [
-    {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"},
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+    {file = "arrow-1.4.0-py3-none-any.whl", hash = "sha256:749f0769958ebdc79c173ff0b0670d59051a535fa26e8eba02953dc19eb43205"},
+    {file = "arrow-1.4.0.tar.gz", hash = "sha256:ed0cc050e98001b8779e84d461b0098c4ac597e88704a655582b21d116e526d7"},
 ]
 
 [package.dependencies]
 python-dateutil = ">=2.7.0"
-types-python-dateutil = ">=2.8.10"
+tzdata = {version = "*", markers = "python_version >= \"3.9\""}
 
 [package.extras]
 doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
-test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
+test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2025.2)", "simplejson (==3.*)"]
 
 [[package]]
 name = "asttokens"
-version = "3.0.0"
+version = "3.0.1"
 description = "Annotate AST trees with source code positions"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"},
-    {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"},
+    {file = "asttokens-3.0.1-py3-none-any.whl", hash = "sha256:15a3ebc0f43c2d0a50eeafea25e19046c68398e487b9f1f5b517f7c0f40f976a"},
+    {file = "asttokens-3.0.1.tar.gz", hash = "sha256:71a4ee5de0bde6a31d64f6b13f2293ac190344478f081c3d1bccfcf5eacb0cb7"},
 ]
 
 [package.extras]
-astroid = ["astroid (>=2,<4)"]
-test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"]
+astroid = ["astroid (>=2,<5)"]
+test = ["astroid (>=2,<5)", "pytest (<9.0)", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "async-lru"
@@ -226,24 +221,16 @@ typing_extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "attrs"
-version = "25.3.0"
+version = "25.4.0"
 description = "Classes Without Boilerplate"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["main", "dev"]
 files = [
-    {file = "attrs-25.3.0-py3-none-any.whl", hash = "sha256:427318ce031701fea540783410126f03899a97ffc6f61596ad581ac2e40e3bc3"},
-    {file = "attrs-25.3.0.tar.gz", hash = "sha256:75d7cefc7fb576747b2c81b4442d4d4a1ce0900973527c011d1030fd3bf4af1b"},
+    {file = "attrs-25.4.0-py3-none-any.whl", hash = "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373"},
+    {file = "attrs-25.4.0.tar.gz", hash = "sha256:16d5969b87f0859ef33a48b35d55ac1be6e42ae49d5e853b597db70c35c57e11"},
 ]
 
-[package.extras]
-benchmark = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-cov = ["cloudpickle ; platform_python_implementation == \"CPython\"", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-dev = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier"]
-tests = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-tests-mypy = ["mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\""]
-
 [[package]]
 name = "babel"
 version = "2.17.0"
@@ -273,14 +260,14 @@ files = [
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.13.4"
+version = "4.14.2"
 description = "Screen-scraping library"
 optional = false
 python-versions = ">=3.7.0"
 groups = ["main", "dev"]
 files = [
-    {file = "beautifulsoup4-4.13.4-py3-none-any.whl", hash = "sha256:9bbbb14bfde9d79f38b8cd5f8c7c85f4b8f2523190ebed90e950a8dea4cb1c4b"},
-    {file = "beautifulsoup4-4.13.4.tar.gz", hash = "sha256:dbb3c4e1ceae6aefebdaf2423247260cd062430a410e38c66f2baa50a8437195"},
+    {file = "beautifulsoup4-4.14.2-py3-none-any.whl", hash = "sha256:5ef6fa3a8cbece8488d66985560f97ed091e22bbc4e9c2338508a9d5de6d4515"},
+    {file = "beautifulsoup4-4.14.2.tar.gz", hash = "sha256:2a98ab9f944a11acee9cc848508ec28d9228abfd522ef0fad6a02a72e0ded69e"},
 ]
 
 [package.dependencies]
@@ -296,14 +283,15 @@ lxml = ["lxml"]
 
 [[package]]
 name = "bioregistry"
-version = "0.12.13"
+version = "0.12.36"
 description = "Integrated registry of biological databases and nomenclatures"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
-    {file = "bioregistry-0.12.13-py3-none-any.whl", hash = "sha256:d2a9d3d7bf40aecd2f5f54cbe61cea222d1192b6315058ebceea22ff1c2365dd"},
-    {file = "bioregistry-0.12.13.tar.gz", hash = "sha256:1e5d462cede81c27e121081aaac467a6f3839135a2841ec2581e1c906b63a9e7"},
+    {file = "bioregistry-0.12.36-py3-none-any.whl", hash = "sha256:1f6cac6bf2700c52dbc8ef4ebc6b7638ed8e762dc495e22cb83c56ca4fec3f94"},
+    {file = "bioregistry-0.12.36.tar.gz", hash = "sha256:f31d113e55d62cc8bea94dce15dfb49abffee3a09d2762f48f01426ac16ec421"},
 ]
 
 [package.dependencies]
@@ -311,7 +299,7 @@ click = "*"
 curies = ">=0.7.0"
 more_click = ">=0.1.2"
 pydantic = {version = ">=2.0", extras = ["email"]}
-pystow = ">=0.1.13"
+pystow = ">=0.7.7"
 requests = "*"
 tqdm = "*"
 
@@ -324,8 +312,42 @@ gha = ["more_itertools"]
 health = ["click_default_group", "jinja2", "pandas", "pyyaml", "tabulate"]
 mapping-checking = ["pandas", "sentence_transformers"]
 paper-ranking = ["indra", "pandas", "scikit-learn", "tabulate"]
-tests = ["coverage", "httpx", "indra", "more_itertools", "pytest", "scikit-learn"]
-web = ["a2wsgi", "bootstrap-flask", "curies[fastapi]", "fastapi", "flask (>=3.0.0)", "markdown", "pyyaml", "rdflib", "rdflib-endpoint (>=0.5.3)", "rdflib-jsonld", "uvicorn", "werkzeug (>=3.0.0)"]
+tests = ["coverage", "httpx", "more_itertools", "pytest", "scikit-learn"]
+web = ["a2wsgi", "api-analytics[fastapi]", "bootstrap-flask", "curies[fastapi]", "fastapi", "flask (>=3.0.0)", "markdown", "pyyaml", "rdflib", "rdflib-endpoint (>=0.5.3)", "rdflib-jsonld", "uvicorn", "werkzeug (>=3.0.0)"]
+
+[[package]]
+name = "bioregistry"
+version = "0.13.7"
+description = "Integrated registry of biological databases and nomenclatures"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "bioregistry-0.13.7-py3-none-any.whl", hash = "sha256:e3f5f5e5ad20a6e17959a7d9ae2f3b32fc15a92264a300327e6c72f010870ef5"},
+    {file = "bioregistry-0.13.7.tar.gz", hash = "sha256:fbe809ceff71ef02df5d3a438adba6d083f03e39240eb0849653447e6c29d994"},
+]
+
+[package.dependencies]
+click = "*"
+curies = ">=0.12.2"
+more-click = ">=0.1.2"
+pydantic = {version = ">=2.0", extras = ["email"]}
+pystow = ">=0.7.7"
+requests = "*"
+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 (>=8)", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme (>=3.0)"]
+export = ["ndex2", "pyyaml", "rdflib", "rdflib-jsonld"]
+gha = ["more-itertools"]
+health = ["click-default-group", "jinja2", "pandas", "pyyaml", "tabulate"]
+mapping-checking = ["pandas", "sentence-transformers"]
+paper-ranking = ["pandas", "pubmed-downloader (>=0.0.12)", "scikit-learn", "tabulate"]
+tests = ["coverage", "httpx", "more-itertools", "pytest", "scikit-learn"]
+web = ["a2wsgi", "api-analytics[fastapi]", "bootstrap-flask", "curies[fastapi]", "fastapi", "flask (>=3.0.0)", "markdown", "pyyaml", "rdflib", "rdflib-endpoint (>=0.5.3)", "rdflib-jsonld", "uvicorn", "werkzeug (>=3.0.0)"]
 
 [[package]]
 name = "bleach"
@@ -334,6 +356,7 @@ description = "An easy safelist-based HTML-sanitizing tool."
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"},
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@@ -346,136 +369,173 @@ webencodings = "*"
 [package.extras]
 css = ["tinycss2 (>=1.1.0,<1.5)"]
 
+[[package]]
+name = "bleach"
+version = "6.3.0"
+description = "An easy safelist-based HTML-sanitizing tool."
+optional = false
+python-versions = ">=3.10"
+groups = ["dev"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "bleach-6.3.0-py3-none-any.whl", hash = "sha256:fe10ec77c93ddf3d13a73b035abaac7a9f5e436513864ccdad516693213c65d6"},
+    {file = "bleach-6.3.0.tar.gz", hash = "sha256:6f3b91b1c0a02bb9a78b5a454c92506aa0fdf197e1d5e114d2e00c6f64306d22"},
+]
+
+[package.dependencies]
+tinycss2 = {version = ">=1.1.0,<1.5", optional = true, markers = "extra == \"css\""}
+webencodings = "*"
+
+[package.extras]
+css = ["tinycss2 (>=1.1.0,<1.5)"]
+
 [[package]]
 name = "cachetools"
-version = "5.5.2"
+version = "6.2.2"
 description = "Extensible memoizing collections and decorators"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
 groups = ["main"]
 files = [
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+    {file = "cachetools-6.2.2-py3-none-any.whl", hash = "sha256:6c09c98183bf58560c97b2abfcedcbaf6a896a490f534b031b661d3723b45ace"},
+    {file = "cachetools-6.2.2.tar.gz", hash = "sha256:8e6d266b25e539df852251cfd6f990b4bc3a141db73b939058d809ebd2590fc6"},
 ]
 
 [[package]]
 name = "cattrs"
-version = "24.1.3"
+version = "25.3.0"
 description = "Composable complex class support for attrs and dataclasses."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["main"]
 files = [
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+    {file = "cattrs-25.3.0.tar.gz", hash = "sha256:1ac88d9e5eda10436c4517e390a4142d88638fe682c436c93db7ce4a277b884a"},
 ]
 
 [package.dependencies]
-attrs = ">=23.1.0"
+attrs = ">=25.4.0"
 exceptiongroup = {version = ">=1.1.1", markers = "python_version < \"3.11\""}
-typing-extensions = {version = ">=4.1.0,<4.6.3 || >4.6.3", markers = "python_version < \"3.11\""}
+typing-extensions = ">=4.14.0"
 
 [package.extras]
 bson = ["pymongo (>=4.4.0)"]
 cbor2 = ["cbor2 (>=5.4.6)"]
 msgpack = ["msgpack (>=1.0.5)"]
-msgspec = ["msgspec (>=0.18.5) ; implementation_name == \"cpython\""]
-orjson = ["orjson (>=3.9.2) ; implementation_name == \"cpython\""]
+msgspec = ["msgspec (>=0.19.0) ; implementation_name == \"cpython\""]
+orjson = ["orjson (>=3.11.3) ; implementation_name == \"cpython\""]
 pyyaml = ["pyyaml (>=6.0)"]
 tomlkit = ["tomlkit (>=0.11.8)"]
-ujson = ["ujson (>=5.7.0)"]
+ujson = ["ujson (>=5.10.0)"]
 
 [[package]]
 name = "certifi"
-version = "2025.4.26"
+version = "2025.11.12"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
-python-versions = ">=3.6"
-groups = ["main", "dev"]
+python-versions = ">=3.7"
+groups = ["main", "dev", "llm"]
 files = [
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 ]
 
 [[package]]
 name = "cffi"
-version = "1.17.1"
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 description = "Foreign Function Interface for Python calling C code."
 optional = false
-python-versions = ">=3.8"
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 groups = ["dev"]
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 [[package]]
 name = "cfgraph"
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 ]
 
 [[package]]
 name = "class-resolver"
-version = "0.6.0"
+version = "0.6.1"
 description = "Lookup and instantiate classes with style."
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
-    {file = "class_resolver-0.6.0-py3-none-any.whl", hash = "sha256:cc629187a10bacff2e360939f8a4e8e7d209583dc8b318485ff91a0d24d5c9d0"},
-    {file = "class_resolver-0.6.0.tar.gz", hash = "sha256:8a3c20ab771925477f65cad8a49bb431e11543c82fbfadbf611c6769228a6cae"},
+    {file = "class_resolver-0.6.1-py3-none-any.whl", hash = "sha256:87a29d3cc863c2d57adaf6bc9590aef0227d8026bcd46a1ba832cb73bf1cc61c"},
+    {file = "class_resolver-0.6.1.tar.gz", hash = "sha256:b30a21b77f9be1d9542f069dc15efa8768f60357c7eb721e03c84037d229d531"},
 ]
 
 [package.dependencies]
@@ -622,7 +704,7 @@ importlib-metadata = {version = ">3.6", markers = "python_full_version < \"3.10.
 typing-extensions = "*"
 
 [package.extras]
-click = ["click"]
+click = ["click (<8.2)"]
 numpy = ["numpy"]
 optuna = ["optuna"]
 sklearn = ["scikit-learn"]
@@ -631,32 +713,40 @@ torch = ["torch"]
 torch-geometric = ["torch", "torch-geometric", "torch-sparse"]
 
 [[package]]
-name = "click"
-version = "8.1.8"
-description = "Composable command line interface toolkit"
+name = "class-resolver"
+version = "0.7.1"
+description = "Lookup and instantiate classes with style."
 optional = false
-python-versions = ">=3.7"
-groups = ["main", "dev"]
-markers = "python_version < \"3.11\""
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version >= \"3.11\""
 files = [
-    {file = "click-8.1.8-py3-none-any.whl", hash = "sha256:63c132bbbed01578a06712a2d1f497bb62d9c1c0d329b7903a866228027263b2"},
-    {file = "click-8.1.8.tar.gz", hash = "sha256:ed53c9d8990d83c2a27deae68e4ee337473f6330c040a31d4225c9574d16096a"},
+    {file = "class_resolver-0.7.1-py3-none-any.whl", hash = "sha256:d177909a48fdf6d6a0c297d117742a83ea799e0f601a922aa9ccb23ca1200e00"},
+    {file = "class_resolver-0.7.1.tar.gz", hash = "sha256:86f73b8cc5ed9111b7d9c5e331b51856a32f205179c66a56a9c520d0f6e82f66"},
 ]
 
 [package.dependencies]
-colorama = {version = "*", markers = "platform_system == \"Windows\""}
+typing-extensions = "*"
+
+[package.extras]
+click = ["click (>=8.2)"]
+numpy = ["numpy"]
+optuna = ["optuna"]
+sklearn = ["scikit-learn"]
+tabulate = ["tabulate"]
+torch = ["torch"]
+torch-geometric = ["torch", "torch-geometric", "torch-sparse"]
 
 [[package]]
 name = "click"
-version = "8.2.0"
+version = "8.1.8"
 description = "Composable command line interface toolkit"
 optional = false
-python-versions = ">=3.10"
-groups = ["main", "dev"]
-markers = "python_version >= \"3.11\""
+python-versions = ">=3.7"
+groups = ["main", "dev", "llm"]
 files = [
-    {file = "click-8.2.0-py3-none-any.whl", hash = "sha256:6b303f0b2aa85f1cb4e5303078fadcbcd4e476f114fab9b5007005711839325c"},
-    {file = "click-8.2.0.tar.gz", hash = "sha256:f5452aeddd9988eefa20f90f05ab66f17fce1ee2a36907fd30b05bbb5953814d"},
+    {file = "click-8.1.8-py3-none-any.whl", hash = "sha256:63c132bbbed01578a06712a2d1f497bb62d9c1c0d329b7903a866228027263b2"},
+    {file = "click-8.1.8.tar.gz", hash = "sha256:ed53c9d8990d83c2a27deae68e4ee337473f6330c040a31d4225c9574d16096a"},
 ]
 
 [package.dependencies]
@@ -666,10 +756,9 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "click-default-group"
 version = "1.2.4"
 description = "click_default_group"
-optional = true
+optional = false
 python-versions = ">=2.7"
-groups = ["main"]
-markers = "extra == \"llm\""
+groups = ["main", "llm"]
 files = [
     {file = "click_default_group-1.2.4-py2.py3-none-any.whl", hash = "sha256:9b60486923720e7fc61731bdb32b617039aba820e22e1c88766b1125592eaa5f"},
     {file = "click_default_group-1.2.4.tar.gz", hash = "sha256:eb3f3c99ec0d456ca6cd2a7f08f7d4e91771bef51b01bdd9580cc6450fe1251e"},
@@ -702,7 +791,7 @@ version = "0.4.6"
 description = "Cross-platform colored terminal text."
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 markers = "platform_system == \"Windows\" or sys_platform == \"win32\""
 files = [
     {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
@@ -711,32 +800,45 @@ files = [
 
 [[package]]
 name = "comm"
-version = "0.2.2"
+version = "0.2.3"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "comm-0.2.2-py3-none-any.whl", hash = "sha256:e6fb86cb70ff661ee8c9c14e7d36d6de3b4066f1441be4063df9c5009f0a64d3"},
-    {file = "comm-0.2.2.tar.gz", hash = "sha256:3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e"},
+    {file = "comm-0.2.3-py3-none-any.whl", hash = "sha256:c615d91d75f7f04f095b30d1c1711babd43bdc6419c1be9886a85f2f4e489417"},
+    {file = "comm-0.2.3.tar.gz", hash = "sha256:2dc8048c10962d55d7ad693be1e7045d891b7ce8d999c97963a5e3e99c055971"},
 ]
 
-[package.dependencies]
-traitlets = ">=4"
-
 [package.extras]
 test = ["pytest"]
 
+[[package]]
+name = "condense-json"
+version = "0.1.3"
+description = "Python function for condensing JSON using replacement strings"
+optional = false
+python-versions = ">=3.9"
+groups = ["llm"]
+files = [
+    {file = "condense_json-0.1.3-py3-none-any.whl", hash = "sha256:e0a3d42db4f44a89e74af8737d8e517e97420be0f7e5437087f4decfd38c3366"},
+    {file = "condense_json-0.1.3.tar.gz", hash = "sha256:25fe8d434fdafd849e8d98f21a3e18f96ae2d6dbc2c17565f29e4843d039d2bc"},
+]
+
+[package.extras]
+test = ["mypy", "pytest"]
+
 [[package]]
 name = "curies"
-version = "0.10.19"
+version = "0.10.23"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
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 [package.dependencies]
@@ -751,6 +853,35 @@ fastapi = ["defusedxml", "fastapi", "httpx", "python-multipart", "uvicorn"]
 flask = ["defusedxml", "flask"]
 pandas = ["pandas"]
 rdflib = ["rdflib"]
+sqlalchemy = ["sqlalchemy"]
+sqlmodel = ["sqlmodel"]
+tests = ["coverage[toml]", "pytest", "requests"]
+
+[[package]]
+name = "curies"
+version = "0.12.4"
+description = "Idiomatic conversion between URIs and compact URIs (CURIEs)"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version >= \"3.11\""
+files = [
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+]
+
+[package.dependencies]
+pydantic = ">=2.0"
+typing-extensions = "*"
+
+[package.extras]
+docs = ["sphinx (>=8)", "sphinx-automodapi", "sphinx-rtd-theme (>=3.0)"]
+fastapi = ["defusedxml", "fastapi", "httpx", "python-multipart", "uvicorn"]
+flask = ["defusedxml", "flask"]
+pandas = ["pandas"]
+rdflib = ["rdflib"]
+sqlalchemy = ["sqlalchemy"]
+sqlmodel = ["sqlmodel"]
 tests = ["coverage[toml]", "pytest", "requests"]
 
 [[package]]
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+version = "1.8.17"
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 optional = false
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 groups = ["dev"]
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 [[package]]
@@ -827,18 +962,18 @@ files = [
 
 [[package]]
 name = "deprecated"
-version = "1.2.18"
+version = "1.3.1"
 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
 groups = ["main"]
 files = [
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 [package.dependencies]
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+wrapt = ">=1.10,<3"
 
 [package.extras]
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@@ -860,28 +995,28 @@ packaging = "*"
 
 [[package]]
 name = "deptry"
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 description = "A command line utility to check for unused, missing and transitive dependencies in a Python project."
 optional = false
 python-versions = ">=3.9"
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 ]
 
 [package.dependencies]
@@ -889,16 +1024,15 @@ click = ">=8.0.0,<9"
 colorama = {version = ">=0.4.6", markers = "sys_platform == \"win32\""}
 packaging = ">=23.2"
 requirements-parser = ">=0.11.0,<1"
-tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+tomli = {version = ">=2.0.1", markers = "python_full_version < \"3.11.0\""}
 
 [[package]]
 name = "distro"
 version = "1.9.0"
 description = "Distro - an OS platform information API"
-optional = true
+optional = false
 python-versions = ">=3.6"
-groups = ["main"]
-markers = "extra == \"llm\""
+groups = ["main", "llm"]
 files = [
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@@ -911,6 +1045,7 @@ description = "DNS toolkit"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
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@@ -925,6 +1060,28 @@ idna = ["idna (>=3.7)"]
 trio = ["trio (>=0.23)"]
 wmi = ["wmi (>=1.5.1)"]
 
+[[package]]
+name = "dnspython"
+version = "2.8.0"
+description = "DNS toolkit"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version >= \"3.11\""
+files = [
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+]
+
+[package.extras]
+dev = ["black (>=25.1.0)", "coverage (>=7.0)", "flake8 (>=7)", "hypercorn (>=0.17.0)", "mypy (>=1.17)", "pylint (>=3)", "pytest (>=8.4)", "pytest-cov (>=6.2.0)", "quart-trio (>=0.12.0)", "sphinx (>=8.2.0)", "sphinx-rtd-theme (>=3.0.0)", "twine (>=6.1.0)", "wheel (>=0.45.0)"]
+dnssec = ["cryptography (>=45)"]
+doh = ["h2 (>=4.2.0)", "httpcore (>=1.0.0)", "httpx (>=0.28.0)"]
+doq = ["aioquic (>=1.2.0)"]
+idna = ["idna (>=3.10)"]
+trio = ["trio (>=0.30)"]
+wmi = ["wmi (>=1.5.1) ; platform_system == \"Windows\""]
+
 [[package]]
 name = "docopt"
 version = "0.6.2"
@@ -1008,14 +1165,14 @@ files = [
 
 [[package]]
 name = "email-validator"
-version = "2.2.0"
+version = "2.3.0"
 description = "A robust email address syntax and deliverability validation library."
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
 files = [
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 ]
 
 [package.dependencies]
@@ -1056,15 +1213,15 @@ dev = ["flake8", "ipython", "mock", "pytest", "pytest-cov", "restview", "setupto
 
 [[package]]
 name = "eval-type-backport"
-version = "0.2.2"
+version = "0.3.0"
 description = "Like `typing._eval_type`, but lets older Python versions use newer typing features."
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version == \"3.9\""
+markers = "python_version < \"3.10\""
 files = [
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 ]
 
 [package.extras]
@@ -1076,7 +1233,7 @@ version = "1.3.0"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 markers = "python_version < \"3.11\""
 files = [
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@@ -1091,14 +1248,14 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "executing"
-version = "2.2.0"
+version = "2.2.1"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
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 ]
 
 [package.extras]
@@ -1106,14 +1263,14 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
 name = "fastjsonschema"
-version = "2.21.1"
+version = "2.21.2"
 description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
 groups = ["dev"]
 files = [
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 ]
 
 [package.extras]
@@ -1121,47 +1278,53 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "fastobo"
-version = "0.13.0"
+version = "0.14.1"
 description = "Faultless AST for Open Biomedical Ontologies in Python."
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
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 ]
 
 [[package]]
@@ -1213,14 +1376,14 @@ beautifulsoup4 = "*"
 
 [[package]]
 name = "google-api-core"
-version = "2.24.2"
+version = "2.28.1"
 description = "Google API client core library"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
-    {file = "google_api_core-2.24.2-py3-none-any.whl", hash = "sha256:810a63ac95f3c441b7c0e43d344e372887f62ce9071ba972eacf32672e072de9"},
-    {file = "google_api_core-2.24.2.tar.gz", hash = "sha256:81718493daf06d96d6bc76a91c23874dbf2fac0adbbf542831b805ee6e974696"},
+    {file = "google_api_core-2.28.1-py3-none-any.whl", hash = "sha256:4021b0f8ceb77a6fb4de6fde4502cecab45062e66ff4f2895169e0b35bc9466c"},
+    {file = "google_api_core-2.28.1.tar.gz", hash = "sha256:2b405df02d68e68ce0fbc138559e6036559e685159d148ae5861013dc201baf8"},
 ]
 
 [package.dependencies]
@@ -1234,21 +1397,21 @@ protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4
 requests = ">=2.18.0,<3.0.0"
 
 [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) ; python_version >= \"3.11\"", "grpcio-status (>=1.33.2,<2.0.dev0)", "grpcio-status (>=1.49.1,<2.0.dev0) ; python_version >= \"3.11\""]
-grpcgcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
-grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
+async-rest = ["google-auth[aiohttp] (>=2.35.0,<3.0.0)"]
+grpc = ["grpcio (>=1.33.2,<2.0.0)", "grpcio (>=1.49.1,<2.0.0) ; python_version >= \"3.11\"", "grpcio (>=1.75.1,<2.0.0) ; python_version >= \"3.14\"", "grpcio-status (>=1.33.2,<2.0.0)", "grpcio-status (>=1.49.1,<2.0.0) ; python_version >= \"3.11\"", "grpcio-status (>=1.75.1,<2.0.0) ; python_version >= \"3.14\""]
+grpcgcp = ["grpcio-gcp (>=0.2.2,<1.0.0)"]
+grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.0)"]
 
 [[package]]
 name = "google-api-python-client"
-version = "2.169.0"
+version = "2.187.0"
 description = "Google API Client Library for Python"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
-    {file = "google_api_python_client-2.169.0-py3-none-any.whl", hash = "sha256:dae3e882dc0e6f28e60cf09c1f13fedfd881db84f824dd418aa9e44def2fe00d"},
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+    {file = "google_api_python_client-2.187.0.tar.gz", hash = "sha256:e98e8e8f49e1b5048c2f8276473d6485febc76c9c47892a8b4d1afa2c9ec8278"},
 ]
 
 [package.dependencies]
@@ -1260,18 +1423,18 @@ uritemplate = ">=3.0.1,<5"
 
 [[package]]
 name = "google-auth"
-version = "2.40.1"
+version = "2.43.0"
 description = "Google Authentication Library"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
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+    {file = "google_auth-2.43.0.tar.gz", hash = "sha256:88228eee5fc21b62a1b5fe773ca15e67778cb07dc8363adcb4a8827b52d81483"},
 ]
 
 [package.dependencies]
-cachetools = ">=2.0.0,<6.0"
+cachetools = ">=2.0.0,<7.0"
 pyasn1-modules = ">=0.2.1"
 rsa = ">=3.1.4,<5"
 
@@ -1282,24 +1445,24 @@ pyjwt = ["cryptography (<39.0.0) ; python_version < \"3.8\"", "cryptography (>=3
 pyopenssl = ["cryptography (<39.0.0) ; python_version < \"3.8\"", "cryptography (>=38.0.3)", "pyopenssl (>=20.0.0)"]
 reauth = ["pyu2f (>=0.1.5)"]
 requests = ["requests (>=2.20.0,<3.0.0)"]
-testing = ["aiohttp (<3.10.0)", "aiohttp (>=3.6.2,<4.0.0)", "aioresponses", "cryptography (<39.0.0) ; python_version < \"3.8\"", "cryptography (>=38.0.3)", "flask", "freezegun", "grpcio", "mock", "oauth2client", "packaging", "pyjwt (>=2.0)", "pyopenssl (<24.3.0)", "pyopenssl (>=20.0.0)", "pytest", "pytest-asyncio", "pytest-cov", "pytest-localserver", "pyu2f (>=0.1.5)", "requests (>=2.20.0,<3.0.0)", "responses", "urllib3"]
+testing = ["aiohttp (<3.10.0)", "aiohttp (>=3.6.2,<4.0.0)", "aioresponses", "cryptography (<39.0.0) ; python_version < \"3.8\"", "cryptography (<39.0.0) ; python_version < \"3.8\"", "cryptography (>=38.0.3)", "cryptography (>=38.0.3)", "flask", "freezegun", "grpcio", "mock", "oauth2client", "packaging", "pyjwt (>=2.0)", "pyopenssl (<24.3.0)", "pyopenssl (>=20.0.0)", "pytest", "pytest-asyncio", "pytest-cov", "pytest-localserver", "pyu2f (>=0.1.5)", "requests (>=2.20.0,<3.0.0)", "responses", "urllib3"]
 urllib3 = ["packaging", "urllib3"]
 
 [[package]]
 name = "google-auth-httplib2"
-version = "0.2.0"
+version = "0.2.1"
 description = "Google Authentication Library: httplib2 transport"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
 groups = ["main"]
 files = [
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+    {file = "google_auth_httplib2-0.2.1-py3-none-any.whl", hash = "sha256:1be94c611db91c01f9703e7f62b0a59bbd5587a95571c7b6fade510d648bc08b"},
+    {file = "google_auth_httplib2-0.2.1.tar.gz", hash = "sha256:5ef03be3927423c87fb69607b42df23a444e434ddb2555b73b3679793187b7de"},
 ]
 
 [package.dependencies]
-google-auth = "*"
-httplib2 = ">=0.19.0"
+google-auth = ">=1.32.0,<3.0.0"
+httplib2 = ">=0.19.0,<1.0.0"
 
 [[package]]
 name = "google-auth-oauthlib"
@@ -1322,14 +1485,14 @@ tool = ["click (>=6.0.0)"]
 
 [[package]]
 name = "googleapis-common-protos"
-version = "1.70.0"
+version = "1.72.0"
 description = "Common protobufs used in Google APIs"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
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+    {file = "googleapis_common_protos-1.72.0-py3-none-any.whl", hash = "sha256:4299c5a82d5ae1a9702ada957347726b167f9f8d1fc352477702a1e851ff4038"},
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 ]
 
 [package.dependencies]
@@ -1340,90 +1503,101 @@ grpc = ["grpcio (>=1.44.0,<2.0.0)"]
 
 [[package]]
 name = "graphviz"
-version = "0.20.3"
+version = "0.21"
 description = "Simple Python interface for Graphviz"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["main"]
 files = [
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+    {file = "graphviz-0.21.tar.gz", hash = "sha256:20743e7183be82aaaa8ad6c93f8893c923bd6658a04c32ee115edb3c8a835f78"},
 ]
 
 [package.extras]
-dev = ["flake8", "pep8-naming", "tox (>=3)", "twine", "wheel"]
-docs = ["sphinx (>=5,<7)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"]
+dev = ["Flake8-pyproject", "build", "flake8", "pep8-naming", "tox (>=3)", "twine", "wheel"]
+docs = ["sphinx (>=5,<7)", "sphinx-autodoc-typehints", "sphinx-rtd-theme (>=0.2.5)"]
 test = ["coverage", "pytest (>=7,<8.1)", "pytest-cov", "pytest-mock (>=3)"]
 
 [[package]]
 name = "greenlet"
-version = "3.2.2"
+version = "3.2.4"
 description = "Lightweight in-process concurrent programming"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version <= \"3.13\" 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\")"
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 ]
 
 [package.extras]
 docs = ["Sphinx", "furo"]
-test = ["objgraph", "psutil"]
+test = ["objgraph", "psutil", "setuptools"]
 
 [[package]]
 name = "gspread"
@@ -1461,12 +1635,11 @@ version = "0.16.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
 optional = false
 python-versions = ">=3.8"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 files = [
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 ]
-markers = {main = "extra == \"llm\""}
 
 [[package]]
 name = "hbreader"
@@ -1486,12 +1659,11 @@ version = "1.0.9"
 description = "A minimal low-level HTTP client."
 optional = false
 python-versions = ">=3.8"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 files = [
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 ]
-markers = {main = "extra == \"llm\""}
 
 [package.dependencies]
 certifi = "*"
@@ -1505,18 +1677,18 @@ trio = ["trio (>=0.22.0,<1.0)"]
 
 [[package]]
 name = "httplib2"
-version = "0.22.0"
+version = "0.31.0"
 description = "A comprehensive HTTP client library."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.6"
 groups = ["main"]
 files = [
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 [package.dependencies]
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+pyparsing = ">=3.0.4,<4"
 
 [[package]]
 name = "httpx"
@@ -1524,12 +1696,11 @@ version = "0.28.1"
 description = "The next generation HTTP client."
 optional = false
 python-versions = ">=3.8"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 files = [
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 ]
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 [package.dependencies]
 anyio = "*"
@@ -1546,14 +1717,14 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "idna"
-version = "3.10"
+version = "3.11"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.6"
-groups = ["main", "dev"]
+python-versions = ">=3.8"
+groups = ["main", "dev", "llm"]
 files = [
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 ]
 
 [package.extras]
@@ -1561,97 +1732,107 @@ all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2
 
 [[package]]
 name = "ijson"
-version = "3.4.0"
+version = "3.4.0.post0"
 description = "Iterative JSON parser with standard Python iterator interfaces"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
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+    {file = "ijson-3.4.0.post0.tar.gz", hash = "sha256:9aa02dc70bb245670a6ca7fba737b992aeeb4895360980622f7e568dbf23e41e"},
 ]
 
 [[package]]
@@ -1673,7 +1854,7 @@ description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev"]
-markers = "python_version == \"3.9\""
+markers = "python_version < \"3.10\""
 files = [
     {file = "importlib_metadata-8.7.0-py3-none-any.whl", hash = "sha256:e5dd1551894c77868a30651cef00984d50e1002d06942a7101d34870c5f02afd"},
     {file = "importlib_metadata-8.7.0.tar.gz", hash = "sha256:d13b81ad223b890aa16c5471f2ac3056cf76c5f10f82d6f9292f0b415f389000"},
@@ -1698,6 +1879,7 @@ description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "importlib_resources-6.5.2-py3-none-any.whl", hash = "sha256:789cfdc3ed28c78b67a06acb8126751ced69a3d5f79c095a98298cd8a760ccec"},
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@@ -1745,44 +1927,94 @@ description = "brain-dead simple config-ini parsing"
 optional = false
 python-versions = ">=3.8"
 groups = ["main", "dev"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760"},
     {file = "iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7"},
 ]
 
+[[package]]
+name = "iniconfig"
+version = "2.3.0"
+description = "brain-dead simple config-ini parsing"
+optional = false
+python-versions = ">=3.10"
+groups = ["main", "dev"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "iniconfig-2.3.0-py3-none-any.whl", hash = "sha256:f631c04d2c48c52b84d0d0549c99ff3859c98df65b3101406327ecc7d53fbf12"},
+    {file = "iniconfig-2.3.0.tar.gz", hash = "sha256:c76315c77db068650d49c5b56314774a7804df16fee4402c1f19d6d15d8c4730"},
+]
+
 [[package]]
 name = "ipykernel"
-version = "6.29.5"
+version = "6.31.0"
 description = "IPython Kernel for Jupyter"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["dev"]
+markers = "python_version < \"3.11\""
 files = [
-    {file = "ipykernel-6.29.5-py3-none-any.whl", hash = "sha256:afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5"},
-    {file = "ipykernel-6.29.5.tar.gz", hash = "sha256:f093a22c4a40f8828f8e330a9c297cb93dcab13bd9678ded6de8e5cf81c56215"},
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 ]
 
 [package.dependencies]
-appnope = {version = "*", markers = "platform_system == \"Darwin\""}
+appnope = {version = ">=0.1.2", markers = "platform_system == \"Darwin\""}
 comm = ">=0.1.1"
 debugpy = ">=1.6.5"
 ipython = ">=7.23.1"
-jupyter-client = ">=6.1.12"
+jupyter-client = ">=8.0.0"
 jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 matplotlib-inline = ">=0.1"
-nest-asyncio = "*"
-packaging = "*"
-psutil = "*"
-pyzmq = ">=24"
-tornado = ">=6.1"
+nest-asyncio = ">=1.4"
+packaging = ">=22"
+psutil = ">=5.7"
+pyzmq = ">=25"
+tornado = ">=6.2"
 traitlets = ">=5.4.0"
 
 [package.extras]
-cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"]
-docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
+cov = ["coverage[toml]", "matplotlib", "pytest-cov", "trio"]
+docs = ["intersphinx-registry", "myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
 pyqt5 = ["pyqt5"]
 pyside6 = ["pyside6"]
-test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0,<9)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
+
+[[package]]
+name = "ipykernel"
+version = "7.1.0"
+description = "IPython Kernel for Jupyter"
+optional = false
+python-versions = ">=3.10"
+groups = ["dev"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "ipykernel-7.1.0-py3-none-any.whl", hash = "sha256:763b5ec6c5b7776f6a8d7ce09b267693b4e5ce75cb50ae696aaefb3c85e1ea4c"},
+    {file = "ipykernel-7.1.0.tar.gz", hash = "sha256:58a3fc88533d5930c3546dc7eac66c6d288acde4f801e2001e65edc5dc9cf0db"},
+]
+
+[package.dependencies]
+appnope = {version = ">=0.1.2", markers = "platform_system == \"Darwin\""}
+comm = ">=0.1.1"
+debugpy = ">=1.6.5"
+ipython = ">=7.23.1"
+jupyter-client = ">=8.0.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+matplotlib-inline = ">=0.1"
+nest-asyncio = ">=1.4"
+packaging = ">=22"
+psutil = ">=5.7"
+pyzmq = ">=25"
+tornado = ">=6.2"
+traitlets = ">=5.4.0"
+
+[package.extras]
+cov = ["coverage[toml]", "matplotlib", "pytest-cov", "trio"]
+docs = ["intersphinx-registry", "myst-parser", "pydata-sphinx-theme", "sphinx (<8.2.0)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
+pyqt5 = ["pyqt5"]
+pyside6 = ["pyside6"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0,<9)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "ipython"
@@ -1825,37 +2057,37 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pa
 
 [[package]]
 name = "ipython"
-version = "9.2.0"
+version = "9.7.0"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.11"
 groups = ["dev"]
 markers = "python_version >= \"3.11\""
 files = [
-    {file = "ipython-9.2.0-py3-none-any.whl", hash = "sha256:fef5e33c4a1ae0759e0bba5917c9db4eb8c53fee917b6a526bd973e1ca5159f6"},
-    {file = "ipython-9.2.0.tar.gz", hash = "sha256:62a9373dbc12f28f9feaf4700d052195bf89806279fc8ca11f3f54017d04751b"},
+    {file = "ipython-9.7.0-py3-none-any.whl", hash = "sha256:bce8ac85eb9521adc94e1845b4c03d88365fd6ac2f4908ec4ed1eb1b0a065f9f"},
+    {file = "ipython-9.7.0.tar.gz", hash = "sha256:5f6de88c905a566c6a9d6c400a8fed54a638e1f7543d17aae2551133216b1e4e"},
 ]
 
 [package.dependencies]
-colorama = {version = "*", markers = "sys_platform == \"win32\""}
-decorator = "*"
-ipython-pygments-lexers = "*"
-jedi = ">=0.16"
-matplotlib-inline = "*"
+colorama = {version = ">=0.4.4", markers = "sys_platform == \"win32\""}
+decorator = ">=4.3.2"
+ipython-pygments-lexers = ">=1.0.0"
+jedi = ">=0.18.1"
+matplotlib-inline = ">=0.1.5"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
 prompt_toolkit = ">=3.0.41,<3.1.0"
-pygments = ">=2.4.0"
-stack_data = "*"
+pygments = ">=2.11.0"
+stack_data = ">=0.6.0"
 traitlets = ">=5.13.0"
 typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
 
 [package.extras]
 all = ["ipython[doc,matplotlib,test,test-extra]"]
 black = ["black"]
-doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinx_toml (==0.0.4)", "typing_extensions"]
-matplotlib = ["matplotlib"]
-test = ["packaging", "pytest", "pytest-asyncio (<0.22)", "testpath"]
-test-extra = ["curio", "ipykernel", "ipython[test]", "jupyter_ai", "matplotlib (!=3.2.0)", "nbclient", "nbformat", "numpy (>=1.23)", "pandas", "trio"]
+doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[matplotlib,test]", "setuptools (>=70.0)", "sphinx (>=8.0)", "sphinx-rtd-theme (>=0.1.8)", "sphinx_toml (==0.0.4)", "typing_extensions"]
+matplotlib = ["matplotlib (>3.9)"]
+test = ["packaging (>=20.1.0)", "pytest (>=7.0.0)", "pytest-asyncio (>=1.0.0)", "setuptools (>=61.2)", "testpath (>=0.2)"]
+test-extra = ["curio", "ipykernel (>6.30)", "ipython[matplotlib]", "ipython[test]", "jupyter_ai", "nbclient", "nbformat", "numpy (>=1.27)", "pandas (>2.1)", "trio (>=0.1.0)"]
 
 [[package]]
 name = "ipython-pygments-lexers"
@@ -1875,14 +2107,14 @@ pygments = "*"
 
 [[package]]
 name = "ipywidgets"
-version = "8.1.7"
+version = "8.1.8"
 description = "Jupyter interactive widgets"
 optional = false
 python-versions = ">=3.7"
 groups = ["dev"]
 files = [
-    {file = "ipywidgets-8.1.7-py3-none-any.whl", hash = "sha256:764f2602d25471c213919b8a1997df04bef869251db4ca8efba1b76b1bd9f7bb"},
-    {file = "ipywidgets-8.1.7.tar.gz", hash = "sha256:15f1ac050b9ccbefd45dccfbb2ef6bed0029d8278682d569d71b8dd96bee0376"},
+    {file = "ipywidgets-8.1.8-py3-none-any.whl", hash = "sha256:ecaca67aed704a338f88f67b1181b58f821ab5dc89c1f0f5ef99db43c1c2921e"},
+    {file = "ipywidgets-8.1.8.tar.gz", hash = "sha256:61f969306b95f85fba6b6986b7fe45d73124d1d9e3023a8068710d47a22ea668"},
 ]
 
 [package.dependencies]
@@ -1962,90 +2194,114 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jiter"
-version = "0.10.0"
+version = "0.12.0"
 description = "Fast iterable JSON parser."
-optional = true
+optional = false
 python-versions = ">=3.9"
-groups = ["main"]
-markers = "extra == \"llm\""
-files = [
-    {file = "jiter-0.10.0-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:cd2fb72b02478f06a900a5782de2ef47e0396b3e1f7d5aba30daeb1fce66f303"},
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-    {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
+    {file = "jsonschema-4.25.1-py3-none-any.whl", hash = "sha256:3fba0169e345c7175110351d456342c364814cfcf3b964ba4587f22915230a63"},
+    {file = "jsonschema-4.25.1.tar.gz", hash = "sha256:e4a9655ce0da0c0b67a085847e00a3a51449e1157f4f75e9fb5aa545e122eb85"},
 ]
 
 [package.dependencies]
@@ -2171,6 +2427,7 @@ rfc3339-validator = [
 ]
 rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
 rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
+rfc3987-syntax = {version = ">=1.1.0", optional = true, markers = "extra == \"format-nongpl\""}
 rpds-py = ">=0.7.1"
 uri-template = [
     {version = "*", optional = true, markers = "extra == \"format\""},
@@ -2183,18 +2440,18 @@ webcolors = [
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
-format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=24.6.0)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "rfc3987-syntax (>=1.1.0)", "uri-template", "webcolors (>=24.6.0)"]
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2025.4.1"
+version = "2025.9.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev"]
 files = [
-    {file = "jsonschema_specifications-2025.4.1-py3-none-any.whl", hash = "sha256:4653bffbd6584f7de83a67e0d620ef16900b390ddc7939d56684d6c81e33f1af"},
-    {file = "jsonschema_specifications-2025.4.1.tar.gz", hash = "sha256:630159c9f4dbea161a6a2205c3011cc4f18ff381b189fff48bb39b9bf26ae608"},
+    {file = "jsonschema_specifications-2025.9.1-py3-none-any.whl", hash = "sha256:98802fee3a11ee76ecaca44429fda8a41bff98b00a0f2838151b113f210cc6fe"},
+    {file = "jsonschema_specifications-2025.9.1.tar.gz", hash = "sha256:b540987f239e745613c7a9176f3edb72b832a4ac465cf02712288397832b5e8d"},
 ]
 
 [package.dependencies]
@@ -2271,14 +2528,15 @@ test = ["flaky", "pexpect", "pytest"]
 
 [[package]]
 name = "jupyter-core"
-version = "5.7.2"
+version = "5.8.1"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
+markers = "python_version < \"3.11\""
 files = [
-    {file = "jupyter_core-5.7.2-py3-none-any.whl", hash = "sha256:4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409"},
-    {file = "jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9"},
+    {file = "jupyter_core-5.8.1-py3-none-any.whl", hash = "sha256:c28d268fc90fb53f1338ded2eb410704c5449a358406e8a948b75706e24863d0"},
+    {file = "jupyter_core-5.8.1.tar.gz", hash = "sha256:0a5f9706f70e64786b75acba995988915ebd4601c8a52e534a40b51c95f59941"},
 ]
 
 [package.dependencies]
@@ -2287,8 +2545,29 @@ pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_
 traitlets = ">=5.3"
 
 [package.extras]
-docs = ["myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
-test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"]
+docs = ["intersphinx-registry", "myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-spelling", "traitlets"]
+test = ["ipykernel", "pre-commit", "pytest (<9)", "pytest-cov", "pytest-timeout"]
+
+[[package]]
+name = "jupyter-core"
+version = "5.9.1"
+description = "Jupyter core package. A base package on which Jupyter projects rely."
+optional = false
+python-versions = ">=3.10"
+groups = ["dev"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "jupyter_core-5.9.1-py3-none-any.whl", hash = "sha256:ebf87fdc6073d142e114c72c9e29a9d7ca03fad818c5d300ce2adc1fb0743407"},
+    {file = "jupyter_core-5.9.1.tar.gz", hash = "sha256:4d09aaff303b9566c3ce657f580bd089ff5c91f5f89cf7d8846c3cdf465b5508"},
+]
+
+[package.dependencies]
+platformdirs = ">=2.5"
+traitlets = ">=5.3"
+
+[package.extras]
+docs = ["intersphinx-registry", "myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-spelling", "traitlets"]
+test = ["ipykernel", "pre-commit", "pytest (<9)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-events"
@@ -2319,30 +2598,30 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p
 
 [[package]]
 name = "jupyter-lsp"
-version = "2.2.5"
+version = "2.3.0"
 description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "jupyter-lsp-2.2.5.tar.gz", hash = "sha256:793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001"},
-    {file = "jupyter_lsp-2.2.5-py3-none-any.whl", hash = "sha256:45fbddbd505f3fbfb0b6cb2f1bc5e15e83ab7c79cd6e89416b248cb3c00c11da"},
+    {file = "jupyter_lsp-2.3.0-py3-none-any.whl", hash = "sha256:e914a3cb2addf48b1c7710914771aaf1819d46b2e5a79b0f917b5478ec93f34f"},
+    {file = "jupyter_lsp-2.3.0.tar.gz", hash = "sha256:458aa59339dc868fb784d73364f17dbce8836e906cd75fd471a325cba02e0245"},
 ]
 
 [package.dependencies]
-importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
-jupyter-server = ">=1.1.2"
+importlib_metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
+jupyter_server = ">=1.1.2"
 
 [[package]]
 name = "jupyter-server"
-version = "2.16.0"
+version = "2.17.0"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
 files = [
-    {file = "jupyter_server-2.16.0-py3-none-any.whl", hash = "sha256:3d8db5be3bc64403b1c65b400a1d7f4647a5ce743f3b20dbdefe8ddb7b55af9e"},
-    {file = "jupyter_server-2.16.0.tar.gz", hash = "sha256:65d4b44fdf2dcbbdfe0aa1ace4a842d4aaf746a2b7b168134d5aaed35621b7f6"},
+    {file = "jupyter_server-2.17.0-py3-none-any.whl", hash = "sha256:e8cb9c7db4251f51ed307e329b81b72ccf2056ff82d50524debde1ee1870e13f"},
+    {file = "jupyter_server-2.17.0.tar.gz", hash = "sha256:c38ea898566964c888b4772ae1ed58eca84592e88251d2cfc4d171f81f7e99d5"},
 ]
 
 [package.dependencies]
@@ -2355,7 +2634,7 @@ jupyter-events = ">=0.11.0"
 jupyter-server-terminals = ">=0.4.4"
 nbconvert = ">=6.4.4"
 nbformat = ">=5.3.0"
-overrides = ">=5.0"
+overrides = {version = ">=5.0", markers = "python_version < \"3.12\""}
 packaging = ">=22.0"
 prometheus-client = ">=0.9"
 pywinpty = {version = ">=2.0.1", markers = "os_name == \"nt\""}
@@ -2392,26 +2671,26 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 
 [[package]]
 name = "jupyterlab"
-version = "4.4.2"
+version = "4.5.0"
 description = "JupyterLab computational environment"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
 files = [
-    {file = "jupyterlab-4.4.2-py3-none-any.whl", hash = "sha256:857111a50bed68542bf55dca784522fe728f9f88b4fe69e8c585db5c50900419"},
-    {file = "jupyterlab-4.4.2.tar.gz", hash = "sha256:afa9caf28c0cb966488be18e5e8daba9f018a1c4273a406b7d5006344cbc6d16"},
+    {file = "jupyterlab-4.5.0-py3-none-any.whl", hash = "sha256:88e157c75c1afff64c7dc4b801ec471450b922a4eae4305211ddd40da8201c8a"},
+    {file = "jupyterlab-4.5.0.tar.gz", hash = "sha256:aec33d6d8f1225b495ee2cf20f0514f45e6df8e360bdd7ac9bace0b7ac5177ea"},
 ]
 
 [package.dependencies]
 async-lru = ">=1.0.0"
-httpx = ">=0.25.0"
+httpx = ">=0.25.0,<1"
 importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
-ipykernel = ">=6.5.0"
+ipykernel = ">=6.5.0,<6.30.0 || >6.30.0"
 jinja2 = ">=3.0.3"
 jupyter-core = "*"
 jupyter-lsp = ">=2.0.0"
 jupyter-server = ">=2.4.0,<3"
-jupyterlab-server = ">=2.27.1,<3"
+jupyterlab-server = ">=2.28.0,<3"
 notebook-shim = ">=0.2"
 packaging = "*"
 setuptools = ">=41.1.0"
@@ -2420,9 +2699,9 @@ tornado = ">=6.2.0"
 traitlets = "*"
 
 [package.extras]
-dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.11.4)"]
+dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.11.12)"]
 docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-jupyter", "sphinx (>=1.8,<8.2.0)", "sphinx-copybutton"]
-docs-screenshots = ["altair (==5.5.0)", "ipython (==8.16.1)", "ipywidgets (==8.1.5)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.3.post1)", "matplotlib (==3.10.0)", "nbconvert (>=7.0.0)", "pandas (==2.2.3)", "scipy (==1.15.1)", "vega-datasets (==0.9.0)"]
+docs-screenshots = ["altair (==6.0.0)", "ipython (==8.16.1)", "ipywidgets (==8.1.5)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.3.post1)", "matplotlib (==3.10.0)", "nbconvert (>=7.0.0)", "pandas (==2.2.3)", "scipy (==1.15.1)"]
 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)"]
 
@@ -2440,14 +2719,14 @@ files = [
 
 [[package]]
 name = "jupyterlab-server"
-version = "2.27.3"
+version = "2.28.0"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "jupyterlab_server-2.27.3-py3-none-any.whl", hash = "sha256:e697488f66c3db49df675158a77b3b017520d772c6e1548c7d9bcc5df7944ee4"},
-    {file = "jupyterlab_server-2.27.3.tar.gz", hash = "sha256:eb36caca59e74471988f0ae25c77945610b887f777255aa21f8065def9e51ed4"},
+    {file = "jupyterlab_server-2.28.0-py3-none-any.whl", hash = "sha256:e4355b148fdcf34d312bbbc80f22467d6d20460e8b8736bf235577dd18506968"},
+    {file = "jupyterlab_server-2.28.0.tar.gz", hash = "sha256:35baa81898b15f93573e2deca50d11ac0ae407ebb688299d3a5213265033712c"},
 ]
 
 [package.dependencies]
@@ -2467,14 +2746,14 @@ test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-v
 
 [[package]]
 name = "jupyterlab-widgets"
-version = "3.0.15"
+version = "3.0.16"
 description = "Jupyter interactive widgets for JupyterLab"
 optional = false
 python-versions = ">=3.7"
 groups = ["dev"]
 files = [
-    {file = "jupyterlab_widgets-3.0.15-py3-none-any.whl", hash = "sha256:d59023d7d7ef71400d51e6fee9a88867f6e65e10a4201605d2d7f3e8f012a31c"},
-    {file = "jupyterlab_widgets-3.0.15.tar.gz", hash = "sha256:2920888a0c2922351a9202817957a68c07d99673504d6cd37345299e971bb08b"},
+    {file = "jupyterlab_widgets-3.0.16-py3-none-any.whl", hash = "sha256:45fa36d9c6422cf2559198e4db481aa243c7a32d9926b500781c830c80f7ecf8"},
+    {file = "jupyterlab_widgets-3.0.16.tar.gz", hash = "sha256:423da05071d55cf27a9e602216d35a3a65a3e41cdf9c5d3b643b814ce38c19e0"},
 ]
 
 [[package]]
@@ -2513,14 +2792,14 @@ prefixmaps = ">=0.2.0,<0.3.0"
 
 [[package]]
 name = "lark"
-version = "1.2.2"
+version = "1.3.1"
 description = "a modern parsing library"
 optional = false
 python-versions = ">=3.8"
-groups = ["main"]
+groups = ["main", "dev"]
 files = [
-    {file = "lark-1.2.2-py3-none-any.whl", hash = "sha256:c2276486b02f0f1b90be155f2c8ba4a8e194d42775786db622faccd652d8e80c"},
-    {file = "lark-1.2.2.tar.gz", hash = "sha256:ca807d0162cd16cef15a8feecb862d7319e7a09bdb13aef927968e45040fed80"},
+    {file = "lark-1.3.1-py3-none-any.whl", hash = "sha256:c629b661023a014c37da873b4ff58a817398d12635d3bbb2c5a03be7fe5d1e12"},
+    {file = "lark-1.3.1.tar.gz", hash = "sha256:b426a7a6d6d53189d318f2b6236ab5d6429eaf09259f1ca33eb716eed10d2905"},
 ]
 
 [package.extras]
@@ -2531,26 +2810,26 @@ regex = ["regex"]
 
 [[package]]
 name = "linkml"
-version = "1.9.2"
+version = "1.9.5"
 description = "Linked Open Data Modeling Language"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "linkml-1.9.2-py3-none-any.whl", hash = "sha256:4c9cf217948367df8a20cdf68e8f6da24ba23ab97a551f8ae32e9d4264e702cc"},
-    {file = "linkml-1.9.2.tar.gz", hash = "sha256:2f9141d2bc8a93bfe1d4b86a015ad0acbb94c2af099177f5687a50d3331d2b34"},
+    {file = "linkml-1.9.5-py3-none-any.whl", hash = "sha256:7544c8221a083029ee37ec12eeaa3978237c8181f08d6f2abf9789561375a58f"},
+    {file = "linkml-1.9.5.tar.gz", hash = "sha256:736765dfdf35054497452771f8fd5653f7a2b6aec735b4e9e8171730ddf93582"},
 ]
 
 [package.dependencies]
 antlr4-python3-runtime = ">=4.9.0,<4.10"
-click = ">=7.0"
+click = ">=8.0,<8.2"
 graphviz = ">=0.10.1"
 hbreader = "*"
 isodate = ">=0.6.0"
 jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = {version = ">=4.0.0", extras = ["format"]}
-linkml-runtime = ">=1.9.2,<2.0.0"
+linkml-runtime = ">=1.9.5,<2.0.0"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
@@ -2568,14 +2847,6 @@ 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)"]
-pandera = ["pandera (>=0.19.0)"]
-polars-lts-cpu = ["polars-lts-cpu (>=1.0.0)"]
-shacl = ["pyshacl (>=0.25.0)"]
-tests = ["black (>=24.0.0)", "numpydantic (>=1.6.1)", "pyshacl (>=0.25.0)"]
-
 [[package]]
 name = "linkml-renderer"
 version = "0.3.1"
@@ -2596,14 +2867,14 @@ pydantic = "*"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.9.2"
+version = "1.9.5"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "linkml_runtime-1.9.2-py3-none-any.whl", hash = "sha256:ff9fd51d38e5c6b991b88e90fb603120629b9da28861f334ea48139c7266f941"},
-    {file = "linkml_runtime-1.9.2.tar.gz", hash = "sha256:d37b3ca479464ec1fec04551f98e8e0e74620ee62a45bbd80da1ff2022132d92"},
+    {file = "linkml_runtime-1.9.5-py3-none-any.whl", hash = "sha256:fece3e8aa25a4246165c6528b6a7fe83a929b985d2ce1951cc8a0f4da1a30b90"},
+    {file = "linkml_runtime-1.9.5.tar.gz", hash = "sha256:78dc1383adf11ad5f20bb11b6adde56ed566fbd2429a292d57699ad4596c738a"},
 ]
 
 [package.dependencies]
@@ -2626,10 +2897,9 @@ requests = "*"
 name = "llm"
 version = "0.21"
 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 = true
+optional = false
 python-versions = ">=3.9"
-groups = ["main"]
-markers = "extra == \"llm\""
+groups = ["main", "llm"]
 files = [
     {file = "llm-0.21-py3-none-any.whl", hash = "sha256:d045276c92d0eb4e5f2978123ad1a0f607085cdd454ef055731a55487ae5c0a6"},
     {file = "llm-0.21.tar.gz", hash = "sha256:ac1717e7cb68275271ad90d8f045407e59215a69b4ccc222ef4e60c43edeb95e"},
@@ -2653,13 +2923,44 @@ sqlite-utils = ">=3.37"
 [package.extras]
 test = ["black (==24.10.0)", "cogapp", "mypy (>=1.10.0)", "numpy", "pytest", "pytest-asyncio", "pytest-httpx (>=0.33.0)", "ruff", "types-PyYAML", "types-click", "types-setuptools"]
 
+[[package]]
+name = "llm"
+version = "0.27.1"
+description = "CLI utility and Python library for interacting with Large Language Models from organizations like OpenAI, Anthropic and Gemini plus local models installed on your own machine."
+optional = false
+python-versions = ">=3.9"
+groups = ["llm"]
+files = [
+    {file = "llm-0.27.1-py3-none-any.whl", hash = "sha256:a884a575062fbea8c2b129708a80e146fa9682bd1c444d8d7b028196107de727"},
+    {file = "llm-0.27.1.tar.gz", hash = "sha256:02b0b393e31cf0e0ee1f2a6006c451c74ec18c7ec3973218de56e76fd72baa80"},
+]
+
+[package.dependencies]
+click = "*"
+click-default-group = ">=1.2.3"
+condense-json = ">=0.1.3"
+openai = ">=1.55.3"
+pip = "*"
+pluggy = "*"
+puremagic = "*"
+pydantic = ">=2.0.0"
+pyreadline3 = {version = "*", markers = "sys_platform == \"win32\""}
+python-ulid = "*"
+PyYAML = "*"
+setuptools = "*"
+sqlite-migrate = ">=0.1a2"
+sqlite-utils = ">=3.37"
+
+[package.extras]
+test = ["black (>=25.1.0)", "build", "click (<8.2.0)", "cogapp", "llm-echo (==0.3a3)", "mypy (>=1.10.0)", "numpy", "pytest", "pytest-asyncio", "pytest-httpx (>=0.33.0)", "pytest-recording", "ruff", "syrupy", "types-PyYAML", "types-click", "types-setuptools"]
+
 [[package]]
 name = "lxml"
 version = "5.4.0"
 description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
 optional = false
 python-versions = ">=3.6"
-groups = ["main", "dev"]
+groups = ["main", "llm"]
 files = [
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@@ -2802,26 +3103,43 @@ html5 = ["html5lib"]
 htmlsoup = ["BeautifulSoup4"]
 source = ["Cython (>=3.0.11,<3.1.0)"]
 
+[[package]]
+name = "lxml-stubs"
+version = "0.5.1"
+description = "Type annotations for the lxml package"
+optional = false
+python-versions = "*"
+groups = ["dev"]
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+
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+
 [[package]]
 name = "mariadb"
-version = "1.1.12"
+version = "1.1.14"
 description = "Python MariaDB extension"
 optional = true
 python-versions = ">=3.8"
 groups = ["main"]
 markers = "extra == \"mariadb\""
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 ]
 
 [package.dependencies]
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+version = "3.0.3"
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 python-versions = ">=3.9"
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+    {file = "matplotlib_inline-0.2.1-py3-none-any.whl", hash = "sha256:d56ce5156ba6085e00a9d54fead6ed29a9c47e215cd1bba2e976ef39f5710a76"},
+    {file = "matplotlib_inline-0.2.1.tar.gz", hash = "sha256:e1ee949c340d771fc39e241ea75683deb94762c8fa5f2927ec57c83c4dffa9fe"},
 ]
 
 [package.dependencies]
 traitlets = "*"
 
+[package.extras]
+test = ["flake8", "nbdime", "nbval", "notebook", "pytest"]
+
 [[package]]
 name = "mdit-py-plugins"
 version = "0.4.2"
@@ -2945,6 +3294,7 @@ description = "Collection of plugins for markdown-it-py"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "mdit_py_plugins-0.4.2-py3-none-any.whl", hash = "sha256:0c673c3f889399a33b95e88d2f0d111b4447bdfea7f237dab2d488f459835636"},
     {file = "mdit_py_plugins-0.4.2.tar.gz", hash = "sha256:5f2cd1fdb606ddf152d37ec30e46101a60512bc0e5fa1a7002c36647b09e26b5"},
@@ -2958,6 +3308,27 @@ code-style = ["pre-commit"]
 rtd = ["myst-parser", "sphinx-book-theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
+[[package]]
+name = "mdit-py-plugins"
+version = "0.5.0"
+description = "Collection of plugins for markdown-it-py"
+optional = false
+python-versions = ">=3.10"
+groups = ["dev"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "mdit_py_plugins-0.5.0-py3-none-any.whl", hash = "sha256:07a08422fc1936a5d26d146759e9155ea466e842f5ab2f7d2266dd084c8dab1f"},
+    {file = "mdit_py_plugins-0.5.0.tar.gz", hash = "sha256:f4918cb50119f50446560513a8e311d574ff6aaed72606ddae6d35716fe809c6"},
+]
+
+[package.dependencies]
+markdown-it-py = ">=2.0.0,<5.0.0"
+
+[package.extras]
+code-style = ["pre-commit"]
+rtd = ["myst-parser", "sphinx-book-theme"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
+
 [[package]]
 name = "mdurl"
 version = "0.1.2"
@@ -2972,14 +3343,14 @@ files = [
 
 [[package]]
 name = "mistune"
-version = "3.1.3"
+version = "3.1.4"
 description = "A sane and fast Markdown parser with useful plugins and renderers"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "mistune-3.1.3-py3-none-any.whl", hash = "sha256:1a32314113cff28aa6432e99e522677c8587fd83e3d51c29b82a52409c842bd9"},
-    {file = "mistune-3.1.3.tar.gz", hash = "sha256:a7035c21782b2becb6be62f8f25d3df81ccb4d6fa477a6525b15af06539f02a0"},
+    {file = "mistune-3.1.4-py3-none-any.whl", hash = "sha256:93691da911e5d9d2e23bc54472892aff676df27a75274962ff9edc210364266d"},
+    {file = "mistune-3.1.4.tar.gz", hash = "sha256:b5a7f801d389f724ec702840c11d8fc48f2b33519102fc7ee739e8177b672164"},
 ]
 
 [package.dependencies]
@@ -2992,6 +3363,7 @@ description = "More click."
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "more_click-0.1.2-py3-none-any.whl", hash = "sha256:f6387af37ef7e7423bd94b72a81a53c79c5086a3bfe5cc035da534ff0c2a0a9e"},
     {file = "more_click-0.1.2.tar.gz", hash = "sha256:085da66d5a9b823c5d912a888dca1fa0c8b3a14ed1b21ea9c8a1b814857a3981"},
@@ -3003,16 +3375,32 @@ click = "*"
 [package.extras]
 tests = ["coverage", "pytest"]
 
+[[package]]
+name = "more-click"
+version = "0.1.3"
+description = "Implementations of common CLI patterns on top of Click"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "more_click-0.1.3-py3-none-any.whl", hash = "sha256:12f0f3da94c84d39daaaec08e9503df8877f493812f8ebc3f0713081da48d282"},
+    {file = "more_click-0.1.3.tar.gz", hash = "sha256:c170987d37334278169fe3b9b388f1fcd9fc96439579354fd7c537537a182128"},
+]
+
+[package.dependencies]
+click = "*"
+
 [[package]]
 name = "more-itertools"
-version = "10.7.0"
+version = "10.8.0"
 description = "More routines for operating on iterables, beyond itertools"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "more_itertools-10.7.0-py3-none-any.whl", hash = "sha256:d43980384673cb07d2f7d2d918c616b30c659c089ee23953f601d6609c67510e"},
-    {file = "more_itertools-10.7.0.tar.gz", hash = "sha256:9fddd5403be01a94b204faadcff459ec3568cf110265d3c54323e1e866ad29d3"},
+    {file = "more_itertools-10.8.0-py3-none-any.whl", hash = "sha256:52d4362373dcf7c52546bc4af9a86ee7c4579df9a8dc268be0a2f949d376cc9b"},
+    {file = "more_itertools-10.8.0.tar.gz", hash = "sha256:f638ddf8a1a0d134181275fb5d58b086ead7c6a72429ad725c67503f13ba30bd"},
 ]
 
 [[package]]
@@ -3168,14 +3556,14 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
 
 [[package]]
 name = "ndex2"
-version = "3.10.0"
+version = "3.11.0"
 description = "Nice CX Python includes a client and a data model."
 optional = false
 python-versions = "*"
 groups = ["main"]
 files = [
-    {file = "ndex2-3.10.0-py2.py3-none-any.whl", hash = "sha256:fdb8307ccdbdf49044c9119373852242ca24a4926df1c5566e94965e59b70b67"},
-    {file = "ndex2-3.10.0.tar.gz", hash = "sha256:7e8cfc3fc940cddfd612810fc8c913ab61e01a43e4f482608e86c6548b81b7e1"},
+    {file = "ndex2-3.11.0-py2.py3-none-any.whl", hash = "sha256:cafb2efa38e9faf3f7e47805429d2498cfd127b5a452df020bf3c8e199c9c072"},
+    {file = "ndex2-3.11.0.tar.gz", hash = "sha256:3fbf4d96254f0e85a2162c9f77d970687fe5a41622671a553111238e81350512"},
 ]
 
 [package.dependencies]
@@ -3222,48 +3610,49 @@ test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "networkx"
-version = "3.4.2"
+version = "3.5"
 description = "Python package for creating and manipulating graphs and networks"
 optional = false
-python-versions = ">=3.10"
+python-versions = ">=3.11"
 groups = ["main"]
 markers = "python_version >= \"3.11\""
 files = [
-    {file = "networkx-3.4.2-py3-none-any.whl", hash = "sha256:df5d4365b724cf81b8c6a7312509d0c22386097011ad1abe274afd5e9d3bbc5f"},
-    {file = "networkx-3.4.2.tar.gz", hash = "sha256:307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1"},
+    {file = "networkx-3.5-py3-none-any.whl", hash = "sha256:0030d386a9a06dee3565298b4a734b68589749a544acbb6c412dc9e2489ec6ec"},
+    {file = "networkx-3.5.tar.gz", hash = "sha256:d4c6f9cf81f52d69230866796b82afbccdec3db7ae4fbd1b65ea750feed50037"},
 ]
 
 [package.extras]
-default = ["matplotlib (>=3.7)", "numpy (>=1.24)", "pandas (>=2.0)", "scipy (>=1.10,!=1.11.0,!=1.11.1)"]
-developer = ["changelist (==0.5)", "mypy (>=1.1)", "pre-commit (>=3.2)", "rtoml"]
-doc = ["intersphinx-registry", "myst-nb (>=1.1)", "numpydoc (>=1.8.0)", "pillow (>=9.4)", "pydata-sphinx-theme (>=0.15)", "sphinx (>=7.3)", "sphinx-gallery (>=0.16)", "texext (>=0.6.7)"]
-example = ["cairocffi (>=1.7)", "contextily (>=1.6)", "igraph (>=0.11)", "momepy (>=0.7.2)", "osmnx (>=1.9)", "scikit-learn (>=1.5)", "seaborn (>=0.13)"]
+default = ["matplotlib (>=3.8)", "numpy (>=1.25)", "pandas (>=2.0)", "scipy (>=1.11.2)"]
+developer = ["mypy (>=1.15)", "pre-commit (>=4.1)"]
+doc = ["intersphinx-registry", "myst-nb (>=1.1)", "numpydoc (>=1.8.0)", "pillow (>=10)", "pydata-sphinx-theme (>=0.16)", "sphinx (>=8.0)", "sphinx-gallery (>=0.18)", "texext (>=0.6.7)"]
+example = ["cairocffi (>=1.7)", "contextily (>=1.6)", "igraph (>=0.11)", "momepy (>=0.7.2)", "osmnx (>=2.0.0)", "scikit-learn (>=1.5)", "seaborn (>=0.13)"]
 extra = ["lxml (>=4.6)", "pydot (>=3.0.1)", "pygraphviz (>=1.14)", "sympy (>=1.10)"]
-test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
+test = ["pytest (>=7.2)", "pytest-cov (>=4.0)", "pytest-xdist (>=3.0)"]
+test-extras = ["pytest-mpl", "pytest-randomly"]
 
 [[package]]
 name = "notebook"
-version = "7.4.2"
+version = "7.5.0"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["dev"]
 files = [
-    {file = "notebook-7.4.2-py3-none-any.whl", hash = "sha256:9ccef602721aaa5530852e3064710b8ae5415c4e2ce26f8896d0433222755259"},
-    {file = "notebook-7.4.2.tar.gz", hash = "sha256:e739defd28c3f615a6bfb0a2564bd75018a9cc6613aa00bbd9c15e68eed2de1b"},
+    {file = "notebook-7.5.0-py3-none-any.whl", hash = "sha256:3300262d52905ca271bd50b22617681d95f08a8360d099e097726e6d2efb5811"},
+    {file = "notebook-7.5.0.tar.gz", hash = "sha256:3b27eaf9913033c28dde92d02139414c608992e1df4b969c843219acf2ff95e4"},
 ]
 
 [package.dependencies]
 jupyter-server = ">=2.4.0,<3"
-jupyterlab = ">=4.4.0,<4.5"
-jupyterlab-server = ">=2.27.1,<3"
+jupyterlab = ">=4.5.0rc0,<4.6"
+jupyterlab-server = ">=2.28.0,<3"
 notebook-shim = ">=0.2,<0.3"
 tornado = ">=6.2.0"
 
 [package.extras]
 dev = ["hatch", "pre-commit"]
 docs = ["myst-parser", "nbsphinx", "pydata-sphinx-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
-test = ["importlib-resources (>=5.0) ; python_version < \"3.10\"", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.27.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"]
+test = ["importlib-resources (>=5.0) ; python_version < \"3.10\"", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.28.0,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"]
 
 [[package]]
 name = "notebook-shim"
@@ -3346,14 +3735,14 @@ files = [
 
 [[package]]
 name = "oaklib"
-version = "0.6.22"
+version = "0.6.23"
 description = "Ontology Access Kit: Python library for common ontology operations over a variety of backends"
 optional = false
 python-versions = "<4.0.0,>=3.9"
 groups = ["main"]
 files = [
-    {file = "oaklib-0.6.22-py3-none-any.whl", hash = "sha256:c945538c071da6682ca5ebc04eb02d4e85b770aea94f4540fd6dcc6e3ce9becc"},
-    {file = "oaklib-0.6.22.tar.gz", hash = "sha256:bd557aeab6d8aca7ef8840f8e68da66110e33447f946107dc9f463a500a27674"},
+    {file = "oaklib-0.6.23-py3-none-any.whl", hash = "sha256:2e20732f49f91b21f85e55c0ddaba8365ecc473ce0b07929c7ec68c0ca500ace"},
+    {file = "oaklib-0.6.23.tar.gz", hash = "sha256:66cab87f2a672910d779c39e85dca90fdf8fc6728f37dd70d81f683791db52ff"},
 ]
 
 [package.dependencies]
@@ -3395,14 +3784,14 @@ semsimian = ["semsimian (>=0.2.18)"]
 
 [[package]]
 name = "oauthlib"
-version = "3.2.2"
+version = "3.3.1"
 description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 groups = ["main"]
 files = [
-    {file = "oauthlib-3.2.2-py3-none-any.whl", hash = "sha256:8139f29aac13e25d502680e9e19963e83f16838d48a0d71c287fe40e7067fbca"},
-    {file = "oauthlib-3.2.2.tar.gz", hash = "sha256:9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918"},
+    {file = "oauthlib-3.3.1-py3-none-any.whl", hash = "sha256:88119c938d2b8fb88561af5f6ee0eec8cc8d552b7bb1f712743136eb7523b7a1"},
+    {file = "oauthlib-3.3.1.tar.gz", hash = "sha256:0f0f8aa759826a193cf66c12ea1af1637f87b9b4622d46e866952bb022e538c9"},
 ]
 
 [package.extras]
@@ -3417,6 +3806,7 @@ description = "A client to the EBI Ontology Lookup Service"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "ols_client-0.1.4-py3-none-any.whl", hash = "sha256:7bdca0590042e07cc7ee3ef3fba99c3b6862cde6c8835afb129de31284b3e010"},
     {file = "ols_client-0.1.4.tar.gz", hash = "sha256:cd2a0f39107f39eaf0f40b9098f12d442cf3d43e28228e63feb407d0aeb44470"},
@@ -3433,6 +3823,29 @@ requests = "*"
 docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
 tests = ["coverage", "pytest"]
 
+[[package]]
+name = "ols-client"
+version = "0.2.1"
+description = "A client to the EBI Ontology Lookup Service"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "ols_client-0.2.1-py3-none-any.whl", hash = "sha256:e6d094b8d49711ed2b173b06bd3fbc62be4c8becd21def3bf4efec59096fcca8"},
+    {file = "ols_client-0.2.1.tar.gz", hash = "sha256:c5078446f025e2fbe24a1a2bbb924d7372216ca05e7ff11dba87aa7721be008a"},
+]
+
+[package.dependencies]
+class-resolver = "*"
+click = "*"
+more-click = "*"
+pystow = "*"
+requests = "*"
+
+[package.extras]
+similarity = ["numpy", "scikit-learn"]
+
 [[package]]
 name = "ontodev-cogs"
 version = "0.3.3"
@@ -3477,28 +3890,28 @@ tests = ["coverage", "pytest", "unittest-templates"]
 
 [[package]]
 name = "openai"
-version = "1.79.0"
+version = "2.8.1"
 description = "The official Python library for the openai API"
-optional = true
-python-versions = ">=3.8"
-groups = ["main"]
-markers = "extra == \"llm\""
+optional = false
+python-versions = ">=3.9"
+groups = ["main", "llm"]
 files = [
-    {file = "openai-1.79.0-py3-none-any.whl", hash = "sha256:d5050b92d5ef83f869cb8dcd0aca0b2291c3413412500eec40c66981b3966992"},
-    {file = "openai-1.79.0.tar.gz", hash = "sha256:e3b627aa82858d3e42d16616edc22aa9f7477ee5eb3e6819e9f44a961d899a4c"},
+    {file = "openai-2.8.1-py3-none-any.whl", hash = "sha256:c6c3b5a04994734386e8dad3c00a393f56d3b68a27cd2e8acae91a59e4122463"},
+    {file = "openai-2.8.1.tar.gz", hash = "sha256:cb1b79eef6e809f6da326a7ef6038719e35aa944c42d081807bfa1be8060f15f"},
 ]
 
 [package.dependencies]
 anyio = ">=3.5.0,<5"
 distro = ">=1.7.0,<2"
 httpx = ">=0.23.0,<1"
-jiter = ">=0.4.0,<1"
+jiter = ">=0.10.0,<1"
 pydantic = ">=1.9.0,<3"
 sniffio = "*"
 tqdm = ">4"
 typing-extensions = ">=4.11,<5"
 
 [package.extras]
+aiohttp = ["aiohttp", "httpx-aiohttp (>=0.1.9)"]
 datalib = ["numpy (>=1)", "pandas (>=1.2.3)", "pandas-stubs (>=1.1.0.11)"]
 realtime = ["websockets (>=13,<16)"]
 voice-helpers = ["numpy (>=2.0.2)", "sounddevice (>=0.5.1)"]
@@ -3525,6 +3938,7 @@ description = "A decorator to automatically detect mismatch when overriding a me
 optional = false
 python-versions = ">=3.6"
 groups = ["dev"]
+markers = "python_version <= \"3.11\""
 files = [
     {file = "overrides-7.7.0-py3-none-any.whl", hash = "sha256:c7ed9d062f78b8e4c1a7b70bd8796b35ead4d9f510227ef9c5dc7626c60d7e49"},
     {file = "overrides-7.7.0.tar.gz", hash = "sha256:55158fa3d93b98cc75299b1e67078ad9003ca27945c76162c1c0766d6f91820a"},
@@ -3536,7 +3950,7 @@ version = "25.0"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.8"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 files = [
     {file = "packaging-25.0-py3-none-any.whl", hash = "sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484"},
     {file = "packaging-25.0.tar.gz", hash = "sha256:d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f"},
@@ -3544,54 +3958,67 @@ files = [
 
 [[package]]
 name = "pandas"
-version = "2.2.3"
+version = "2.3.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "pandas-2.2.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1948ddde24197a0f7add2bdc4ca83bf2b1ef84a1bc8ccffd95eda17fd836ecb5"},
-    {file = "pandas-2.2.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:381175499d3802cde0eabbaf6324cce0c4f5d52ca6f8c377c29ad442f50f6348"},
-    {file = "pandas-2.2.3-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:d9c45366def9a3dd85a6454c0e7908f2b3b8e9c138f5dc38fed7ce720d8453ed"},
-    {file = "pandas-2.2.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:86976a1c5b25ae3f8ccae3a5306e443569ee3c3faf444dfd0f41cda24667ad57"},
-    {file = "pandas-2.2.3-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:b8661b0238a69d7aafe156b7fa86c44b881387509653fdf857bebc5e4008ad42"},
-    {file = "pandas-2.2.3-cp310-cp310-musllinux_1_2_x86_64.whl", hash = "sha256:37e0aced3e8f539eccf2e099f65cdb9c8aa85109b0be6e93e2baff94264bdc6f"},
-    {file = "pandas-2.2.3-cp310-cp310-win_amd64.whl", hash = "sha256:56534ce0746a58afaf7942ba4863e0ef81c9c50d3f0ae93e9497d6a41a057645"},
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 [package.dependencies]
@@ -3631,14 +4058,14 @@ xml = ["lxml (>=4.9.2)"]
 
 [[package]]
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 optional = false
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+    {file = "pandera-0.26.1.tar.gz", hash = "sha256:81a55a6429770d31b3bf4c3e8e1096a38296bd3009f9eca5780fad3c3c17fd82"},
 ]
 
 [package.dependencies]
@@ -3649,11 +4076,12 @@ typing_extensions = "*"
 typing_inspect = ">=0.6.0"
 
 [package.extras]
-all = ["black", "dask[dataframe]", "distributed", "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"]
+all = ["black", "dask[dataframe]", "distributed", "fastapi", "frictionless (<=4.40.8)", "geopandas (<1.1.0)", "hypothesis (>=6.92.7)", "ibis-framework (>=9.0.0)", "modin", "pandas-stubs", "polars (>=0.20.0)", "pyspark[connect] (>=3.2.0,<4.0.0)", "pyyaml (>=5.1)", "ray", "scipy", "shapely"]
 dask = ["dask[dataframe]", "distributed"]
 fastapi = ["fastapi"]
-geopandas = ["geopandas", "shapely"]
+geopandas = ["geopandas (<1.1.0)", "shapely"]
 hypotheses = ["scipy"]
+ibis = ["ibis-framework (>=9.0.0)"]
 io = ["black", "frictionless (<=4.40.8)", "pyyaml (>=5.1)"]
 modin = ["dask[dataframe]", "distributed", "modin", "ray"]
 modin-dask = ["dask[dataframe]", "distributed", "modin"]
@@ -3661,7 +4089,7 @@ modin-ray = ["modin", "ray"]
 mypy = ["pandas-stubs"]
 pandas = ["numpy (>=1.24.4)", "pandas (>=2.1.1)"]
 polars = ["polars (>=0.20.0)"]
-pyspark = ["pyspark[connect] (>=3.2.0)"]
+pyspark = ["pyspark[connect] (>=3.2.0,<4.0.0)"]
 strategies = ["hypothesis (>=6.92.7)"]
 
 [[package]]
@@ -3683,6 +4111,7 @@ description = "sqldf for pandas"
 optional = false
 python-versions = "*"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "pansql-0.0.1-py3-none-any.whl", hash = "sha256:0c49d8c23e418ac065af767ed350c544c0d6d96dc04e2faa1f8b37851d404988"},
     {file = "pansql-0.0.1.tar.gz", hash = "sha256:61091112442c5d663ea5c042b6327a9b6b94c6687831677dddda46f292532e29"},
@@ -3707,14 +4136,14 @@ files = [
 
 [[package]]
 name = "parso"
-version = "0.8.4"
+version = "0.8.5"
 description = "A Python Parser"
 optional = false
 python-versions = ">=3.6"
 groups = ["dev"]
 files = [
-    {file = "parso-0.8.4-py2.py3-none-any.whl", hash = "sha256:a418670a20291dacd2dddc80c377c5c3791378ee1e8d12bffc35420643d43f18"},
-    {file = "parso-0.8.4.tar.gz", hash = "sha256:eb3a7b58240fb99099a345571deecc0f9540ea5f4dd2fe14c2a99d6b281ab92d"},
+    {file = "parso-0.8.5-py2.py3-none-any.whl", hash = "sha256:646204b5ee239c396d040b90f9e272e9a8017c630092bf59980beb62fd033887"},
+    {file = "parso-0.8.5.tar.gz", hash = "sha256:034d7354a9a018bdce352f48b2a8a450f05e9d6ee85db84764e9b6bd96dafe5a"},
 ]
 
 [package.extras]
@@ -3739,27 +4168,27 @@ ptyprocess = ">=0.5"
 
 [[package]]
 name = "pip"
-version = "25.1.1"
+version = "25.3"
 description = "The PyPA recommended tool for installing Python packages."
-optional = true
+optional = false
 python-versions = ">=3.9"
-groups = ["main"]
-markers = "extra == \"llm\""
+groups = ["main", "llm"]
 files = [
-    {file = "pip-25.1.1-py3-none-any.whl", hash = "sha256:2913a38a2abf4ea6b64ab507bd9e967f3b53dc1ede74b01b0931e1ce548751af"},
-    {file = "pip-25.1.1.tar.gz", hash = "sha256:3de45d411d308d5054c2168185d8da7f9a2cd753dbac8acbfa88a8909ecd9077"},
+    {file = "pip-25.3-py3-none-any.whl", hash = "sha256:9655943313a94722b7774661c21049070f6bbb0a1516bf02f7c8d5d9201514cd"},
+    {file = "pip-25.3.tar.gz", hash = "sha256:8d0538dbbd7babbd207f261ed969c65de439f6bc9e5dbd3b3b9a77f25d95f343"},
 ]
 
 [[package]]
 name = "platformdirs"
-version = "4.3.8"
+version = "4.4.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev"]
+markers = "python_version < \"3.11\""
 files = [
-    {file = "platformdirs-4.3.8-py3-none-any.whl", hash = "sha256:ff7059bb7eb1179e2685604f4aaf157cfd9535242bd23742eadc3c13542139b4"},
-    {file = "platformdirs-4.3.8.tar.gz", hash = "sha256:3d512d96e16bcb959a814c9f348431070822a6496326a4be0911c40b5a74c2bc"},
+    {file = "platformdirs-4.4.0-py3-none-any.whl", hash = "sha256:abd01743f24e5287cd7a5db3752faf1a2d65353f38ec26d98e25a6db65958c85"},
+    {file = "platformdirs-4.4.0.tar.gz", hash = "sha256:ca753cf4d81dc309bc67b0ea38fd15dc97bc30ce419a7f58d13eb3bf14c4febf"},
 ]
 
 [package.extras]
@@ -3767,13 +4196,31 @@ docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.1.3)", "sphinx-a
 test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.4)", "pytest-cov (>=6)", "pytest-mock (>=3.14)"]
 type = ["mypy (>=1.14.1)"]
 
+[[package]]
+name = "platformdirs"
+version = "4.5.0"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
+optional = false
+python-versions = ">=3.10"
+groups = ["main", "dev"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "platformdirs-4.5.0-py3-none-any.whl", hash = "sha256:e578a81bb873cbb89a41fcc904c7ef523cc18284b7e3b3ccf06aca1403b7ebd3"},
+    {file = "platformdirs-4.5.0.tar.gz", hash = "sha256:70ddccdd7c99fc5942e9fc25636a8b34d04c24b335100223152c2803e4063312"},
+]
+
+[package.extras]
+docs = ["furo (>=2025.9.25)", "proselint (>=0.14)", "sphinx (>=8.2.3)", "sphinx-autodoc-typehints (>=3.2)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.4.2)", "pytest-cov (>=7)", "pytest-mock (>=3.15.1)"]
+type = ["mypy (>=1.18.2)"]
+
 [[package]]
 name = "pluggy"
 version = "1.6.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.9"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 files = [
     {file = "pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746"},
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@@ -3819,14 +4266,14 @@ pyyaml = ">=5.3.1"
 
 [[package]]
 name = "prometheus-client"
-version = "0.22.0"
+version = "0.23.1"
 description = "Python client for the Prometheus monitoring system."
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
 files = [
-    {file = "prometheus_client-0.22.0-py3-none-any.whl", hash = "sha256:c8951bbe64e62b96cd8e8f5d917279d1b9b91ab766793f33d4dce6c228558713"},
-    {file = "prometheus_client-0.22.0.tar.gz", hash = "sha256:18da1d2241ac2d10c8d2110f13eedcd5c7c0c8af18c926e8731f04fc10cd575c"},
+    {file = "prometheus_client-0.23.1-py3-none-any.whl", hash = "sha256:dd1913e6e76b59cfe44e7a4b83e01afc9873c1bdfd2ed8739f1e76aeca115f99"},
+    {file = "prometheus_client-0.23.1.tar.gz", hash = "sha256:6ae8f9081eaaaf153a2e959d2e6c4f4fb57b12ef76c8c7980202f1e57b48b2ce"},
 ]
 
 [package.extras]
@@ -3834,14 +4281,14 @@ twisted = ["twisted"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.51"
+version = "3.0.52"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "prompt_toolkit-3.0.51-py3-none-any.whl", hash = "sha256:52742911fde84e2d423e2f9a4cf1de7d7ac4e51958f648d9540e0fb8db077b07"},
-    {file = "prompt_toolkit-3.0.51.tar.gz", hash = "sha256:931a162e3b27fc90c86f1b48bb1fb2c528c2761475e57c9c06de13311c7b54ed"},
+    {file = "prompt_toolkit-3.0.52-py3-none-any.whl", hash = "sha256:9aac639a3bbd33284347de5ad8d68ecc044b91a762dc39b7c21095fcd6a19955"},
+    {file = "prompt_toolkit-3.0.52.tar.gz", hash = "sha256:28cde192929c8e7321de85de1ddbe736f1375148b02f2e17edd840042b1be855"},
 ]
 
 [package.dependencies]
@@ -3849,19 +4296,19 @@ wcwidth = "*"
 
 [[package]]
 name = "pronto"
-version = "2.7.0"
+version = "2.7.2"
 description = "Python frontend to ontologies."
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
-    {file = "pronto-2.7.0-py3-none-any.whl", hash = "sha256:da4fb4a6fd67ed7958cc3fc02ad0360ef81e48d2282b8e3fb9715209fcc64952"},
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+    {file = "pronto-2.7.2-py3-none-any.whl", hash = "sha256:9c4b037ae1f9598398f38a55306eb1af7c3cdf8be7d535925500b978b32d1450"},
+    {file = "pronto-2.7.2.tar.gz", hash = "sha256:ba3a07d4d84f71deb56ff4dea987ea513c21ad9c3ce172375647ff2471982b36"},
 ]
 
 [package.dependencies]
 chardet = ">=5.0,<6.0"
-fastobo = ">=0.13.0,<0.14.0"
+fastobo = ">=0.13.0,<0.15.0"
 networkx = ">=2.3,<4.0"
 python-dateutil = ">=2.8,<3.0"
 
@@ -3885,124 +4332,133 @@ testing = ["google-api-core (>=1.31.5)"]
 
 [[package]]
 name = "protobuf"
-version = "6.31.0"
+version = "6.33.1"
 description = ""
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
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 ]
 
 [[package]]
 name = "psutil"
-version = "7.0.0"
-description = "Cross-platform lib for process and system monitoring in Python.  NOTE: the syntax of this script MUST be kept compatible with Python 2.7."
+version = "7.1.3"
+description = "Cross-platform lib for process and system monitoring."
 optional = false
 python-versions = ">=3.6"
 groups = ["dev"]
 files = [
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 [[package]]
@@ -4035,15 +4491,14 @@ tests = ["pytest"]
 
 [[package]]
 name = "puremagic"
-version = "1.29"
+version = "1.30"
 description = "Pure python implementation of magic file detection"
-optional = true
+optional = false
 python-versions = "*"
-groups = ["main"]
-markers = "extra == \"llm\""
+groups = ["main", "llm"]
 files = [
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 [[package]]
@@ -4075,34 +4530,35 @@ pyasn1 = ">=0.6.1,<0.7.0"
 
 [[package]]
 name = "pycparser"
-version = "2.22"
+version = "2.23"
 description = "C parser in Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
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+version = "2.12.4"
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 python-versions = ">=3.9"
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 [package.dependencies]
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-pydantic-core = "2.33.2"
-typing-extensions = ">=4.12.2"
-typing-inspection = ">=0.4.0"
+pydantic-core = "2.41.5"
+typing-extensions = ">=4.14.1"
+typing-inspection = ">=0.4.2"
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
@@ -4110,126 +4566,148 @@ timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows
 
 [[package]]
 name = "pydantic-core"
-version = "2.33.2"
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 description = "Core functionality for Pydantic validation and serialization"
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 python-versions = ">=3.9"
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+]
+
+[package.dependencies]
+typing-extensions = ">=4.14.1"
 
 [[package]]
 name = "pydbml"
-version = "1.2.0"
+version = "1.2.1"
 description = "Python parser and builder for DBML"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
 files = [
-    {file = "pydbml-1.2.0-py3-none-any.whl", hash = "sha256:dc663786647c97bbb6ef61f7a5becd5e7bb304770bb3e2e01d3f43748d33064f"},
-    {file = "pydbml-1.2.0.tar.gz", hash = "sha256:c4fdb602f62b42e2b28674ea45e72f3d0e88bc6d186ea3a683685c41662ece14"},
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+    {file = "pydbml-1.2.1.tar.gz", hash = "sha256:8c1232291948fd5857792aa732a33e71418c47f6a2badea869dc37377394566b"},
 ]
 
 [package.dependencies]
@@ -4237,14 +4715,14 @@ pyparsing = ">=3.0.0"
 
 [[package]]
 name = "pygments"
-version = "2.19.1"
+version = "2.19.2"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.8"
 groups = ["main", "dev"]
 files = [
-    {file = "pygments-2.19.1-py3-none-any.whl", hash = "sha256:9ea1544ad55cecf4b8242fab6dd35a93bbce657034b0611ee383099054ab6d8c"},
-    {file = "pygments-2.19.1.tar.gz", hash = "sha256:61c16d2a8576dc0649d9f39e089b5f02bcd27fba10d8fb4dcc28173f7a45151f"},
+    {file = "pygments-2.19.2-py3-none-any.whl", hash = "sha256:86540386c03d588bb81d44bc3928634ff26449851e99741617ecb9037ee5ec0b"},
+    {file = "pygments-2.19.2.tar.gz", hash = "sha256:636cb2477cec7f8952536970bc533bc43743542f70392ae026374600add5b887"},
 ]
 
 [package.extras]
@@ -4268,14 +4746,14 @@ jsonasobj = ">=1.2.1"
 
 [[package]]
 name = "pyparsing"
-version = "3.2.3"
-description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+version = "3.2.5"
+description = "pyparsing - Classes and methods to define and execute parsing grammars"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "pyparsing-3.2.3-py3-none-any.whl", hash = "sha256:a749938e02d6fd0b59b356ca504a24982314bb090c383e3cf201c95ef7e2bfcf"},
-    {file = "pyparsing-3.2.3.tar.gz", hash = "sha256:b9c13f1ab8b3b542f72e28f634bad4de758ab3ce4546e4301970ad6fa77c38be"},
+    {file = "pyparsing-3.2.5-py3-none-any.whl", hash = "sha256:e38a4f02064cf41fe6593d328d0512495ad1f3d8a91c4f73fc401b3079a59a5e"},
+    {file = "pyparsing-3.2.5.tar.gz", hash = "sha256:2df8d5b7b2802ef88e8d016a2eb9c7aeaa923529cd251ed0fe4608275d4105b6"},
 ]
 
 [package.extras]
@@ -4285,10 +4763,10 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "pyreadline3"
 version = "3.5.4"
 description = "A python implementation of GNU readline."
-optional = true
+optional = false
 python-versions = ">=3.8"
-groups = ["main"]
-markers = "extra == \"llm\" and sys_platform == \"win32\""
+groups = ["main", "llm"]
+markers = "sys_platform == \"win32\""
 files = [
     {file = "pyreadline3-3.5.4-py3-none-any.whl", hash = "sha256:eaf8e6cc3c49bcccf145fc6067ba8643d1df34d604a1ec0eccbf7a18e6d3fae6"},
     {file = "pyreadline3-3.5.4.tar.gz", hash = "sha256:8d57d53039a1c75adba8e50dd3d992b28143480816187ea5efbd5c78e6c885b7"},
@@ -4347,6 +4825,7 @@ description = "Lightweight Python client for Apache Solr"
 optional = false
 python-versions = "*"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "pysolr-3.10.0.tar.gz", hash = "sha256:127b4a2dd169234acb1586643a6cd1e3e94b917921e69bf569d7b2a2aa0ef409"},
 ]
@@ -4358,16 +4837,35 @@ setuptools = "*"
 [package.extras]
 solrcloud = ["kazoo (>=2.5.0)"]
 
+[[package]]
+name = "pysolr"
+version = "3.11.0"
+description = "Lightweight Python client for Apache Solr"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "pysolr-3.11.0.tar.gz", hash = "sha256:bbd0e7467835316880f994b55386c9bc3c146733c17d85a3fed317755976c40a"},
+]
+
+[package.dependencies]
+requests = ">=2.32.5"
+setuptools = "*"
+
+[package.extras]
+solrcloud = ["kazoo (>=2.5.0)"]
+
 [[package]]
 name = "pystow"
-version = "0.7.0"
+version = "0.7.11"
 description = "Easily pick a place to store data for your Python code"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "pystow-0.7.0-py3-none-any.whl", hash = "sha256:5b6ed4b322a625f0163471f76989bae3b870fd20d64fed55a9150c68d34eb39d"},
-    {file = "pystow-0.7.0.tar.gz", hash = "sha256:5f8935a76d5f03b0645bedbe5dfcb3b777a0e755fda3e3fd3e4be7a1d2d058d0"},
+    {file = "pystow-0.7.11-py3-none-any.whl", hash = "sha256:bcafe098310499b2e91fedb8671b13e206058605319ad6987ecc2388ec8b5200"},
+    {file = "pystow-0.7.11.tar.gz", hash = "sha256:2b8b10dbf78b13d36a7fcd71efd47921cea1c5c9f1078b7c3cf49f658278f0e9"},
 ]
 
 [package.dependencies]
@@ -4378,34 +4876,61 @@ typing-extensions = "*"
 
 [package.extras]
 aws = ["boto3"]
+bs4 = ["bs4"]
 docs = ["sphinx (>=8)", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme (>=3.0)"]
 pandas = ["pandas"]
+ratelimit = ["ratelimit"]
 rdf = ["rdflib"]
 tests = ["coverage[toml]", "pytest", "requests-file"]
 xml = ["lxml"]
 
 [[package]]
 name = "pytest"
-version = "8.3.5"
+version = "8.4.2"
 description = "pytest: simple powerful testing with Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["main", "dev"]
+markers = "python_version < \"3.11\""
 files = [
-    {file = "pytest-8.3.5-py3-none-any.whl", hash = "sha256:c69214aa47deac29fad6c2a4f590b9c4a9fdb16a403176fe154b79c0b4d4d820"},
-    {file = "pytest-8.3.5.tar.gz", hash = "sha256:f4efe70cc14e511565ac476b57c279e12a855b11f48f212af1080ef2263d3845"},
+    {file = "pytest-8.4.2-py3-none-any.whl", hash = "sha256:872f880de3fc3a5bdc88a11b39c9710c3497a547cfa9320bc3c5e62fbf272e79"},
+    {file = "pytest-8.4.2.tar.gz", hash = "sha256:86c0d0b93306b961d58d62a4db4879f27fe25513d4b969df351abdddb3c30e01"},
 ]
 
 [package.dependencies]
-colorama = {version = "*", markers = "sys_platform == \"win32\""}
-exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
-iniconfig = "*"
-packaging = "*"
+colorama = {version = ">=0.4", markers = "sys_platform == \"win32\""}
+exceptiongroup = {version = ">=1", markers = "python_version < \"3.11\""}
+iniconfig = ">=1"
+packaging = ">=20"
 pluggy = ">=1.5,<2"
+pygments = ">=2.7.2"
 tomli = {version = ">=1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "requests", "setuptools", "xmlschema"]
+
+[[package]]
+name = "pytest"
+version = "9.0.1"
+description = "pytest: simple powerful testing with Python"
+optional = false
+python-versions = ">=3.10"
+groups = ["main", "dev"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "pytest-9.0.1-py3-none-any.whl", hash = "sha256:67be0030d194df2dfa7b556f2e56fb3c3315bd5c8822c6951162b92b32ce7dad"},
+    {file = "pytest-9.0.1.tar.gz", hash = "sha256:3e9c069ea73583e255c3b21cf46b8d3c56f6e3a1a8f6da94ccb0fcf57b9d73c8"},
+]
+
+[package.dependencies]
+colorama = {version = ">=0.4", markers = "sys_platform == \"win32\""}
+iniconfig = ">=1.0.1"
+packaging = ">=22"
+pluggy = ">=1.5,<2"
+pygments = ">=2.7.2"
+
+[package.extras]
+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-logging"
@@ -4427,7 +4952,7 @@ version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 files = [
     {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
     {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
@@ -4438,14 +4963,14 @@ six = ">=1.5"
 
 [[package]]
 name = "python-json-logger"
-version = "3.3.0"
+version = "4.0.0"
 description = "JSON Log Formatter for the Python Logging Package"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "python_json_logger-3.3.0-py3-none-any.whl", hash = "sha256:dd980fae8cffb24c13caf6e158d3d61c0d6d22342f932cb6e9deedab3d35eec7"},
-    {file = "python_json_logger-3.3.0.tar.gz", hash = "sha256:12b7e74b17775e7d565129296105bbe3910842d9d0eb083fc83a6a617aa8df84"},
+    {file = "python_json_logger-4.0.0-py3-none-any.whl", hash = "sha256:af09c9daf6a813aa4cc7180395f50f2a9e5fa056034c9953aec92e381c5ba1e2"},
+    {file = "python_json_logger-4.0.0.tar.gz", hash = "sha256:f58e68eb46e1faed27e0f574a55a0455eecd7b8a5b88b85a784519ba3cff047f"},
 ]
 
 [package.dependencies]
@@ -4456,15 +4981,14 @@ dev = ["backports.zoneinfo ; python_version < \"3.9\"", "black", "build", "freez
 
 [[package]]
 name = "python-ulid"
-version = "3.0.0"
+version = "3.1.0"
 description = "Universally unique lexicographically sortable identifier"
-optional = true
+optional = false
 python-versions = ">=3.9"
-groups = ["main"]
-markers = "extra == \"llm\""
+groups = ["main", "llm"]
 files = [
-    {file = "python_ulid-3.0.0-py3-none-any.whl", hash = "sha256:e4c4942ff50dbd79167ad01ac725ec58f924b4018025ce22c858bfcff99a5e31"},
-    {file = "python_ulid-3.0.0.tar.gz", hash = "sha256:e50296a47dc8209d28629a22fc81ca26c00982c78934bd7766377ba37ea49a9f"},
+    {file = "python_ulid-3.1.0-py3-none-any.whl", hash = "sha256:e2cdc979c8c877029b4b7a38a6fba3bc4578e4f109a308419ff4d3ccf0a46619"},
+    {file = "python_ulid-3.1.0.tar.gz", hash = "sha256:ff0410a598bc5f6b01b602851a3296ede6f91389f913a5d5f8c496003836f636"},
 ]
 
 [package.extras]
@@ -4477,6 +5001,7 @@ description = "A pure Python implementation of the trie data structure."
 optional = false
 python-versions = "*"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "PyTrie-0.4.0-py3-none-any.whl", hash = "sha256:f687c224ee8c66cda8e8628a903011b692635ffbb08d4b39c5f92b18eb78c950"},
     {file = "PyTrie-0.4.0.tar.gz", hash = "sha256:8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379"},
@@ -4499,213 +5024,238 @@ files = [
 
 [[package]]
 name = "pywin32"
-version = "310"
+version = "311"
 description = "Python for Window Extensions"
 optional = false
 python-versions = "*"
 groups = ["dev"]
-markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""
-files = [
-    {file = "pywin32-310-cp310-cp310-win32.whl", hash = "sha256:6dd97011efc8bf51d6793a82292419eba2c71cf8e7250cfac03bba284454abc1"},
-    {file = "pywin32-310-cp310-cp310-win_amd64.whl", hash = "sha256:c3e78706e4229b915a0821941a84e7ef420bf2b77e08c9dae3c76fd03fd2ae3d"},
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@@ -4802,6 +5352,7 @@ description = "JSON Referencing + Python"
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 python-versions = ">=3.9"
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+typing-extensions = {version = ">=4.4.0", markers = "python_version < \"3.13\""}
+
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 name = "requests"
-version = "2.32.3"
+version = "2.32.5"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["main", "dev"]
 files = [
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 ]
 
 [package.dependencies]
 certifi = ">=2017.4.17"
-charset-normalizer = ">=2,<4"
+charset_normalizer = ">=2,<4"
 idna = ">=2.5,<4"
 urllib3 = ">=1.21.1,<3"
 
@@ -4901,19 +5470,18 @@ requests = ">=2.0.1,<3.0.0"
 
 [[package]]
 name = "requirements-parser"
-version = "0.11.0"
+version = "0.13.0"
 description = "This is a small Python module for parsing Pip requirement files."
 optional = false
 python-versions = "<4.0,>=3.8"
-groups = ["dev"]
+groups = ["llm"]
 files = [
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 [package.dependencies]
 packaging = ">=23.2"
-types-setuptools = ">=69.1.0"
 
 [[package]]
 name = "rfc3339-validator"
@@ -4954,6 +5522,24 @@ files = [
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 ]
 
+[[package]]
+name = "rfc3987-syntax"
+version = "1.1.0"
+description = "Helper functions to syntactically validate strings according to RFC 3987."
+optional = false
+python-versions = ">=3.9"
+groups = ["dev"]
+files = [
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+]
+
+[package.dependencies]
+lark = ">=1.2.2"
+
+[package.extras]
+testing = ["pytest (>=8.3.5)"]
+
 [[package]]
 name = "roman-numerals-py"
 version = "3.1.0"
@@ -4973,126 +5559,294 @@ test = ["pytest (>=8)"]
 
 [[package]]
 name = "rpds-py"
-version = "0.25.0"
+version = "0.27.1"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev"]
+markers = "python_version < \"3.11\""
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-
-[package.dependencies]
-numpy = ">=1.23.5,<2.5"
-
-[package.extras]
-dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"]
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-test = ["Cython", "array-api-strict (>=2.0,<2.1.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja ; sys_platform != \"emscripten\"", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
-
 [[package]]
 name = "semsql"
 version = "0.4.0"
@@ -5274,14 +5963,14 @@ win32 = ["pywin32 ; sys_platform == \"win32\""]
 
 [[package]]
 name = "setuptools"
-version = "80.7.1"
+version = "80.9.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.9"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 files = [
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 [package.extras]
@@ -5314,7 +6003,7 @@ version = "1.17.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 files = [
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@@ -5326,12 +6015,11 @@ version = "1.3.1"
 description = "Sniff out which async library your code is running under"
 optional = false
 python-versions = ">=3.7"
-groups = ["main", "dev"]
+groups = ["main", "dev", "llm"]
 files = [
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 [[package]]
 name = "snowballstemmer"
@@ -5352,6 +6040,7 @@ description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
 optional = false
 python-versions = "*"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
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-version = "2.7"
+version = "2.8"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
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 [[package]]
@@ -5489,6 +6178,7 @@ description = "Sphinx extension that automatically documents click applications"
 optional = false
 python-versions = ">=3.8"
 groups = ["main", "dev"]
+markers = "python_version < \"3.11\""
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@@ -5499,15 +6189,37 @@ click = ">=8.0"
 docutils = "*"
 sphinx = ">=4.0"
 
+[[package]]
+name = "sphinx-click"
+version = "6.1.0"
+description = "Sphinx extension that automatically documents click applications"
+optional = false
+python-versions = ">=3.10"
+groups = ["main", "dev"]
+markers = "python_version >= \"3.11\""
+files = [
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+[package.dependencies]
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+docutils = "*"
+sphinx = ">=4.0"
+
+[package.extras]
+docs = ["reno"]
+test = ["pytest", "pytest-cov"]
+
 [[package]]
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-version = "0.5.0"
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 description = "A cool theme for sphinx documentation"
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 python-versions = "*"
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 files = [
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 [[package]]
@@ -5578,14 +6290,14 @@ test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-mermaid"
-version = "1.0.0"
+version = "1.1.0"
 description = "Mermaid diagrams in yours Sphinx powered docs"
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 groups = ["dev"]
 files = [
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 ]
 
 [package.dependencies]
@@ -5631,73 +6343,73 @@ test = ["pytest"]
 
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+version = "2.0.44"
 description = "Database Abstraction Library"
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+
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+greenlet = {version = ">=1", markers = "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]
@@ -5758,10 +6470,9 @@ url = ["furl (>=0.4.1)"]
 name = "sqlite-fts4"
 version = "1.0.3"
 description = "Python functions for working with SQLite FTS4 search"
-optional = true
+optional = false
 python-versions = "*"
-groups = ["main"]
-markers = "extra == \"llm\""
+groups = ["main", "llm"]
 files = [
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@@ -5774,10 +6485,9 @@ test = ["pytest"]
 name = "sqlite-migrate"
 version = "0.1b0"
 description = "A simple database migration system for SQLite, based on sqlite-utils"
-optional = true
+optional = false
 python-versions = "*"
-groups = ["main"]
-markers = "extra == \"llm\""
+groups = ["main", "llm"]
 files = [
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@@ -5793,10 +6503,9 @@ test = ["black", "mypy", "pytest", "ruff"]
 name = "sqlite-utils"
 version = "3.38"
 description = "CLI tool and Python library for manipulating SQLite databases"
-optional = true
+optional = false
 python-versions = ">=3.8"
-groups = ["main"]
-markers = "extra == \"llm\""
+groups = ["main", "llm"]
 files = [
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@@ -5819,19 +6528,20 @@ tui = ["trogon"]
 
 [[package]]
 name = "sssom"
-version = "0.4.15"
+version = "0.4.16"
 description = "Operations on SSSOM mapping tables"
 optional = false
 python-versions = "<4.0.0,>=3.9"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
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 ]
 
 [package.dependencies]
 click = ">=8.1.6"
-curies = ">=0.7.3"
+curies = ">=0.10.18"
 deprecation = ">=2.1.0,<3.0.0"
 importlib-resources = ">=6.1.1,<7.0.0"
 linkml = ">1.7.10"
@@ -5846,6 +6556,39 @@ sparqlwrapper = ">=2.0.0"
 sssom-schema = ">=1.0.0,<2.0.0"
 validators = ">=0.20.0"
 
+[[package]]
+name = "sssom"
+version = "0.4.17"
+description = "Operations on SSSOM mapping tables"
+optional = false
+python-versions = "<4.0.0,>=3.10"
+groups = ["main"]
+markers = "python_version >= \"3.11\""
+files = [
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+curies = ">=0.10.18"
+deprecation = ">=2.1.0"
+linkml = ">1.7.10"
+linkml-runtime = ">=1.7.5"
+pandas = ">1.0.3"
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+rdflib = ">=6.0.0"
+sparqlwrapper = ">=2.0.0"
+sssom-schema = "1.0.0"
+validators = ">=0.20.0"
+
+[package.extras]
+docs = ["myst-parser (>=0.18.1)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-click (>=4.3.0)", "sphinx-rtd-theme (>=1.0.0)"]
+networkx = ["networkx (>=3.1)"]
+pansql = ["pansql (>=0.0.1)"]
+rdflib-endpoint = ["fastapi", "httpx", "rdflib-endpoint", "uvicorn"]
+scipy = ["scipy"]
+
 [[package]]
 name = "sssom-schema"
 version = "1.0.0"
@@ -5899,7 +6642,7 @@ version = "0.9.0"
 description = "Pretty-print tabular data"
 optional = false
 python-versions = ">=3.7"
-groups = ["main"]
+groups = ["main", "llm"]
 files = [
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@@ -5931,6 +6674,7 @@ description = "ANSI color formatting for output in terminal"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
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@@ -5939,6 +6683,22 @@ files = [
 [package.extras]
 tests = ["pytest", "pytest-cov"]
 
+[[package]]
+name = "termcolor"
+version = "3.2.0"
+description = "ANSI color formatting for output in terminal"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version >= \"3.11\""
+files = [
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+
+[package.extras]
+tests = ["pytest", "pytest-cov"]
+
 [[package]]
 name = "terminado"
 version = "0.18.1"
@@ -5982,79 +6742,89 @@ test = ["pytest", "ruff"]
 
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 python-versions = ">=3.9"
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 ]
 
 [[package]]
@@ -6063,7 +6833,7 @@ version = "4.67.1"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
-groups = ["main"]
+groups = ["main", "llm"]
 files = [
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@@ -6097,58 +6867,30 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 
 [[package]]
 name = "typeguard"
-version = "4.4.2"
+version = "4.4.4"
 description = "Run-time type checker for Python"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
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 [package.dependencies]
 importlib_metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
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-
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-doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.3.0)"]
-test = ["coverage[toml] (>=7)", "mypy (>=1.2.0) ; platform_python_implementation != \"PyPy\"", "pytest (>=7)"]
-
-[[package]]
-name = "types-python-dateutil"
-version = "2.9.0.20250516"
-description = "Typing stubs for python-dateutil"
-optional = false
-python-versions = ">=3.9"
-groups = ["main", "dev"]
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+typing_extensions = ">=4.14.0"
 
 [[package]]
 name = "typing-extensions"
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-description = "Backported and Experimental Type Hints for Python 3.8+"
+version = "4.15.0"
+description = "Backported and Experimental Type Hints for Python 3.9+"
 optional = false
-python-versions = ">=3.8"
-groups = ["main", "dev"]
+python-versions = ">=3.9"
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 ]
 
 [[package]]
@@ -6169,14 +6911,14 @@ typing-extensions = ">=3.7.4"
 
 [[package]]
 name = "typing-inspection"
-version = "0.4.0"
+version = "0.4.2"
 description = "Runtime typing introspection tools"
 optional = false
 python-versions = ">=3.9"
-groups = ["main"]
+groups = ["main", "llm"]
 files = [
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 ]
 
 [package.dependencies]
@@ -6188,7 +6930,7 @@ version = "2025.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
-groups = ["main"]
+groups = ["main", "dev"]
 files = [
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@@ -6211,14 +6953,14 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 
 [[package]]
 name = "uritemplate"
-version = "4.1.1"
+version = "4.2.0"
 description = "Implementation of RFC 6570 URI Templates"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.9"
 groups = ["main"]
 files = [
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 ]
 
 [[package]]
@@ -6241,14 +6983,14 @@ dev = ["mypy", "pre-commit", "pytest", "pytest-cov", "pytest-socket", "ruff"]
 
 [[package]]
 name = "urllib3"
-version = "2.4.0"
+version = "2.5.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev"]
 files = [
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 ]
 
 [package.extras]
@@ -6317,14 +7059,14 @@ watchmedo = ["PyYAML (>=3.10)"]
 
 [[package]]
 name = "wcwidth"
-version = "0.2.13"
+version = "0.2.14"
 description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 groups = ["dev"]
 files = [
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 ]
 
 [[package]]
@@ -6334,11 +7076,25 @@ description = "A library for working with the color formats defined by HTML and
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev"]
+markers = "python_version < \"3.11\""
 files = [
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 ]
 
+[[package]]
+name = "webcolors"
+version = "25.10.0"
+description = "A library for working with the color formats defined by HTML and CSS."
+optional = false
+python-versions = ">=3.10"
+groups = ["main", "dev"]
+markers = "python_version >= \"3.11\""
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+
 [[package]]
 name = "webencodings"
 version = "0.5.1"
@@ -6353,133 +7109,164 @@ files = [
 
 [[package]]
 name = "websocket-client"
-version = "1.8.0"
+version = "1.9.0"
 description = "WebSocket client for Python with low level API options"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["dev"]
 files = [
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 [package.extras]
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+docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx_rtd_theme (>=1.1.0)"]
 optional = ["python-socks", "wsaccel"]
-test = ["websockets"]
+test = ["pytest", "websockets"]
 
 [[package]]
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+version = "4.0.15"
 description = "Jupyter interactive widgets for Jupyter Notebook"
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 python-versions = ">=3.7"
 groups = ["dev"]
 files = [
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 [[package]]
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 python-versions = ">=3.8"
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+    {file = "wrapt-2.0.1.tar.gz", hash = "sha256:9c9c635e78497cacb81e84f8b11b23e0aacac7a136e73b8e5b2109a1d9fc468f"},
+]
+
+[package.extras]
+dev = ["pytest", "setuptools"]
 
 [[package]]
 name = "zipp"
-version = "3.21.0"
+version = "3.23.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev"]
-markers = "python_version == \"3.9\""
+markers = "python_version < \"3.10\""
 files = [
-    {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"},
-    {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"},
+    {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"},
+    {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"},
 ]
 
 [package.extras]
@@ -6487,7 +7274,7 @@ check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"
 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 = ["big-O", "importlib-resources ; python_version < \"3.9\"", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
 type = ["pytest-mypy"]
 
 [extras]
@@ -6500,4 +7287,4 @@ postgres = ["psycopg2-binary"]
 [metadata]
 lock-version = "2.1"
 python-versions = "^3.9"
-content-hash = "36592b2404117e8f8e38e7c1b6b170def08c65c362e74c4e35bfd190d8a9225b"
+content-hash = "07bbec33b4f317fabfecb4a6e99fba309e185f9703634b8c0b4c47eb7822d7bd"
diff --git a/pyproject.toml b/pyproject.toml
index 9533229..2fb34b3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -56,6 +56,7 @@ rdflib = "^7.1.1"
 jsonasobj2 = "^1.0.4"
 deprecation = "^2.1.0"
 numpy = "<2.0"
+lxml = "^5.3.0"
 pydbml = "^1.1.2"
 pyyaml = "^6.0.2"
 llm = {version = "^0.21", optional = true}
@@ -68,6 +69,10 @@ sphinx-click = ">=3.1.0"
 sphinxcontrib-mermaid = ">=0.9.2"
 myst-parser = "*"
 jupyter = ">=1.0.0"
+lxml-stubs = "^0.5.1"
+
+[tool.poetry.group.llm.dependencies]
+llm = ">=0.12"
 lxml = ">=4.9.1"
 deptry = "^0.23.0"
 
diff --git a/schema_automator/cli.py b/schema_automator/cli.py
index 780d0b3..641abd8 100644
--- a/schema_automator/cli.py
+++ b/schema_automator/cli.py
@@ -32,6 +32,7 @@
 from schema_automator.importers.rdfs_import_engine import RdfsImportEngine
 from schema_automator.importers.sql_import_engine import SqlImportEngine
 from schema_automator.importers.tabular_import_engine import TableImportEngine
+from schema_automator.importers.xsd_import_engine import XsdImportEngine
 from schema_automator.utils.schemautils import write_schema
 from schema_automator import __version__
 
@@ -497,6 +498,23 @@ def import_rdfs(rdfsfile: str, output: str, metamodel_mappings: str, schema_name
     schema = sie.convert(rdfsfile, name=schema_name, **args)
     write_schema(schema, output)
 
+@main.command()
+@click.argument('xsd')
+@output_option
+@schema_name_option
+@click.option('--output', '-o', help="Path to saved yaml schema")
+def import_xsd(xsd: str, output: str, **kwargs):
+    """
+    Import an XML Schema Definition Language (XSD) schema to LinkML
+
+    Example:
+
+        schemauto import-xsd schema.xml -o prov.yaml
+    """
+    engine = XsdImportEngine()
+    schema = engine.convert(xsd, **kwargs)
+    write_schema(schema, output)
+
 @main.command()
 @click.argument('rdffile')
 @output_option
diff --git a/schema_automator/importers/__init__.py b/schema_automator/importers/__init__.py
index 2011d25..21d1c8f 100644
--- a/schema_automator/importers/__init__.py
+++ b/schema_automator/importers/__init__.py
@@ -3,3 +3,13 @@
 from schema_automator.importers.dosdp_import_engine import DOSDPImportEngine
 from schema_automator.importers.frictionless_import_engine import FrictionlessImportEngine
 from schema_automator.importers.cadsr_import_engine import CADSRImportEngine
+from schema_automator.importers.xsd_import_engine import XsdImportEngine
+
+__all__ = [
+    'JsonSchemaImportEngine',
+    'OwlImportEngine',
+    'DOSDPImportEngine',
+    'FrictionlessImportEngine',
+    'CADSRImportEngine',
+    'XsdImportEngine'
+]
diff --git a/schema_automator/importers/xsd_import_engine.py b/schema_automator/importers/xsd_import_engine.py
new file mode 100644
index 0000000..259767c
--- /dev/null
+++ b/schema_automator/importers/xsd_import_engine.py
@@ -0,0 +1,633 @@
+from __future__ import annotations
+from dataclasses import dataclass, field
+import re
+from types import GenericAlias
+from typing import Any, Iterable, Type, cast, TypeVar
+from urllib.parse import urljoin
+from linkml.utils.schema_builder import SchemaBuilder
+from linkml_runtime.linkml_model import (
+    SchemaDefinition,
+    SlotDefinition,
+    ClassDefinition,
+)
+from linkml_runtime.linkml_model.meta import AnonymousSlotExpression
+from linkml_runtime.utils import formatutils
+from lxml import etree
+
+
+from linkml_runtime.linkml_model import SchemaDefinition
+from schema_automator.importers.import_engine import ImportEngine
+
+# Mapping between https://www.w3.org/TR/2012/REC-xmlschema11-2-20120405/datatypes.html#built-in-primitive-datatypes and https://linkml.io/linkml-model/latest/docs/#types
+TYPE_MAP = {
+    "anyURI": "Uri",
+    "boolean": "Boolean",
+    "date": "Date",
+    "dateTime": "DateTime",
+    "decimal": "Decimal",
+    "double": "Double",
+    "float": "Float",
+    "string": "String",
+    "time": "Time",
+    "int": "Integer",
+    "integer": "Integer",
+    # NMTOKEN is basically just a string inside an attribute
+    "NMTOKEN": "String",
+}
+PLACEHOLDER_NAME = "PLACEHOLDER"
+Attributes = dict[str, SlotDefinition]
+MISSING_TYPES = {
+    "base64Binary",
+    "duration",
+    "hexBinary",
+    "gDay",
+    "gMonth",
+    "gMonthDay",
+    "gYear",
+    "gYearMonth",
+    "NOTATION",
+    "QName",
+    "normalizedString",
+    "token",
+    "language",
+    "NMTOKEN",
+    "NMTOKENS",
+    "Name",
+    "NCName",
+    "ID",
+    "IDREF",
+    "IDREFS",
+    "ENTITY",
+    "ENTITIES",
+    "nonPositiveInteger",
+    "negativeInteger",
+    "long",
+    "short",
+    "byte",
+    "nonNegativeInteger",
+    "unsignedLong",
+    "unsignedInt",
+    "unsignedShort",
+    "unsignedByte",
+    "positiveInteger",
+}
+XSD = "http://www.w3.org/2001/XMLSchema"
+NAMESPACES = {"xsd": "http://www.w3.org/2001/XMLSchema"}
+SCHEMA = etree.QName(XSD, "schema")
+COMPLEX_TYPE = etree.QName(XSD, "complexType")
+SIMPLE_TYPE = etree.QName(XSD, "simpleType")
+DOCUMENTATION = etree.QName(XSD, "documentation")
+ANNOTATION = etree.QName(XSD, "annotation")
+LIST = etree.QName(XSD, "list")
+COMPLEX_CONTENT = etree.QName(XSD, "complexContent")
+SIMPLE_CONTENT = etree.QName(XSD, "simpleContent")
+ELEMENT = etree.QName(XSD, "element")
+SEQUENCE = etree.QName(XSD, "sequence")
+CHOICE = etree.QName(XSD, "choice")
+RESTRICTION = etree.QName(XSD, "restriction")
+EXTENSION = etree.QName(XSD, "extension")
+UNION = etree.QName(XSD, "union")
+ALL = etree.QName(XSD, "all")
+MIN_LENGTH = etree.QName(XSD, "minLength")
+MAX_LENGTH = etree.QName(XSD, "maxLength")
+PATTERN = etree.QName(XSD, "pattern")
+ATTRIBUTE = etree.QName(XSD, "attribute")
+MIN_INCLUSIVE = etree.QName(XSD, "minInclusive")
+MAX_INCLUSIVE = etree.QName(XSD, "maxInclusive")
+GROUP = etree.QName(XSD, "group")
+
+T = TypeVar("T")
+def assert_type(x: Any, t: Type[T]) -> T:
+    """
+    Utility function to assert that a value is of a certain type.
+    Useful when we know that, say, `element.text` is a string and not bytes.
+    Unlike `cast`, this function will raise an error if the type is incorrect to avoid silent failures.
+    """
+    # Allow generics such as list[t] to be passed in, but only check the base type such as list
+    if isinstance(t, GenericAlias):
+        base_type = t.__origin__
+    else:
+        base_type = t
+    if not isinstance(x, base_type):
+        raise TypeError(f"Expected {t}, got {type(x)}")
+    return x
+
+def xsd_to_linkml_type(xsd_type: etree.QName) -> str:
+    """
+    Returns the LinkML type from an XSD type
+    """
+    if xsd_type.namespace == XSD:
+        if xsd_type.localname in TYPE_MAP:
+            # Atomic XSD types can be looked up
+            return TYPE_MAP[xsd_type.localname]
+        elif xsd_type.localname in MISSING_TYPES:
+            raise ValueError(
+                f"Atomic type {xsd_type} does not have a corresponding LinkML type"
+            )
+        else:
+            raise ValueError(f"Atomic type {xsd_type} is not defined in the standard")
+    else:
+        # Assume any remaining type is a complex type that we have or will define separately
+        return xsd_type.localname
+
+
+def resolve_type(el: etree._Element, attribute: str) -> etree.QName:
+    """
+    Returns the fully resolved type of an XSD element
+
+    Params:
+        el: the element to resolve the type of. Must be either an <xsd:element> or <xsd:attribute>, with a 'type' attribute.
+        attribute: the attribute that holds the type information, e.g. "type" or "base"
+    """
+    typ: str = el.attrib.get(attribute, "string")
+    if typ.count(":") == 1:
+        # Hacky fallback for when a custom namespace is used
+        prefix, name = typ.split(":")
+        return etree.QName(el.nsmap[prefix], name)
+    else:
+        return etree.QName(typ)
+
+
+def element_to_linkml_type(el: etree._Element, attribute: str) -> str:
+    """
+    Returns the LinkML type of an XSD element
+
+    Params:
+        el: the element to resolve the type of. Must be either an <xsd:element> or <xsd:attribute>, with a 'type' attribute.
+        attribute: the attribute that holds the type information, e.g. "type" or "base"
+    """
+    return xsd_to_linkml_type(resolve_type(el, attribute))
+
+
+def find_class_name(el: etree._Element, root_name: str = "Root") -> str:
+    """
+    Returns the name of the class that this element is a slot for
+
+    Params:
+        el: the element that will be a slot for the class whose name we want to find
+        root_name: class name to assign to the schema's root
+    """
+    for parent in el.iterancestors():
+        if "name" in parent.attrib:
+            return assert_type(parent.attrib["name"], str)
+        elif parent.tag == SCHEMA:
+            return root_name
+    raise ValueError("Could not find class name for element")
+
+def get_value_element(cls: ClassDefinition) -> SlotDefinition:
+    if not isinstance(cls.attributes, dict):
+        raise ValueError("cls.attributes should be a dictionary at this point")
+    if "value" not in cls.attributes:
+        raise ValueError("Value element should have been added by this stage")
+    return cast(SlotDefinition, cls.attributes["value"])
+
+@dataclass
+class XsdImportEngine(ImportEngine):
+    sb: SchemaBuilder = field(default_factory=lambda: SchemaBuilder())
+    target_ns: str | None = None
+
+    def __post_init__(self):
+        self.sb.add_defaults()
+        self.sb.add_prefix("xsd", XSD)
+
+    def visit_element(self, el: etree._Element) -> SlotDefinition:
+        """
+        Converts an `<xsd:element>` into a SlotDefinition
+
+        See 3.3.2 XML Representation of Element Declaration Schema Components: https://www.w3.org/TR/2012/REC-xmlschema11-1-20120405/structures.html#declare-element
+        """
+
+        slot_name = formatutils.lcamelcase(assert_type(el.attrib["name"], str)) if "name" in el.attrib else PLACEHOLDER_NAME
+        slot = SlotDefinition(
+            name=formatutils.lcamelcase(slot_name) if "name" in el.attrib else PLACEHOLDER_NAME,
+            slot_uri=urljoin(self.target_ns, slot_name) if self.target_ns else None,
+            instantiates=["xsd:element"],
+            range = "boolean"
+        )
+        """
+        XML supports empty elements, which we can represent as booleans.
+        For example this XML data:
+        ```xml
+        <parent>
+            <some_flag></some_flag>
+        </parent>
+        ```
+        Can be represented as:
+        ```yaml
+        parent:
+            some_flag: true
+        ```
+        """
+
+        # First pass, to determine if this is simple or complex
+        for child in el:
+            if child.tag == COMPLEX_TYPE:
+                # If we find a complex type, we need to create a class
+                cls_name: str = el.attrib.get("name", PLACEHOLDER_NAME)
+                cls = ClassDefinition(
+                    name=cls_name,
+                    class_uri=urljoin(self.target_ns, cls_name) if self.target_ns else None
+                )
+                self.sb.add_class(cls)
+                slot.range = cls_name
+                self.visit_complex_type(child, cls)
+            elif child.tag == SIMPLE_TYPE:
+                # If we find a simple type, the range is a restriction of a primitive type
+                self.visit_simple_type(child, slot)
+
+
+        if "type" in el.attrib:
+            slot.range = element_to_linkml_type(el, "type")
+
+        if "ref" in el.attrib:
+            # If we find a ref, we're creating a slot. Also, that slot's range is a reference to another class.
+            # We can make up a name for the slot using the referenced class, although the slot doesn't actually have a name in XSD
+            slot.range = assert_type(el.attrib["ref"], str)
+
+            if slot.name == PLACEHOLDER_NAME:
+                slot.name = formatutils.lcamelcase(assert_type(el.attrib["ref"], str))
+        
+        # Second pass, to add annotations
+        for child in el:
+            if child.tag == ANNOTATION:
+                # If we find an annotation, we can use it as documentation
+                slot.description = self.visit_annotation(child, slot.description)
+
+        return slot
+
+    def visit_documentation(self, el: etree._Element) -> str:
+        """
+        Converts an `<xsd:documentation>` into a string
+        """
+        return re.sub(r"\s+", " ", assert_type(el.text, str)).strip()
+
+    def visit_annotation(self, el: etree._Element, existing: str | None = None) -> str:
+        """
+        Converts an annotation into a string to be used for documentation
+
+        See 3.15.2 XML Representation of Annotation Schema Components: https://www.w3.org/TR/2012/REC-xmlschema11-1-20120405/structures.html#declare-annotation
+
+        Params:
+            el: the `<xsd:annotation>` element
+            existing: any existing documentation to append to
+        """
+        # Note: This only supports xsd:documentation, other annotation types are ignored
+        text = []
+        if existing is not None:
+            text.append(existing)
+        for child in el:
+            if child.tag == DOCUMENTATION:
+                text.append(self.visit_documentation(child))
+        return "\n".join(text)
+
+    def visit_simple_type_restriction(self, el: etree._Element, slot: SlotDefinition | AnonymousSlotExpression) -> None:
+        """"
+        Visits an <xsd:restriction> and applies type restrictions to a slot.
+
+        Despite the name, this can be used for both simple types:
+            ```xml
+            <xsd:simpleType>
+                <xsd:restriction>
+                ...
+                </xsd:restriction>
+            </xsd:simpleType>
+            ```
+        and complex types:
+            ```xml
+            <xsd:complexType>
+                <xsd:simpleContent>
+                    <xsd:restriction>
+                    ...
+                    </xsd:restriction>
+                </xsd:simpleContent>
+            </xsd:complexType>
+            ```
+        Since there are a subset of elements that can be used inside both.
+        """
+        slot.range = element_to_linkml_type(el, "base")
+        for child in el:
+            value = assert_type(child.attrib["value"], str)
+            if child.tag == MIN_INCLUSIVE:
+                slot.minimum_value = value
+            elif child.tag == MAX_INCLUSIVE:
+                slot.maximum_value = value
+            elif child.tag == PATTERN:
+                slot.pattern = value
+            elif child.tag == MIN_LENGTH:
+                slot.minimum_cardinality = int(value)
+            elif child.tag == MAX_LENGTH:
+                slot.maximum_cardinality = int(value)
+
+    def visit_simple_content_restriction(self, el: etree._Element, cls: ClassDefinition) -> None:
+        """
+        Visit a restriction inside a simple content element:
+        ```xml
+        <xsd:complexType>
+            <xsd:simpleContent>
+                <xsd:restriction>
+                ...
+                </xsd:restriction>
+            </xsd:simpleContent>
+        </xsd:complexType>
+        ```
+        """
+        value = get_value_element(cls)
+        self.visit_simple_type_restriction(el, value)
+        for child in el:
+            if child.tag == ATTRIBUTE:
+                if cls.attributes is None:
+                    cls.attributes = {}
+                attributes = assert_type(cls.attributes, Attributes)
+                name = assert_type(child.attrib["name"], str)
+                attributes[name] = self.visit_attribute(child)
+
+    def visit_simple_content_extension(self, el: etree._Element, cls: ClassDefinition) -> None:
+        """
+        Visit a:
+        ```xml
+        <xsd:complexType>
+            <xsd:simpleContent>
+                <xsd:extension>
+                ...
+                </xsd:extension>
+            </xsd:simpleContent>
+        </xsd:complexType>
+        ```
+        """
+        cls.is_a = element_to_linkml_type(el, "base")
+        for child in el:
+            if child.tag == ATTRIBUTE:
+                name = assert_type(child.attrib["name"], str)
+                attributes = assert_type(cls.attributes, dict[str, SlotDefinition])
+                attributes[name] = self.visit_attribute(child)
+
+    def visit_simple_content(self, el: etree._Element, cls: ClassDefinition) -> None:
+        """
+        Visit a:
+        ```xml
+        <xsd:complexType>
+            <xsd:simpleContent>
+                ...
+            </xsd:simpleContent>
+        </xsd:complexType>
+        ```
+        See 3.4.2.2 Mapping Rules for Complex Types with Simple Content: https://www.w3.org/TR/2012/REC-xmlschema11-2-20120405/datatypes.html#xr-defn
+
+        simpleContent maps to a ClassDefinition as it can have multiple values due to XML attributes. 
+        It must also have a main value which is the content inside the XML element. Therefore:
+        ```xml
+        <xsd:complexType name="SomeClass">
+            <xsd:simpleContent>
+                <xsd:restriction base="xsd:string">
+                    <xsd:attribute name="someAttr" type="xsd:integer"/>
+                </xsd:restriction>
+            </xsd:simpleContent>
+        </xsd:complexType>
+        ```
+        Would be represented as:
+        ```yaml
+        SomeClass:
+            attributes:
+                someAttr:
+                    range: integer
+                value:
+                    range: string
+        ```
+        """
+        value_slot = SlotDefinition(
+            name="value",
+            comments=["Mapped from the main content of the element"],
+        )
+
+        attributes = assert_type(cls.attributes, Attributes)
+        attributes["value"] = value_slot
+        for child in el:
+            if child.tag == RESTRICTION:
+                self.visit_simple_content_restriction(child, cls)
+            elif child.tag == EXTENSION:
+                self.visit_simple_content_extension(child, cls)
+            elif child.tag == ANNOTATION:
+                # Annotations inside simple content are applied to the value slot, not the class
+                value_slot.description = self.visit_annotation(child, value_slot.description)
+
+    def visit_simple_type(self, el: etree._Element, slot: SlotDefinition | AnonymousSlotExpression) -> None:
+        """
+        Converts an `<xsd:simpleType>` into a LinkML type
+
+        A simple type always maps to a slot in LinkML since it cannot have attributes or children.
+        e.g.
+        ```xml
+        <xsd:attribute>
+            <xsd:simpleType>
+             ...
+            </xsd:simpleType>
+          </xsd:attribute>
+        ```
+
+        See 3.16.2 XML Representation of Simple Type Definition Schema Components: https://www.w3.org/TR/xmlschema11-1/#declare-datatype
+
+        Params:
+            el: a <xsd:simpleType> element
+            slot: the slot to annotate
+        """
+        for child in el:
+            if child.tag == ANNOTATION:
+                slot.description = self.visit_annotation(child, slot.description)
+            elif child.tag == RESTRICTION:
+                self.visit_simple_type_restriction(child, slot)
+            elif child.tag == LIST:
+                slot.multivalued = True
+                if "itemType" in child.attrib:
+                    slot.range = assert_type(child.attrib["itemType"], str)
+                else:
+                    slot.range = AnonymousSlotExpression()
+                    for list_child in child:
+                        if list_child.tag == SIMPLE_TYPE:
+                            self.visit_simple_type(list_child, slot.range)
+                        else:
+                            raise ValueError("Only xsd:simpleType is allowed inside xsd:list")
+                raise ValueError("xsd:list must have an itemType attribute or an xsd:simpleType child element")
+            elif child.tag == UNION:
+                slot.any_of = []
+                for union_child in child:
+                    union_slot = AnonymousSlotExpression()
+                    self.visit_simple_type(union_child, union_slot)
+                    slot.any_of.append(union_slot)
+
+    def visit_attribute(self, el: etree._Element) -> SlotDefinition:
+        """
+        Converts an `<xsd:attribute>` into a SlotDefinition
+        """
+        description: str | None = None
+
+        for child in el:
+            if child.tag == ANNOTATION:
+                description = self.visit_annotation(child)
+
+        return SlotDefinition(
+            name=formatutils.lcamelcase(assert_type(el.attrib["name"], str)),
+            slot_uri=(
+                urljoin(self.target_ns, assert_type(el.attrib["name"], str)) if self.target_ns else None
+            ),
+            range=element_to_linkml_type(el, "type"),
+            required=el.attrib.get("use") == "required",
+            instantiates=["xsd:attribute"],
+            description=description
+        )
+    
+    def visit_complex_content_child(self, el: etree._Element, cls: ClassDefinition) -> None:
+        """
+        Visit any of the following children of an xsd:complexContent element.
+        We can reuse the functionality since each of these elements can contain sequence, group, choice etc
+
+        ```xml
+        <xsd:complexType>
+            <xsd:complexContent>
+                <xsd:extension>
+                    ...
+                </xsd:extension>
+            </xsd:complexContent>
+        </xsd:complexType>,
+        ```, or
+
+        ```xml
+        <xsd:complexType>
+            <xsd:complexContent>
+                <xsd:restriction>
+                    ...
+                </xsd:restriction>
+            </xsd:complexContent>
+        </xsd:complexType>
+        ```
+        """
+        if "base" in el.attrib:
+            cls.is_a = element_to_linkml_type(el, "base")
+
+        attributes = assert_type(cls.attributes, Attributes)
+        if el.tag == SEQUENCE:
+            attributes |= {
+                slot.name: slot for slot in self.visit_sequence(el)
+            }
+        elif el.tag == GROUP:
+            raise NotImplementedError("xsd:group is not yet supported")
+        elif el.tag == ALL:
+            raise NotImplementedError("xsd:all is not yet supported")
+        elif el.tag == CHOICE:
+            attributes |= {
+                slot.name: slot for slot in self.visit_choice(el)
+            }
+        elif el.tag == ATTRIBUTE:
+            slot = self.visit_attribute(el)
+            attributes[slot.name] = slot
+        elif el.tag == ANNOTATION:
+            cls.description = self.visit_annotation(el, cls.description)
+    
+    def visit_complex_content(self, el: etree._Element, cls: ClassDefinition) -> None:
+        """
+        Visit a:
+        ```xml
+        <xsd:complexType>
+            <xsd:complexContent>
+                ...
+            </xsd:complexContent>
+        </xsd:complexType>
+        ```
+
+        See 3.4.2.3 Mapping Rules for Complex Types with Complex Content: https://www.w3.org/TR/xmlschema11-1/#dcl.ctd.ctcc
+
+        Params:
+            el: the <xsd:complexContent> element
+            cls: the class to annotate, derived from the enclosing <xsd:complexType> element
+        """
+        #: If we have found an extension or restriction
+        for child in el:
+            if child.tag == EXTENSION:
+                self.visit_complex_content_child(child, cls)
+            elif child.tag == RESTRICTION:
+                self.visit_complex_content_child(child, cls)
+            elif child.tag == ANNOTATION:
+                cls.description = self.visit_annotation(child, cls.description)
+                
+    def visit_complex_type(self, el: etree._Element, cls: ClassDefinition) -> None:
+        """
+        Adds information from a `<xsd:complexType>` onto a ClassDefinition
+
+        See 3.4 Complex Type Definitions: https://www.w3.org/TR/xmlschema11-1/#Complex_Type_Definitions
+        """
+        # Update the class name using the complex type's name, if we don't already have one
+        if cls.name == PLACEHOLDER_NAME and "name" in el.attrib:
+            cls.name = assert_type(el.attrib["name"], str)
+            cls.class_uri = urljoin(self.target_ns, cls.name) if self.target_ns else None
+
+        found_content = False
+        for child in el:
+            if child.tag == COMPLEX_CONTENT:
+                self.visit_complex_content(child, cls)
+                found_content = True
+            elif child.tag == SIMPLE_CONTENT:
+                self.visit_simple_content(child, cls)
+                found_content = True
+
+        if not found_content:
+            """ 
+            3.4.2.3.2 Mapping Rules for Complex Types with Implicit Complex Content:
+            > When the <complexType> source declaration has neither <simpleContent> nor <complexContent> as a child, it is taken as shorthand for complex content restricting ·xs:anyType·. 
+            """
+            for child in el:
+                self.visit_complex_content_child(child, cls)
+
+    def visit_choice(self, el: etree._Element) -> Iterable[SlotDefinition]:
+        """
+        Converts an xsd:choice into a list of SlotDefinitions
+        """
+        # TODO: indicate that not all slots can be used at the same time
+        return self.visit_sequence(el)
+
+    def visit_sequence(self, el: etree._Element) -> Iterable[SlotDefinition]:
+        """
+        Converts an xsd:sequence into a list of SlotDefinitions
+        """
+        for child in el:
+            if child.tag == ELEMENT:
+                yield self.visit_element(child)
+            elif child.tag == CHOICE:
+                yield from self.visit_choice(child)
+            elif child.tag == SEQUENCE:
+                yield from self.visit_sequence(child)
+            elif isinstance(child, etree._Comment):
+                pass
+            else:
+                print(f"Skipping unknown tag {child.tag}")
+
+    def visit_schema(self, schema: etree._Element) -> None:
+        """
+        Converts an xsd:schema into a SchemaDefinition
+        """
+        self.target_ns = schema.attrib.get("targetNamespace")
+        if self.target_ns is not None and not self.target_ns.endswith("/"):
+            # Ensure that the target namespace ends with a slash
+            self.target_ns += "/"
+
+        attributes: dict[str, SlotDefinition] = {}
+        for child in schema:
+            if child.tag == ELEMENT:
+                definition = self.visit_element(child)
+                attributes[definition.name] = definition
+            elif child.tag == COMPLEX_TYPE:
+                # complexType can be at the top level
+                cls = ClassDefinition(name=PLACEHOLDER_NAME)
+                self.visit_complex_type(child, cls)
+                self.sb.add_class(cls)
+        schema_root = ClassDefinition(
+            name="SchemaRoot",
+            class_uri=urljoin(self.target_ns, "SchemaRoot") if self.target_ns else None,
+            attributes=attributes,
+            description="Entry point of the schema, treated as a class",
+        )
+        self.sb.add_class(schema_root)
+
+    def convert(self, file: str, **kwargs: Any) -> SchemaDefinition:
+        parser = etree.XMLParser(remove_blank_text=True)
+        tree = etree.parse(file, parser=parser)
+        self.visit_schema(tree.getroot())
+        return self.sb.schema
diff --git a/tests/test_importers/test_xsd_importer.py b/tests/test_importers/test_xsd_importer.py
new file mode 100644
index 0000000..8dc8c2d
--- /dev/null
+++ b/tests/test_importers/test_xsd_importer.py
@@ -0,0 +1,59 @@
+from linkml_runtime import SchemaView
+from schema_automator.importers import XsdImportEngine
+import tempfile
+
+def parse_string(xsd: str) -> SchemaView:
+    engine = XsdImportEngine()
+    with tempfile.NamedTemporaryFile(mode='w', delete=False) as f:
+        f.write('''<xsd:schema
+            xmlns="http://www.dummy/name/space"
+            targetNamespace="http://www.dummy/name/space"
+            xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+            xmlns:xml="http://www.w3.org/XML/1998/namespace"
+            version="2"
+            elementFormDefault="qualified">
+        ''')
+        f.write(xsd)
+        f.write("</xsd:schema>")
+    schema = engine.convert(f.name)
+    return SchemaView(schema)
+
+def test_embedded_type():
+    schema = parse_string('<xsd:element name="AcquisitionDate" type="xsd:dateTime"/>')
+    assert len(schema.all_classes()) == 1
+    root = schema.get_class("SchemaRoot")
+    assert len(root.attributes) == 1
+    assert root.attributes["acquisitionDate"].range == "DateTime"
+    assert "xsd:element" in root.attributes["acquisitionDate"].instantiates
+    assert "xsd" in schema.schema.prefixes
+
+def test_complex_type():
+    schema = parse_string('''
+        <xsd:element name="MyClass">
+            <xsd:annotation>
+                <xsd:documentation>
+                    Some docs
+                </xsd:documentation>
+            </xsd:annotation>
+            <xsd:complexType>
+                <xsd:sequence>
+                    <xsd:element name="elementSlotA" type="xsd:float"/>
+                    <xsd:element name="elementSlotB" type="xsd:integer"/>
+                </xsd:sequence>
+                <xsd:attribute name="attributeSlot" type="xsd:boolean"/>
+            </xsd:complexType>
+        </xsd:element>
+    ''')
+    assert len(schema.all_classes()) == 2
+    my_class = schema.get_class("MyClass")
+    assert len(my_class.attributes) == 3
+    assert my_class.attributes["elementSlotA"].range == "Float"
+    assert my_class.attributes["elementSlotB"].range == "Integer"
+    assert my_class.attributes["attributeSlot"].range == "Boolean"
+    # The annotation should be applied to the slot and not the class
+    assert my_class.description is None
+
+    root = schema.get_class("SchemaRoot")
+    assert len(root.attributes) == 1
+    assert root.attributes["myClass"].range == "MyClass"
+    assert root.attributes["myClass"].description == "Some docs"