diff --git a/kg_covid_19/make_holdouts.py b/kg_covid_19/make_holdouts.py
index 4b27ad85..1d14fa0e 100644
--- a/kg_covid_19/make_holdouts.py
+++ b/kg_covid_19/make_holdouts.py
@@ -203,7 +203,8 @@ def _generate_negative_edges(
             warnings.warn(
                 "Couldn't generate %i negative edges - only %i edges left "
                 "after removing positives and reflexives"
-                % (edges_df.shape[0], negative_edges.shape[0])
+                % (edges_df.shape[0], negative_edges.shape[0]),
+                stacklevel=2
             )
             negative_edges = negative_edges.head(negative_edges.shape[0])
         else:
diff --git a/kg_covid_19/transform_utils/intact/intact.py b/kg_covid_19/transform_utils/intact/intact.py
index 40a58b51..bb055b61 100644
--- a/kg_covid_19/transform_utils/intact/intact.py
+++ b/kg_covid_19/transform_utils/intact/intact.py
@@ -99,7 +99,6 @@ def run(self, data_file: Optional[str] = None):
         os.makedirs(self.output_dir, exist_ok=True)
 
         with open(output_node_file, "w") as node, open(output_edge_file, "w") as edge:
-
             # write node.tsv header
             node.write("\t".join(self.node_header) + "\n")
             edge.write("\t".join(self.edge_header) + "\n")
@@ -170,7 +169,7 @@ def interaction_to_edge(
             interaction_type_str = (
                 interaction_type[0]
                 .getElementsByTagName("shortLabel")[0]
-                .firstChild._data
+                .firstChild._data  # type: ignore
             )
 
             participants = interaction.getElementsByTagName("participant")
@@ -353,7 +352,11 @@ def parse_experiment_info(self, xmldoc: minidom.Document) -> Dict[int, str]:
             # interaction detection method
             try:
                 method = experiment.getElementsByTagName("interactionDetectionMethod")
-                label = method[0].getElementsByTagName("shortLabel")[0].firstChild.data
+                label = (
+                    method[0]
+                    .getElementsByTagName("shortLabel")[0]
+                    .firstChild.data  # type: ignore
+                )
                 exp_dict[exp_id]["detection_method"] = label
             except (KeyError, IndexError, AttributeError):
                 pass
diff --git a/poetry.lock b/poetry.lock
index 1f37cc9c..0a7dc4e7 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,14 +2,14 @@
 
 [[package]]
 name = "alabaster"
-version = "0.7.13"
+version = "0.7.12"
 description = "A configurable sidebar-enabled Sphinx theme"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = "*"
 files = [
-    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
-    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+    {file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"},
+    {file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"},
 ]
 
 [[package]]
@@ -23,6 +23,18 @@ files = [
     {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"},
 ]
 
+[[package]]
+name = "appdirs"
+version = "1.4.4"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
+    {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
+]
+
 [[package]]
 name = "appnope"
 version = "0.1.3"
@@ -36,20 +48,17 @@ files = [
 ]
 
 [[package]]
-name = "arrow"
-version = "1.2.3"
-description = "Better dates & times for Python"
+name = "argparse"
+version = "1.4.0"
+description = "Python command-line parsing library"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = "*"
 files = [
-    {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"},
-    {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"},
+    {file = "argparse-1.4.0-py2.py3-none-any.whl", hash = "sha256:c31647edb69fd3d465a847ea3157d37bed1f95f19760b11a47aa91c04b666314"},
+    {file = "argparse-1.4.0.tar.gz", hash = "sha256:62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4"},
 ]
 
-[package.dependencies]
-python-dateutil = ">=2.7.0"
-
 [[package]]
 name = "asttokens"
 version = "2.2.1"
@@ -70,37 +79,37 @@ test = ["astroid", "pytest"]
 
 [[package]]
 name = "attrs"
-version = "23.1.0"
+version = "22.2.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.6"
 files = [
-    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
-    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
+    {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
+    {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]", "pre-commit"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
-tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
+tests = ["attrs[tests-no-zope]", "zope.interface"]
+tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "babel"
-version = "2.12.1"
+version = "2.11.0"
 description = "Internationalization utilities"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.6"
 files = [
-    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
-    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+    {file = "Babel-2.11.0-py3-none-any.whl", hash = "sha256:1ad3eca1c885218f6dce2ab67291178944f810a10a9b5f3cb8382a5a232b64fe"},
+    {file = "Babel-2.11.0.tar.gz", hash = "sha256:5ef4b3226b0180dedded4229651c8b0e1a3a6a2837d45a073272f313e4cf97f6"},
 ]
 
 [package.dependencies]
-pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
+pytz = ">=2015.7"
 
 [[package]]
 name = "backcall"
@@ -116,125 +125,101 @@ files = [
 
 [[package]]
 name = "bioregistry"
-version = "0.6.108"
+version = "0.9.66"
 description = "Integrated registry of biological databases and nomenclatures"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "bioregistry-0.6.108-py3-none-any.whl", hash = "sha256:e9f83faeb454064fc1413f791d2603afd864d2a82da8b9ec44aee1ae291b98fb"},
-    {file = "bioregistry-0.6.108.tar.gz", hash = "sha256:369a1444a2c6f099b5d02d56b25fb2bcbc57d8964021c5ea13dc86f656f3a649"},
+    {file = "bioregistry-0.9.66-py3-none-any.whl", hash = "sha256:1a830d08613603053ebf251a780ee65ac341e974ede8366ae30f5698134a2652"},
+    {file = "bioregistry-0.9.66.tar.gz", hash = "sha256:8cb8b36eb7dfe91e1da766ac43cfa2025b973f00b050f7285172dd2cdfe852ba"},
 ]
 
 [package.dependencies]
 click = "*"
-curies = ">=0.5.1"
+curies = ">=0.5.6"
 more-click = ">=0.1.2"
-pydantic = "*"
+pydantic = "<2.0"
 pystow = ">=0.1.13"
 requests = "*"
 tqdm = "*"
 
 [package.extras]
 align = ["beautifulsoup4", "class-resolver", "defusedxml", "fairsharing-client (>=0.1.0)", "pyyaml", "tabulate"]
-charts = ["matplotlib", "matplotlib-venn", "pandas", "seaborn"]
+charts = ["jinja2", "matplotlib", "matplotlib-venn", "pandas", "seaborn"]
 docs = ["autodoc-pydantic", "sphinx", "sphinx-autodoc-typehints (==1.21.1)", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
 export = ["ndex2", "pyyaml", "rdflib", "rdflib-jsonld"]
 gha = ["more-itertools"]
-health = ["click-default-group", "pandas", "pyyaml", "tabulate"]
-tests = ["coverage", "more-itertools", "pytest"]
-web = ["bootstrap-flask (<=2.0.0)", "flasgger", "flask", "markdown", "pyyaml", "rdflib", "rdflib-jsonld"]
+health = ["click-default-group", "jinja2", "pandas", "pyyaml", "tabulate"]
+tests = ["coverage", "httpx", "more-itertools", "pytest"]
+web = ["bootstrap-flask (<=2.0.0)", "curies[fastapi]", "fastapi", "flask (<2.2.4)", "markdown", "pyyaml", "rdflib", "rdflib-endpoint", "rdflib-jsonld", "uvicorn", "werkzeug (<2.3.0)"]
 
 [[package]]
 name = "black"
-version = "21.12b0"
+version = "21.6b0"
 description = "The uncompromising code formatter."
 category = "main"
 optional = false
 python-versions = ">=3.6.2"
 files = [
-    {file = "black-21.12b0-py3-none-any.whl", hash = "sha256:a615e69ae185e08fdd73e4715e260e2479c861b5740057fde6e8b4e3b7dd589f"},
-    {file = "black-21.12b0.tar.gz", hash = "sha256:77b80f693a569e2e527958459634f18df9b0ba2625ba4e0c2d5da5be42e6f2b3"},
+    {file = "black-21.6b0-py3-none-any.whl", hash = "sha256:dfb8c5a069012b2ab1e972e7b908f5fb42b6bbabcba0a788b86dc05067c7d9c7"},
+    {file = "black-21.6b0.tar.gz", hash = "sha256:dc132348a88d103016726fe360cb9ede02cecf99b76e3660ce6c596be132ce04"},
 ]
 
 [package.dependencies]
+appdirs = "*"
 click = ">=7.1.2"
 mypy-extensions = ">=0.4.3"
-pathspec = ">=0.9.0,<1"
-platformdirs = ">=2"
-tomli = ">=0.2.6,<2.0.0"
-typing-extensions = [
-    {version = ">=3.10.0.0", markers = "python_version < \"3.10\""},
-    {version = ">=3.10.0.0,<3.10.0.1 || >3.10.0.1", markers = "python_version >= \"3.10\""},
-]
+pathspec = ">=0.8.1,<1"
+regex = ">=2020.1.8"
+toml = ">=0.10.1"
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.7.4)"]
-jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
-python2 = ["typed-ast (>=1.4.3)"]
+d = ["aiohttp (>=3.6.0)", "aiohttp-cors (>=0.4.0)"]
+python2 = ["typed-ast (>=1.4.2)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
-[[package]]
-name = "bleach"
-version = "6.0.0"
-description = "An easy safelist-based HTML-sanitizing tool."
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "bleach-6.0.0-py3-none-any.whl", hash = "sha256:33c16e3353dbd13028ab4799a0f89a83f113405c766e9c122df8a06f5b85b3f4"},
-    {file = "bleach-6.0.0.tar.gz", hash = "sha256:1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414"},
-]
-
-[package.dependencies]
-six = ">=1.9.0"
-webencodings = "*"
-
-[package.extras]
-css = ["tinycss2 (>=1.1.0,<1.2)"]
-
 [[package]]
 name = "bmt"
-version = "0.10.0"
-description = "Biolink Model Toolkit: A Python API for working with the Biolink Model"
+version = "0.8.12"
+description = ""
 category = "main"
 optional = false
-python-versions = ">=3.8,<4.0"
+python-versions = ">=3.7"
 files = [
-    {file = "bmt-0.10.0-py3-none-any.whl", hash = "sha256:30ce2286ecf0135c8f129090ddcbd6ec507cd8d221647efaf115c287cbbdb033"},
-    {file = "bmt-0.10.0.tar.gz", hash = "sha256:680cf55e94c9fa6de4b2d588b9d1d8870621595c55684ad4161aa80d3ef7b4fd"},
+    {file = "bmt-0.8.12-py3-none-any.whl", hash = "sha256:42293a605fc1313052f551e7bd24d13c2464df03cd5bab31f24b58ea51573e98"},
+    {file = "bmt-0.8.12.tar.gz", hash = "sha256:b1f14e87b4f45181ffbb882ebc8bc7400298a7ce8e94cc8b80ba2a319010c47d"},
 ]
 
 [package.dependencies]
-deprecation = ">=2.1.0,<3.0.0"
-linkml-runtime = ">=1.4,<2.0"
-pytest = ">=7.2.0,<8.0.0"
-recommonmark = ">=0.7.1,<0.8.0"
-sphinx-autodoc-typehints = ">=1.19.5,<2.0.0"
-sphinx-click = ">=4.3.0,<5.0.0"
-sphinx-rtd-theme = ">=1.1.1,<2.0.0"
-sphinxcontrib-napoleon = ">=0.7,<0.8"
-stringcase = ">=1.2.0,<2.0.0"
-twine = ">=4.0.1,<5.0.0"
-
-[package.extras]
-docs = ["Sphinx (>=5.3.0,<6.0.0)"]
+black = "<=21.12b0"
+deprecation = ">=2.0.6"
+flake8 = "*"
+linkml = "*"
+linkml-runtime = "*"
+pytest = "*"
+recommonmark = "*"
+sphinx = "*"
+sphinx-rtd-theme = "*"
+sphinxcontrib-napoleon = "*"
+stringcase = ">=1.0.0"
+tox = "*"
 
 [[package]]
 name = "boto3"
-version = "1.26.146"
+version = "1.26.35"
 description = "The AWS SDK for Python"
 category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "boto3-1.26.146-py3-none-any.whl", hash = "sha256:a03e42dfa09c785cd223422d59c06e8babf667983b513a9a172b73c106f3b37e"},
-    {file = "boto3-1.26.146.tar.gz", hash = "sha256:3d7f1b43d2e5a10ee29d4940e714d72a2f6f1a6f6ba856c82ba9328d83062605"},
+    {file = "boto3-1.26.35-py3-none-any.whl", hash = "sha256:f786a12eb036bbe6f473a351182275fd5c43c4e9c523cb8ec9b1946b18830d0d"},
+    {file = "boto3-1.26.35.tar.gz", hash = "sha256:282c9aa0af39fc3f0fac9c91e05f43145ff3d5fee29189b5343490131555981a"},
 ]
 
 [package.dependencies]
-botocore = ">=1.29.146,<1.30.0"
+botocore = ">=1.29.35,<1.30.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.6.0,<0.7.0"
 
@@ -243,14 +228,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.29.146"
+version = "1.29.35"
 description = "Low-level, data-driven core of boto 3."
 category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "botocore-1.29.146-py3-none-any.whl", hash = "sha256:ac57003292f18206ee942eafc381ecd9a3420a3844d6b7e1c1b0f4b88b28263b"},
-    {file = "botocore-1.29.146.tar.gz", hash = "sha256:77f7793cb36074eb84d606a23ad6e1d57c20f7a2eeab7d9136d3e63c584e0504"},
+    {file = "botocore-1.29.35-py3-none-any.whl", hash = "sha256:fc329d2772284dcffdf947023de589eaf72a4eb4737505114b1c0f3a1063b3b6"},
+    {file = "botocore-1.29.35.tar.gz", hash = "sha256:ca673347f46f03fb5f1e56326adc9c696daba860838dffbe85e9bb16a8c54d67"},
 ]
 
 [package.dependencies]
@@ -259,127 +244,50 @@ python-dateutil = ">=2.1,<3.0.0"
 urllib3 = ">=1.25.4,<1.27"
 
 [package.extras]
-crt = ["awscrt (==0.16.9)"]
+crt = ["awscrt (==0.15.3)"]
 
 [[package]]
 name = "cache-decorator"
-version = "2.1.14"
+version = "2.1.13"
 description = "a simple decorator to cache the results of computationally heavy functions"
 category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "cache_decorator-2.1.14.tar.gz", hash = "sha256:430583e6adeaf6f5ab4c2969dd9631ac5f494b2a5c894a0b732af011a3f84a43"},
+    {file = "cache_decorator-2.1.13.tar.gz", hash = "sha256:22a30b4a946fedf77566e197cb8f34e78750418b5ac3f80baf0b64890c7a4f35"},
 ]
 
 [package.dependencies]
 compress_json = ">=1.0.4"
 compress_pickle = ">=2.0.1"
 deflate_dict = "*"
-dict_hash = ">=1.1.32"
+dict_hash = ">=1.1.25"
 humanize = ">=3.4.1"
 
 [[package]]
 name = "cachetools"
-version = "5.3.1"
+version = "5.2.0"
 description = "Extensible memoizing collections and decorators"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = "~=3.7"
 files = [
-    {file = "cachetools-5.3.1-py3-none-any.whl", hash = "sha256:95ef631eeaea14ba2e36f06437f36463aac3a096799e876ee55e5cdccb102590"},
-    {file = "cachetools-5.3.1.tar.gz", hash = "sha256:dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b"},
+    {file = "cachetools-5.2.0-py3-none-any.whl", hash = "sha256:f9f17d2aec496a9aa6b76f53e3b614c965223c061982d434d160f930c698a9db"},
+    {file = "cachetools-5.2.0.tar.gz", hash = "sha256:6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757"},
 ]
 
 [[package]]
 name = "certifi"
-version = "2023.5.7"
+version = "2022.12.7"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.5.7-py3-none-any.whl", hash = "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"},
-    {file = "certifi-2023.5.7.tar.gz", hash = "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7"},
-]
-
-[[package]]
-name = "cffi"
-version = "1.15.1"
-description = "Foreign Function Interface for Python calling C code."
-category = "main"
-optional = false
-python-versions = "*"
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+unicode-backport = ["unicodedata2"]
+
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 [package.dependencies]
@@ -644,68 +473,26 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1
 [package.extras]
 toml = ["tomli"]
 
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-    {file = "cryptography-41.0.1-pp39-pypy39_pp73-macosx_10_12_x86_64.whl", hash = "sha256:5f0ff6e18d13a3de56f609dd1fd11470918f770c6bd5d00d632076c727d35485"},
-    {file = "cryptography-41.0.1-pp39-pypy39_pp73-manylinux_2_28_aarch64.whl", hash = "sha256:7bfc55a5eae8b86a287747053140ba221afc65eb06207bedf6e019b8934b477c"},
-    {file = "cryptography-41.0.1-pp39-pypy39_pp73-manylinux_2_28_x86_64.whl", hash = "sha256:eb8163f5e549a22888c18b0d53d6bb62a20510060a22fd5a995ec8a05268df8a"},
-    {file = "cryptography-41.0.1-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:8dde71c4169ec5ccc1087bb7521d54251c016f126f922ab2dfe6649170a3b8c5"},
-    {file = "cryptography-41.0.1.tar.gz", hash = "sha256:d34579085401d3f49762d2f7d6634d6b6c2ae1242202e860f4d26b046e3a1006"},
-]
-
-[package.dependencies]
-cffi = ">=1.12"
-
-[package.extras]
-docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=1.1.1)"]
-docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"]
-nox = ["nox"]
-pep8test = ["black", "check-sdist", "mypy", "ruff"]
-sdist = ["build"]
-ssh = ["bcrypt (>=3.1.5)"]
-test = ["pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
-test-randomorder = ["pytest-randomly"]
-
 [[package]]
 name = "curies"
-version = "0.5.5"
+version = "0.5.6"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "curies-0.5.5-py3-none-any.whl", hash = "sha256:265ab8c95a2a6478ca22a1f9a2fac2902d71fa7737534b6380297e4dc49decd6"},
-    {file = "curies-0.5.5.tar.gz", hash = "sha256:4c1ddf6e7be2afdccb8e9dad76e4c22c4f9d506bbe0dbb1cfaf2cf29fc488ce2"},
+    {file = "curies-0.5.6-py3-none-any.whl", hash = "sha256:27eee34218bf645fdfb5c457bacfba0274146277bac600d9b9a83d2e5e01abcd"},
+    {file = "curies-0.5.6.tar.gz", hash = "sha256:fd9e72ea9b167911057726bd537c9956ed96d88ce71aecf59f9a47c6ca484ffe"},
 ]
 
 [package.dependencies]
-pydantic = "*"
+pydantic = "<2.0"
 pytrie = "*"
 requests = "*"
 
 [package.extras]
 bioregistry = ["bioregistry (>=0.5.136)"]
-docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-theme"]
+docs = ["sphinx (<7.0)", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-theme"]
 fastapi = ["defusedxml", "fastapi", "httpx", "python-multipart", "uvicorn"]
 flask = ["defusedxml", "flask"]
 pandas = ["pandas"]
@@ -743,21 +530,21 @@ test = ["codacy-coverage", "coveralls", "pytest", "pytest-cov", "random_dict", "
 
 [[package]]
 name = "deprecated"
-version = "1.2.14"
+version = "1.2.13"
 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
-    {file = "Deprecated-1.2.14-py2.py3-none-any.whl", hash = "sha256:6fac8b097794a90302bdbb17b9b815e732d3c4720583ff1b198499d78470466c"},
-    {file = "Deprecated-1.2.14.tar.gz", hash = "sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3"},
+    {file = "Deprecated-1.2.13-py2.py3-none-any.whl", hash = "sha256:64756e3e14c8c5eea9795d93c524551432a0be75629f8f29e67ab8caf076c76d"},
+    {file = "Deprecated-1.2.13.tar.gz", hash = "sha256:43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d"},
 ]
 
 [package.dependencies]
 wrapt = ">=1.10,<2"
 
 [package.extras]
-dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
+dev = ["PyTest", "PyTest (<5)", "PyTest-Cov", "PyTest-Cov (<2.6)", "bump2version (<1)", "configparser (<5)", "importlib-metadata (<3)", "importlib-resources (<4)", "sphinx (<2)", "sphinxcontrib-websupport (<2)", "tox", "zipp (<2)"]
 
 [[package]]
 name = "deprecation"
@@ -776,13 +563,13 @@ packaging = "*"
 
 [[package]]
 name = "dict-hash"
-version = "1.1.32"
+version = "1.1.29"
 description = "Simple python tool to hash dictionaries using both default hash and sha256."
 category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "dict_hash-1.1.32.tar.gz", hash = "sha256:7be40b48dedf3660a05e5958c205ca798e3a13242bdce915a57c27bccb77025a"},
+    {file = "dict_hash-1.1.29.tar.gz", hash = "sha256:7668695426fd6bee2e18aa613c3dfef64114aa6435e0acfbfe48547572e45b35"},
 ]
 
 [package.dependencies]
@@ -818,25 +605,25 @@ files = [
 
 [[package]]
 name = "docker"
-version = "6.1.3"
+version = "4.2.2"
 description = "A Python library for the Docker Engine API."
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
-    {file = "docker-6.1.3-py3-none-any.whl", hash = "sha256:aecd2277b8bf8e506e484f6ab7aec39abe0038e29fa4a6d3ba86c3fe01844ed9"},
-    {file = "docker-6.1.3.tar.gz", hash = "sha256:aa6d17830045ba5ef0168d5eaa34d37beeb113948c413affe1d5991fc11f9a20"},
+    {file = "docker-4.2.2-py2.py3-none-any.whl", hash = "sha256:03a46400c4080cb6f7aa997f881ddd84fef855499ece219d75fbdb53289c17ab"},
+    {file = "docker-4.2.2.tar.gz", hash = "sha256:26eebadce7e298f55b76a88c4f8802476c5eaddbdbe38dbc6cce8781c47c9b54"},
 ]
 
 [package.dependencies]
-packaging = ">=14.0"
-pywin32 = {version = ">=304", markers = "sys_platform == \"win32\""}
-requests = ">=2.26.0"
-urllib3 = ">=1.26.0"
+pypiwin32 = {version = "223", markers = "sys_platform == \"win32\" and python_version >= \"3.6\""}
+requests = ">=2.14.2,<2.18.0 || >2.18.0"
+six = ">=1.4.0"
 websocket-client = ">=0.32.0"
 
 [package.extras]
-ssh = ["paramiko (>=2.4.3)"]
+ssh = ["paramiko (>=2.4.2)"]
+tls = ["cryptography (>=1.3.4)", "idna (>=2.0.0)", "pyOpenSSL (>=17.5.0)"]
 
 [[package]]
 name = "docutils"
@@ -933,14 +720,14 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.1"
+version = "1.0.4"
 description = "Backport of PEP 654 (exception groups)"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.1.1-py3-none-any.whl", hash = "sha256:232c37c63e4f682982c8b6459f33a8981039e5fb8756b2074364e5055c498c9e"},
-    {file = "exceptiongroup-1.1.1.tar.gz", hash = "sha256:d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785"},
+    {file = "exceptiongroup-1.0.4-py3-none-any.whl", hash = "sha256:542adf9dea4055530d6e1279602fa5cb11dab2395fa650b8674eaec35fc4a828"},
+    {file = "exceptiongroup-1.0.4.tar.gz", hash = "sha256:bd14967b79cd9bdb54d97323216f8fdf533e278df937aa2a90089e7d6e06e5ec"},
 ]
 
 [package.extras]
@@ -963,19 +750,19 @@ tests = ["asttokens", "littleutils", "pytest", "rich"]
 
 [[package]]
 name = "filelock"
-version = "3.12.0"
+version = "3.8.2"
 description = "A platform independent file lock."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "filelock-3.12.0-py3-none-any.whl", hash = "sha256:ad98852315c2ab702aeb628412cbf7e95b7ce8c3bf9565670b4eaecf1db370a9"},
-    {file = "filelock-3.12.0.tar.gz", hash = "sha256:fc03ae43288c013d2ea83c8597001b1129db351aad9c57fe2409327916b8e718"},
+    {file = "filelock-3.8.2-py3-none-any.whl", hash = "sha256:8df285554452285f79c035efb0c861eb33a4bcfa5b7a137016e32e6a90f9792c"},
+    {file = "filelock-3.8.2.tar.gz", hash = "sha256:7565f628ea56bfcd8e54e42bdc55da899c85c1abfe1b5bcfd147e9188cebb3b2"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.3.27)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.2.3)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2022.9.29)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"]
+testing = ["covdefaults (>=2.2.2)", "coverage (>=6.5)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"]
 
 [[package]]
 name = "flake8"
@@ -994,18 +781,6 @@ mccabe = ">=0.7.0,<0.8.0"
 pycodestyle = ">=2.9.0,<2.10.0"
 pyflakes = ">=2.5.0,<2.6.0"
 
-[[package]]
-name = "fqdn"
-version = "1.5.1"
-description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers"
-category = "main"
-optional = false
-python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4"
-files = [
-    {file = "fqdn-1.5.1-py3-none-any.whl", hash = "sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014"},
-    {file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"},
-]
-
 [[package]]
 name = "ghp-import"
 version = "2.1.0"
@@ -1049,29 +824,27 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0dev)"]
 
 [[package]]
 name = "google-auth"
-version = "2.19.1"
+version = "2.15.0"
 description = "Google Authentication Library"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*"
 files = [
-    {file = "google-auth-2.19.1.tar.gz", hash = "sha256:a9cfa88b3e16196845e64a3658eb953992129d13ac7337b064c6546f77c17183"},
-    {file = "google_auth-2.19.1-py2.py3-none-any.whl", hash = "sha256:ea165e014c7cbd496558796b627c271aa8c18b4cba79dc1cc962b24c5efdfb85"},
+    {file = "google-auth-2.15.0.tar.gz", hash = "sha256:72f12a6cfc968d754d7bdab369c5c5c16032106e52d32c6dfd8484e4c01a6d1f"},
+    {file = "google_auth-2.15.0-py2.py3-none-any.whl", hash = "sha256:6897b93556d8d807ad70701bb89f000183aea366ca7ed94680828b37437a4994"},
 ]
 
 [package.dependencies]
 cachetools = ">=2.0.0,<6.0"
 pyasn1-modules = ">=0.2.1"
-rsa = ">=3.1.4,<5"
+rsa = {version = ">=3.1.4,<5", markers = "python_version >= \"3.6\""}
 six = ">=1.9.0"
-urllib3 = "<2.0"
 
 [package.extras]
 aiohttp = ["aiohttp (>=3.6.2,<4.0.0dev)", "requests (>=2.20.0,<3.0.0dev)"]
 enterprise-cert = ["cryptography (==36.0.2)", "pyopenssl (==22.0.0)"]
 pyopenssl = ["cryptography (>=38.0.3)", "pyopenssl (>=20.0.0)"]
 reauth = ["pyu2f (>=0.1.5)"]
-requests = ["requests (>=2.20.0,<3.0.0dev)"]
 
 [[package]]
 name = "google-cloud-core"
@@ -1094,14 +867,14 @@ grpc = ["grpcio (>=1.38.0,<2.0dev)"]
 
 [[package]]
 name = "google-cloud-storage"
-version = "2.9.0"
+version = "2.7.0"
 description = "Google Cloud Storage API client library"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-cloud-storage-2.9.0.tar.gz", hash = "sha256:9b6ae7b509fc294bdacb84d0f3ea8e20e2c54a8b4bbe39c5707635fec214eff3"},
-    {file = "google_cloud_storage-2.9.0-py2.py3-none-any.whl", hash = "sha256:83a90447f23d5edd045e0037982c270302e3aeb45fc1288d2c2ca713d27bad94"},
+    {file = "google-cloud-storage-2.7.0.tar.gz", hash = "sha256:1ac2d58d2d693cb1341ebc48659a3527be778d9e2d8989697a2746025928ff17"},
+    {file = "google_cloud_storage-2.7.0-py2.py3-none-any.whl", hash = "sha256:f78a63525e72dd46406b255bbdf858a22c43d6bad8dc5bdeb7851a42967e95a1"},
 ]
 
 [package.dependencies]
@@ -1197,14 +970,14 @@ testing = ["pytest"]
 
 [[package]]
 name = "google-resumable-media"
-version = "2.5.0"
+version = "2.4.0"
 description = "Utilities for Google Media Downloads and Resumable Uploads"
 category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "google-resumable-media-2.5.0.tar.gz", hash = "sha256:218931e8e2b2a73a58eb354a288e03a0fd5fb1c4583261ac6e4c078666468c93"},
-    {file = "google_resumable_media-2.5.0-py2.py3-none-any.whl", hash = "sha256:da1bd943e2e114a56d85d6848497ebf9be6a14d3db23e9fc57581e7c3e8170ec"},
+    {file = "google-resumable-media-2.4.0.tar.gz", hash = "sha256:8d5518502f92b9ecc84ac46779bd4f09694ecb3ba38a3e7ca737a86d15cbca1f"},
+    {file = "google_resumable_media-2.4.0-py2.py3-none-any.whl", hash = "sha256:2aa004c16d295c8f6c33b2b4788ba59d366677c0a25ae7382436cb30f776deaa"},
 ]
 
 [package.dependencies]
@@ -1216,14 +989,14 @@ requests = ["requests (>=2.18.0,<3.0.0dev)"]
 
 [[package]]
 name = "googleapis-common-protos"
-version = "1.59.0"
+version = "1.57.0"
 description = "Common protobufs used in Google APIs"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "googleapis-common-protos-1.59.0.tar.gz", hash = "sha256:4168fcb568a826a52f23510412da405abd93f4d23ba544bb68d943b14ba3cb44"},
-    {file = "googleapis_common_protos-1.59.0-py2.py3-none-any.whl", hash = "sha256:b287dc48449d1d41af0c69f4ea26242b5ae4c3d7249a38b0984c86a4caffff1f"},
+    {file = "googleapis-common-protos-1.57.0.tar.gz", hash = "sha256:27a849d6205838fb6cc3c1c21cb9800707a661bb21c6ce7fb13e99eb1f8a0c46"},
+    {file = "googleapis_common_protos-1.57.0-py2.py3-none-any.whl", hash = "sha256:a9f4a1d7f6d9809657b7f1316a1aa527f6664891531bcfcc13b6696e685f443c"},
 ]
 
 [package.dependencies]
@@ -1337,14 +1110,14 @@ files = [
 
 [[package]]
 name = "humanize"
-version = "4.6.0"
+version = "4.4.0"
 description = "Python humanize utilities"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "humanize-4.6.0-py3-none-any.whl", hash = "sha256:401201aca462749773f02920139f302450cb548b70489b9b4b92be39fe3c3c50"},
-    {file = "humanize-4.6.0.tar.gz", hash = "sha256:5f1f22bc65911eb1a6ffe7659bd6598e33dcfeeb904eb16ee1e705a09bf75916"},
+    {file = "humanize-4.4.0-py3-none-any.whl", hash = "sha256:8830ebf2d65d0395c1bd4c79189ad71e023f277c2c7ae00f263124432e6f2ffa"},
+    {file = "humanize-4.4.0.tar.gz", hash = "sha256:efb2584565cc86b7ea87a977a15066de34cdedaf341b11c851cfcfd2b964779c"},
 ]
 
 [package.extras]
@@ -1364,90 +1137,74 @@ files = [
 
 [[package]]
 name = "ijson"
-version = "3.2.0.post0"
+version = "3.1.4"
 description = "Iterative JSON parser with standard Python iterator interfaces"
 category = "main"
 optional = false
 python-versions = "*"
 files = [
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-    {file = "ijson-3.2.0.post0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a8af68fe579f6f0b9a8b3f033d10caacfed6a4b89b8c7a1d9478a8f5d8aba4a1"},
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 ]
 
 [[package]]
@@ -1464,14 +1221,14 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.6.0"
+version = "5.2.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "importlib_metadata-6.6.0-py3-none-any.whl", hash = "sha256:43dd286a2cd8995d5eaef7fee2066340423b818ed3fd70adf0bad5f1fac53fed"},
-    {file = "importlib_metadata-6.6.0.tar.gz", hash = "sha256:92501cdf9cc66ebd3e612f1b4f0c0765dfa42f0fa38ffb319b6bd84dd675d705"},
+    {file = "importlib_metadata-5.2.0-py3-none-any.whl", hash = "sha256:0eafa39ba42bf225fc00e67f701d71f85aead9f878569caf13c3724f704b970f"},
+    {file = "importlib_metadata-5.2.0.tar.gz", hash = "sha256:404d48d62bba0b7a77ff9d405efd91501bef2e67ff4ace0bed40a0cf28c3c7cd"},
 ]
 
 [package.dependencies]
@@ -1484,33 +1241,33 @@ testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packag
 
 [[package]]
 name = "importlib-resources"
-version = "5.12.0"
+version = "5.10.1"
 description = "Read resources from Python packages"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "importlib_resources-5.12.0-py3-none-any.whl", hash = "sha256:7b1deeebbf351c7578e09bf2f63fa2ce8b5ffec296e0d349139d43cca061a81a"},
-    {file = "importlib_resources-5.12.0.tar.gz", hash = "sha256:4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6"},
+    {file = "importlib_resources-5.10.1-py3-none-any.whl", hash = "sha256:c09b067d82e72c66f4f8eb12332f5efbebc9b007c0b6c40818108c9870adc363"},
+    {file = "importlib_resources-5.10.1.tar.gz", hash = "sha256:32bb095bda29741f6ef0e5278c42df98d135391bee5f932841efc0041f748dc3"},
 ]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
 testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [[package]]
 name = "iniconfig"
-version = "2.0.0"
-description = "brain-dead simple config-ini parsing"
+version = "1.1.1"
+description = "iniconfig: brain-dead simple config-ini parsing"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = "*"
 files = [
-    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
-    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+    {file = "iniconfig-1.1.1-py2.py3-none-any.whl", hash = "sha256:011e24c64b7f47f6ebd835bb12a743f2fbe9a26d4cecaa7f53bc4f35ee9da8b3"},
+    {file = "iniconfig-1.1.1.tar.gz", hash = "sha256:bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32"},
 ]
 
 [[package]]
@@ -1526,14 +1283,14 @@ files = [
 
 [[package]]
 name = "ipython"
-version = "8.12.2"
+version = "8.7.0"
 description = "IPython: Productive Interactive Computing"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipython-8.12.2-py3-none-any.whl", hash = "sha256:ea8801f15dfe4ffb76dea1b09b847430ffd70d827b41735c64a0638a04103bfc"},
-    {file = "ipython-8.12.2.tar.gz", hash = "sha256:c7b80eb7f5a855a88efc971fda506ff7a91c280b42cdae26643e0f601ea281ea"},
+    {file = "ipython-8.7.0-py3-none-any.whl", hash = "sha256:352042ddcb019f7c04e48171b4dd78e4c4bb67bf97030d170e154aac42b656d9"},
+    {file = "ipython-8.7.0.tar.gz", hash = "sha256:882899fe78d5417a0aa07f995db298fa28b58faeba2112d2e3a4c95fe14bb738"},
 ]
 
 [package.dependencies]
@@ -1545,14 +1302,13 @@ jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
 pickleshare = "*"
-prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0"
+prompt-toolkit = ">=3.0.11,<3.1.0"
 pygments = ">=2.4.0"
 stack-data = "*"
 traitlets = ">=5"
-typing-extensions = {version = "*", markers = "python_version < \"3.10\""}
 
 [package.extras]
-all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.21)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
+all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.20)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
 black = ["black"]
 doc = ["docrepr", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
 kernel = ["ipykernel"]
@@ -1562,7 +1318,7 @@ notebook = ["ipywidgets", "notebook"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
 test = ["pytest (<7.1)", "pytest-asyncio", "testpath"]
-test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
+test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.20)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
 
 [[package]]
 name = "isodate"
@@ -1579,40 +1335,6 @@ files = [
 [package.dependencies]
 six = "*"
 
-[[package]]
-name = "isoduration"
-version = "20.11.0"
-description = "Operations with ISO 8601 durations"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"},
-    {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"},
-]
-
-[package.dependencies]
-arrow = ">=0.15.0"
-
-[[package]]
-name = "jaraco-classes"
-version = "3.2.3"
-description = "Utility functions for Python class constructs"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "jaraco.classes-3.2.3-py3-none-any.whl", hash = "sha256:2353de3288bc6b82120752201c6b1c1a14b058267fa424ed5ce5984e3b922158"},
-    {file = "jaraco.classes-3.2.3.tar.gz", hash = "sha256:89559fa5c1d3c34eff6f631ad80bb21f378dbcbb35dd161fd2c6b93f5be2f98a"},
-]
-
-[package.dependencies]
-more-itertools = "*"
-
-[package.extras]
-docs = ["jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
-testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
-
 [[package]]
 name = "jaro-winkler"
 version = "2.0.3"
@@ -1644,22 +1366,6 @@ docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alab
 qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
 testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 
-[[package]]
-name = "jeepney"
-version = "0.8.0"
-description = "Low-level, pure Python DBus protocol wrapper."
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "jeepney-0.8.0-py3-none-any.whl", hash = "sha256:c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755"},
-    {file = "jeepney-0.8.0.tar.gz", hash = "sha256:5efe48d255973902f6badc3ce55e2aa6c5c3b3bc642059ef3a91247bcfcc5806"},
-]
-
-[package.extras]
-test = ["async-timeout", "pytest", "pytest-asyncio (>=0.17)", "pytest-trio", "testpath", "trio"]
-trio = ["async_generator", "trio"]
-
 [[package]]
 name = "jinja2"
 version = "3.1.2"
@@ -1807,17 +1513,9 @@ files = [
 
 [package.dependencies]
 attrs = ">=17.4.0"
-fqdn = {version = "*", optional = true, markers = "extra == \"format\""}
-idna = {version = "*", optional = true, markers = "extra == \"format\""}
 importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
-isoduration = {version = "*", optional = true, markers = "extra == \"format\""}
-jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format\""}
 pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""}
 pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
-rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format\""}
-rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
-uri-template = {version = "*", optional = true, markers = "extra == \"format\""}
-webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\""}
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
@@ -1842,31 +1540,6 @@ six = "*"
 recomended = ["simplejson"]
 test = ["tox"]
 
-[[package]]
-name = "keyring"
-version = "23.13.1"
-description = "Store and access your passwords safely."
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "keyring-23.13.1-py3-none-any.whl", hash = "sha256:771ed2a91909389ed6148631de678f82ddc73737d85a927f382a8a1b157898cd"},
-    {file = "keyring-23.13.1.tar.gz", hash = "sha256:ba2e15a9b35e21908d0aaf4e0a47acc52d6ae33444df0da2b49d41a46ef6d678"},
-]
-
-[package.dependencies]
-importlib-metadata = {version = ">=4.11.4", markers = "python_version < \"3.12\""}
-importlib-resources = {version = "*", markers = "python_version < \"3.9\""}
-"jaraco.classes" = "*"
-jeepney = {version = ">=0.4.2", markers = "sys_platform == \"linux\""}
-pywin32-ctypes = {version = ">=0.2.0", markers = "sys_platform == \"win32\""}
-SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
-
-[package.extras]
-completion = ["shtab"]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
-testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
-
 [[package]]
 name = "kghub-downloader"
 version = "0.3.3"
@@ -1941,31 +1614,32 @@ validators = ">=0.13.0"
 
 [[package]]
 name = "linkml"
-version = "1.5.5"
+version = "1.3.2"
 description = "Linked Open Data Modeling Language"
 category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
-    {file = "linkml-1.5.5-py3-none-any.whl", hash = "sha256:0f7463aa71cd9eea25e452727153ba4fea501793a1e34fa58ae3fac461400fbb"},
-    {file = "linkml-1.5.5.tar.gz", hash = "sha256:46a335512a849966c6980fedfd57eb9ba32b67045f5e6bf6bb6dfcf5be236240"},
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 ]
 
 [package.dependencies]
 antlr4-python3-runtime = ">=4.9.0,<4.10"
+argparse = ">=1.4.0"
 click = ">=7.0"
 graphviz = ">=0.10.1"
 hbreader = "*"
 isodate = ">=0.6.0"
-jinja2 = ">=3.1.0"
+jinja2 = "*"
 jsonasobj2 = ">=1.0.3,<2.0.0"
-jsonschema = {version = ">=4.0.0", extras = ["format"]}
+jsonschema = ">=3.0.1"
 linkml-dataops = "*"
-linkml-runtime = ">=1.5.3"
+linkml-runtime = ">=1.3.0,<2.0.0"
+myst-parser = "*"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
-prefixmaps = ">=0.1.3"
 pydantic = "*"
 pyjsg = ">=0.11.6"
 pyshex = ">=0.7.20"
@@ -1974,9 +1648,13 @@ python-dateutil = "*"
 pyyaml = "*"
 rdflib = ">=6.0.0"
 requests = ">=2.22"
+sphinx-click = "*"
 sqlalchemy = ">=1.4.31"
 watchdog = ">=0.9.0"
 
+[package.extras]
+docs = ["sphinx", "sphinx-rtd-theme"]
+
 [[package]]
 name = "linkml-dataops"
 version = "0.1.0"
@@ -1998,27 +1676,24 @@ linkml-runtime = ">=1.1.6"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.5.3"
+version = "1.4.0"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 category = "main"
 optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = ">=3.7.1,<4.0.0"
 files = [
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 [package.dependencies]
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 deprecated = "*"
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 pyyaml = "*"
 rdflib = ">=6.0.0"
 requests = "*"
@@ -2043,24 +1718,24 @@ testing = ["coverage", "pyyaml"]
 
 [[package]]
 name = "markdown-it-py"
-version = "2.2.0"
+version = "2.1.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
 category = "main"
 optional = false
 python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
 mdurl = ">=0.1,<1.0"
 
 [package.extras]
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-code-style = ["pre-commit (>=3.0,<4.0)"]
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-linkify = ["linkify-it-py (>=1,<3)"]
+benchmarking = ["psutil", "pytest", "pytest-benchmark (>=3.2,<4.0)"]
+code-style = ["pre-commit (==2.6)"]
+compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.3.6,<3.4.0)", "mistletoe (>=0.8.1,<0.9.0)", "mistune (>=2.0.2,<2.1.0)", "panflute (>=2.1.3,<2.2.0)"]
+linkify = ["linkify-it-py (>=1.0,<2.0)"]
 plugins = ["mdit-py-plugins"]
 profiling = ["gprof2dot"]
 rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
@@ -2068,62 +1743,52 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
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-version = "2.1.3"
+version = "2.1.1"
 description = "Safely add untrusted strings to HTML/XML markup."
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 python-versions = ">=3.7"
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+category = "main"
+optional = false
+python-versions = ">=3.7"
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+
+[package.dependencies]
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+
+[package.extras]
+code-style = ["pre-commit"]
+rtd = ["attrs", "myst-parser (>=0.16.1,<0.17.0)", "sphinx-book-theme (>=0.1.0,<0.2.0)"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
+
 [[package]]
 name = "mdurl"
 version = "0.1.2"
@@ -2179,14 +1864,14 @@ files = [
 
 [[package]]
 name = "mkdocs"
-version = "1.4.3"
+version = "1.4.2"
 description = "Project documentation with Markdown."
 category = "main"
 optional = false
 python-versions = ">=3.7"
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 [package.extras]
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 [package.dependencies]
-mypy-extensions = ">=1.0.0"
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 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 typing-extensions = ">=3.10"
 
@@ -2337,16 +2014,43 @@ reports = ["lxml"]
 
 [[package]]
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+python-versions = "*"
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+optional = false
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+
 [[package]]
 name = "neo4j"
 version = "4.3.0"
@@ -2363,59 +2067,59 @@ pytz = "*"
 
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 [[package]]
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 [[package]]
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-version = "3.1.2"
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 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
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 python-versions = ">=3.6"
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 ]
 
 [package.dependencies]
@@ -2468,49 +2172,51 @@ dev = ["black", "mypy", "pytest"]
 
 [[package]]
 name = "packaging"
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+version = "22.0"
 description = "Core utilities for Python packages"
 category = "main"
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 python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -2519,32 +2225,11 @@ numpy = [
     {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
     {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
 ]
-python-dateutil = ">=2.8.2"
+python-dateutil = ">=2.8.1"
 pytz = ">=2020.1"
-tzdata = ">=2022.1"
 
 [package.extras]
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-xml = ["lxml (>=4.6.3)"]
+test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
 
 [[package]]
 name = "parameterized"
@@ -2569,6 +2254,7 @@ category = "main"
 optional = false
 python-versions = "*"
 files = [
+    {file = "parse-1.19.0-py2.py3-none-any.whl", hash = "sha256:6ce007645384a91150cb7cd7c8a9db2559e273c2e2542b508cd1e342508c2601"},
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 ]
 
@@ -2590,14 +2276,14 @@ testing = ["docopt", "pytest (<6.0.0)"]
 
 [[package]]
 name = "pathspec"
-version = "0.11.1"
+version = "0.10.3"
 description = "Utility library for gitignore style pattern matching of file paths."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
@@ -2629,31 +2315,16 @@ files = [
 
 [[package]]
 name = "pip"
-version = "23.1.2"
+version = "22.3.1"
 description = "The PyPA recommended tool for installing Python packages."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "pip-22.3.1.tar.gz", hash = "sha256:65fd48317359f3af8e593943e6ae1506b66325085ea64b706a998c6e83eeaf38"},
 ]
 
-[[package]]
-name = "pkginfo"
-version = "1.9.6"
-description = "Query metadata from sdists / bdists / installed packages."
-category = "main"
-optional = false
-python-versions = ">=3.6"
-files = [
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-]
-
-[package.extras]
-testing = ["pytest", "pytest-cov"]
-
 [[package]]
 name = "pkgutil-resolve-name"
 version = "1.3.10"
@@ -2668,19 +2339,19 @@ files = [
 
 [[package]]
 name = "platformdirs"
-version = "3.5.1"
+version = "2.6.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2022.9.29)", "proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.4)"]
+test = ["appdirs (==1.4.4)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
 
 [[package]]
 name = "pluggy"
@@ -2743,29 +2414,6 @@ pytest-logging = ">=2015.11.4,<2016.0.0"
 PyYAML = ">=6.0,<7.0"
 requests = ">=2.28.1,<3.0.0"
 
-[[package]]
-name = "prefixmaps"
-version = "0.1.5"
-description = "A python library for retrieving semantic prefix maps"
-category = "main"
-optional = false
-python-versions = ">=3.7.6,<4.0.0"
-files = [
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-
-[package.dependencies]
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-greenlet = "2.0.1"
-importlib-metadata = ">=1.0.0"
-pyyaml = ">=5.3.1"
-typing-extensions = ">=4.4.0,<5.0.0"
-
-[package.extras]
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-
 [[package]]
 name = "prologterms"
 version = "0.0.6"
@@ -2780,14 +2428,14 @@ files = [
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.38"
+version = "3.0.36"
 description = "Library for building powerful interactive command lines in Python"
 category = "main"
 optional = false
-python-versions = ">=3.7.0"
+python-versions = ">=3.6.2"
 files = [
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 ]
 
 [package.dependencies]
@@ -2795,25 +2443,26 @@ wcwidth = "*"
 
 [[package]]
 name = "protobuf"
-version = "4.23.2"
+version = "4.21.12"
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 [package.dependencies]
-typing-extensions = ">=4.2.0"
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 [package.extras]
 dotenv = ["python-dotenv (>=0.10.4)"]
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 name = "pygments"
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+version = "2.13.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "main"
 optional = false
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 [[package]]
 name = "pymdown-extensions"
-version = "10.0.1"
+version = "9.9"
 description = "Extension pack for Python Markdown."
 category = "main"
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 [package.dependencies]
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 [[package]]
 name = "pyparsing"
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 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
+[[package]]
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+[package.dependencies]
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 ]
 
 [[package]]
@@ -3142,14 +2788,14 @@ test = ["nose"]
 
 [[package]]
 name = "pystow"
-version = "0.5.0"
+version = "0.4.7"
 description = "Easily pick a place to store data for your python package."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -3167,17 +2813,18 @@ xml = ["lxml"]
 
 [[package]]
 name = "pytest"
-version = "7.3.1"
+version = "7.2.0"
 description = "pytest: simple powerful testing with Python"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
+attrs = ">=19.2.0"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
@@ -3186,18 +2833,18 @@ pluggy = ">=0.12,<2.0"
 tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
+testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
-version = "4.1.0"
+version = "4.0.0"
 description = "Pytest plugin for measuring coverage."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.6"
 files = [
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 ]
 
 [package.dependencies]
@@ -3252,50 +2899,34 @@ sortedcontainers = "*"
 
 [[package]]
 name = "pytz"
-version = "2023.3"
+version = "2022.7"
 description = "World timezone definitions, modern and historical"
 category = "main"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
 name = "pywin32"
-version = "306"
+version = "301"
 description = "Python for Window Extensions"
 category = "main"
 optional = false
 python-versions = "*"
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 ]
 
 [[package]]
@@ -3365,25 +2996,28 @@ pyyaml = "*"
 
 [[package]]
 name = "rdflib"
-version = "6.3.2"
+version = "6.2.0"
 description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
 category = "main"
 optional = false
-python-versions = ">=3.7,<4.0"
+python-versions = ">=3.7"
 files = [
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+    {file = "rdflib-6.2.0.tar.gz", hash = "sha256:62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942"},
 ]
 
 [package.dependencies]
-isodate = ">=0.6.0,<0.7.0"
-pyparsing = ">=2.1.0,<4"
+isodate = "*"
+pyparsing = "*"
+setuptools = "*"
 
 [package.extras]
-berkeleydb = ["berkeleydb (>=18.1.0,<19.0.0)"]
-html = ["html5lib (>=1.0,<2.0)"]
-lxml = ["lxml (>=4.3.0,<5.0.0)"]
-networkx = ["networkx (>=2.0.0,<3.0.0)"]
+berkeleydb = ["berkeleydb"]
+dev = ["black (==22.6.0)", "flake8", "flakeheaven", "isort", "mypy", "pep8-naming", "types-setuptools"]
+docs = ["myst-parser", "sphinx (<6)", "sphinx-autodoc-typehints", "sphinxcontrib-apidoc", "sphinxcontrib-kroki"]
+html = ["html5lib"]
+networkx = ["networkx"]
+tests = ["html5lib", "pytest", "pytest-cov"]
 
 [[package]]
 name = "rdflib-jsonld"
@@ -3416,26 +3050,6 @@ files = [
 rdflib = ">=5.0.0"
 rdflib-jsonld = "0.6.1"
 
-[[package]]
-name = "readme-renderer"
-version = "37.3"
-description = "readme_renderer is a library for rendering \"readme\" descriptions for Warehouse"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
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-
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-docutils = ">=0.13.1"
-Pygments = ">=2.5.1"
-
-[package.extras]
-md = ["cmarkgfm (>=0.8.0)"]
-
 [[package]]
 name = "recommonmark"
 version = "0.7.1"
@@ -3454,103 +3068,124 @@ docutils = ">=0.11"
 sphinx = ">=1.3.1"
 
 [[package]]
-name = "requests"
-version = "2.31.0"
-description = "Python HTTP for Humans."
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
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-]
-
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-certifi = ">=2017.4.17"
-charset-normalizer = ">=2,<4"
-idna = ">=2.5,<4"
-urllib3 = ">=1.21.1,<3"
-
-[package.extras]
-socks = ["PySocks (>=1.5.6,!=1.5.7)"]
-use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
-
-[[package]]
-name = "requests-toolbelt"
-version = "1.0.0"
-description = "A utility belt for advanced users of python-requests"
+name = "regex"
+version = "2022.10.31"
+description = "Alternative regular expression module, to replace re."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.6"
 files = [
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-[package.dependencies]
-requests = ">=2.0.1,<3.0.0"
-
 [[package]]
-name = "rfc3339-validator"
-version = "0.1.4"
-description = "A pure python RFC3339 validator"
+name = "requests"
+version = "2.28.1"
+description = "Python HTTP for Humans."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.7, <4"
 files = [
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 [package.dependencies]
-six = "*"
-
-[[package]]
-name = "rfc3986"
-version = "2.0.0"
-description = "Validating URI References per RFC 3986"
-category = "main"
-optional = false
-python-versions = ">=3.7"
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-]
-
-[package.extras]
-idna2008 = ["idna"]
-
-[[package]]
-name = "rfc3987"
-version = "1.3.8"
-description = "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)"
-category = "main"
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-[[package]]
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-category = "main"
-optional = false
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-
-[package.dependencies]
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-pygments = ">=2.13.0,<3.0.0"
-typing-extensions = {version = ">=4.0.0,<5.0", markers = "python_version < \"3.9\""}
+certifi = ">=2017.4.17"
+charset-normalizer = ">=2,<3"
+idna = ">=2.5,<4"
+urllib3 = ">=1.21.1,<1.27"
 
 [package.extras]
-jupyter = ["ipywidgets (>=7.5.1,<9)"]
+socks = ["PySocks (>=1.5.6,!=1.5.7)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "rsa"
@@ -3569,18 +3204,18 @@ pyasn1 = ">=0.1.3"
 
 [[package]]
 name = "ruamel-yaml"
-version = "0.17.31"
+version = "0.17.21"
 description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
 category = "main"
 optional = false
 python-versions = ">=3"
 files = [
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+    {file = "ruamel.yaml-0.17.21.tar.gz", hash = "sha256:8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af"},
 ]
 
 [package.dependencies]
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+"ruamel.yaml.clib" = {version = ">=0.2.6", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.11\""}
 
 [package.extras]
 docs = ["ryd"]
@@ -3601,7 +3236,8 @@ files = [
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@@ -3634,14 +3270,14 @@ files = [
 
 [[package]]
 name = "s3transfer"
-version = "0.6.1"
+version = "0.6.0"
 description = "An Amazon S3 Transfer Manager"
 category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "s3transfer-0.6.1-py3-none-any.whl", hash = "sha256:3c0da2d074bf35d6870ef157158641178a4204a6e689e82546083e31e0311346"},
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+    {file = "s3transfer-0.6.0-py3-none-any.whl", hash = "sha256:06176b74f3a15f61f1b4f25a1fc29a4429040b7647133a463da8fa5bd28d5ecd"},
+    {file = "s3transfer-0.6.0.tar.gz", hash = "sha256:2ed07d3866f523cc561bf4a00fc5535827981b117dd7876f036b0c1aca42c947"},
 ]
 
 [package.dependencies]
@@ -3651,20 +3287,21 @@ botocore = ">=1.12.36,<2.0a.0"
 crt = ["botocore[crt] (>=1.20.29,<2.0a.0)"]
 
 [[package]]
-name = "secretstorage"
-version = "3.3.3"
-description = "Python bindings to FreeDesktop.org Secret Service API"
+name = "setuptools"
+version = "65.6.3"
+description = "Easily download, build, install, upgrade, and uninstall Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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-[package.dependencies]
-cryptography = ">=2.0"
-jeepney = ">=0.6"
+[package.extras]
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 [[package]]
 name = "shexjsg"
@@ -3791,26 +3428,6 @@ docs = ["sphinxcontrib-websupport"]
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-
 [[package]]
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@@ -3830,34 +3447,33 @@ sphinx = ">=2.0"
 
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+sphinx = ">=1.6,<6"
 
 [package.extras]
 dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 
 [[package]]
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-description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
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+description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books"
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 [package.extras]
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 test = ["html5lib", "pytest"]
 
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 [[package]]
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 version = "1.0.1"
@@ -3976,80 +3577,77 @@ test = ["pytest"]
 
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 ]
 
 [package.dependencies]
-greenlet = {version = "!=0.4.17", 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 = ">=4.2.0"
+greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and platform_machine == \"aarch64\" or python_version >= \"3\" and platform_machine == \"ppc64le\" or python_version >= \"3\" and platform_machine == \"x86_64\" or python_version >= \"3\" and platform_machine == \"amd64\" or python_version >= \"3\" and platform_machine == \"AMD64\" or python_version >= \"3\" and platform_machine == \"win32\" or python_version >= \"3\" and platform_machine == \"WIN32\""}
 
 [package.extras]
 aiomysql = ["aiomysql", "greenlet (!=0.4.17)"]
 aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
-asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
-mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
+asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)"]
 mssql = ["pyodbc"]
 mssql-pymssql = ["pymssql"]
 mssql-pyodbc = ["pyodbc"]
-mypy = ["mypy (>=0.910)"]
-mysql = ["mysqlclient (>=1.4.0)"]
+mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"]
+mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"]
 mysql-connector = ["mysql-connector-python"]
-oracle = ["cx-oracle (>=7)"]
-oracle-oracledb = ["oracledb (>=1.0.1)"]
+oracle = ["cx-oracle (>=7)", "cx-oracle (>=7,<8)"]
 postgresql = ["psycopg2 (>=2.7)"]
 postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
-postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
-postgresql-psycopg = ["psycopg (>=3.0.7)"]
+postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
 postgresql-psycopg2binary = ["psycopg2-binary"]
 postgresql-psycopg2cffi = ["psycopg2cffi"]
-pymysql = ["pymysql"]
+pymysql = ["pymysql", "pymysql (<1)"]
 sqlcipher = ["sqlcipher3-binary"]
 
 [[package]]
@@ -4099,14 +3697,14 @@ test = ["codacy-coverage", "coveralls", "pytest", "pytest-cov", "validate_versio
 
 [[package]]
 name = "tabula-py"
-version = "2.7.0"
+version = "2.6.0"
 description = "Simple wrapper for tabula-java, read tables from PDF into DataFrame"
 category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
 files = [
-    {file = "tabula-py-2.7.0.tar.gz", hash = "sha256:e95d8ff49fe2f86534006ae8bf38d54a9894ae70042831d70d5760800519bae8"},
-    {file = "tabula_py-2.7.0-py3-none-any.whl", hash = "sha256:7151077fedd4a6976a1a4388e36774e87d7a421a4dd0775cc3da25f2fd43ebbe"},
+    {file = "tabula-py-2.6.0.tar.gz", hash = "sha256:b10b83d15e7209fcf65c64dee064bdb2d50b06a7e4e28fc9974b92c9ef14c5cc"},
+    {file = "tabula_py-2.6.0-py3-none-any.whl", hash = "sha256:85e01f05fc8dd646b97b3a3138fda0fd70fedde3366399fe245faa2cd24f3f5e"},
 ]
 
 [package.dependencies]
@@ -4115,7 +3713,7 @@ numpy = "*"
 pandas = ">=0.25.3"
 
 [package.extras]
-dev = ["Flake8-pyproject", "black", "flake8", "isort", "mypy", "pytest"]
+dev = ["black", "flake8", "isort", "mypy", "pytest"]
 doc = ["sphinx", "sphinx-rtd-theme"]
 test = ["pytest"]
 
@@ -4145,26 +3743,26 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "1.2.3"
+version = "2.0.1"
 description = "A lil' TOML parser"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "tomli-1.2.3-py3-none-any.whl", hash = "sha256:e3069e4be3ead9668e21cb9b074cd948f7b3113fd9c8bba083f48247aab8b11c"},
-    {file = "tomli-1.2.3.tar.gz", hash = "sha256:05b6166bff487dc068d322585c7ea4ef78deed501cc124060e0f238e89a9231f"},
+    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
 
 [[package]]
 name = "tox"
-version = "3.25.1"
+version = "3.28.0"
 description = "tox is a generic virtualenv management and test command line tool"
 category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 files = [
-    {file = "tox-3.25.1-py2.py3-none-any.whl", hash = "sha256:c38e15f4733683a9cc0129fba078633e07eb0961f550a010ada879e95fb32632"},
-    {file = "tox-3.25.1.tar.gz", hash = "sha256:c138327815f53bc6da4fe56baec5f25f00622ae69ef3fe4e1e385720e22486f9"},
+    {file = "tox-3.28.0-py2.py3-none-any.whl", hash = "sha256:57b5ab7e8bb3074edc3c0c0b4b192a4f3799d3723b2c5b76f1fa9f2d40316eea"},
+    {file = "tox-3.28.0.tar.gz", hash = "sha256:d0d28f3fe6d6d7195c27f8b054c3e99d5451952b54abdae673b71609a581f640"},
 ]
 
 [package.dependencies]
@@ -4174,7 +3772,7 @@ packaging = ">=14"
 pluggy = ">=0.12.0"
 py = ">=1.4.17"
 six = ">=1.14.0"
-toml = ">=0.9.4"
+tomli = {version = ">=2.0.1", markers = "python_version >= \"3.7\" and python_version < \"3.11\""}
 virtualenv = ">=16.0.0,<20.0.0 || >20.0.0,<20.0.1 || >20.0.1,<20.0.2 || >20.0.2,<20.0.3 || >20.0.3,<20.0.4 || >20.0.4,<20.0.5 || >20.0.5,<20.0.6 || >20.0.6,<20.0.7 || >20.0.7"
 
 [package.extras]
@@ -4183,31 +3781,30 @@ testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "pathlib2 (>=2.3.3)", "psu
 
 [[package]]
 name = "tox-docker"
-version = "4.1.0"
+version = "3.1.0"
 description = "Launch a docker instance around test runs"
 category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "tox-docker-4.1.0.tar.gz", hash = "sha256:0317e692dc80f2197eaf9c905dcb8d1d1f9d5bf2686ecfd83c22a1da9d23fb24"},
-    {file = "tox_docker-4.1.0-py2.py3-none-any.whl", hash = "sha256:444c72192a2443d2b4db5766545d4413ea683cc488523d770e2e216f15fa3086"},
+    {file = "tox-docker-3.1.0.tar.gz", hash = "sha256:e1d7d60254788a2c1956d6cdfbe2a6418ed0c18c7cf2486fd484079fc84d832c"},
+    {file = "tox_docker-3.1.0-py2.py3-none-any.whl", hash = "sha256:3080c436f7fdfb5a7446215aee620638489ccd7abf812d38b6fb860337efd6f2"},
 ]
 
 [package.dependencies]
-docker = ">=4.0,<7.0"
-packaging = "*"
-tox = ">=3.0.0,<5.0"
+docker = ">=2.3.0,<6.0"
+tox = ">=3.0.0,<4.0"
 
 [[package]]
 name = "tqdm"
-version = "4.65.0"
+version = "4.64.1"
 description = "Fast, Extensible Progress Meter"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
 files = [
-    {file = "tqdm-4.65.0-py3-none-any.whl", hash = "sha256:c4f53a17fe37e132815abceec022631be8ffe1b9381c2e6e30aa70edc99e9671"},
-    {file = "tqdm-4.65.0.tar.gz", hash = "sha256:1871fb68a86b8fb3b59ca4cdd3dcccbc7e6d613eeed31f4c332531977b89beb5"},
+    {file = "tqdm-4.64.1-py2.py3-none-any.whl", hash = "sha256:6fee160d6ffcd1b1c68c65f14c829c22832bc401726335ce92c52d395944a6a1"},
+    {file = "tqdm-4.64.1.tar.gz", hash = "sha256:5f4f682a004951c1b450bc753c710e9280c5746ce6ffedee253ddbcbf54cf1e4"},
 ]
 
 [package.dependencies]
@@ -4221,43 +3818,20 @@ telegram = ["requests"]
 
 [[package]]
 name = "traitlets"
-version = "5.9.0"
+version = "5.8.0"
 description = "Traitlets Python configuration system"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "traitlets-5.9.0-py3-none-any.whl", hash = "sha256:9e6ec080259b9a5940c797d58b613b5e31441c2257b87c2e795c5228ae80d2d8"},
-    {file = "traitlets-5.9.0.tar.gz", hash = "sha256:f6cde21a9c68cf756af02035f72d5a723bf607e862e7be33ece505abf4a3bad9"},
+    {file = "traitlets-5.8.0-py3-none-any.whl", hash = "sha256:c864831efa0ba6576d09b44884b34e41defc18c0d7e720b4a2d6698c842cab3e"},
+    {file = "traitlets-5.8.0.tar.gz", hash = "sha256:6cc57d6dc28c85d5365961726ffd19b538739347749e13ebe34e03323a0e8f84"},
 ]
 
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
 test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"]
 
-[[package]]
-name = "twine"
-version = "4.0.2"
-description = "Collection of utilities for publishing packages on PyPI"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "twine-4.0.2-py3-none-any.whl", hash = "sha256:929bc3c280033347a00f847236564d1c52a3e61b1ac2516c97c48f3ceab756d8"},
-    {file = "twine-4.0.2.tar.gz", hash = "sha256:9e102ef5fdd5a20661eb88fad46338806c3bd32cf1db729603fe3697b1bc83c8"},
-]
-
-[package.dependencies]
-importlib-metadata = ">=3.6"
-keyring = ">=15.1"
-pkginfo = ">=1.8.1"
-readme-renderer = ">=35.0"
-requests = ">=2.20"
-requests-toolbelt = ">=0.8.0,<0.9.0 || >0.9.0"
-rfc3986 = ">=1.4.0"
-rich = ">=12.0.0"
-urllib3 = ">=1.26.0"
-
 [[package]]
 name = "typer"
 version = "0.7.0"
@@ -4281,53 +3855,26 @@ test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6.
 
 [[package]]
 name = "typing-extensions"
-version = "4.6.3"
+version = "4.4.0"
 description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "typing_extensions-4.6.3-py3-none-any.whl", hash = "sha256:88a4153d8505aabbb4e13aacb7c486c2b4a33ca3b3f807914a9b4c844c471c26"},
-    {file = "typing_extensions-4.6.3.tar.gz", hash = "sha256:d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5"},
-]
-
-[[package]]
-name = "tzdata"
-version = "2023.3"
-description = "Provider of IANA time zone data"
-category = "main"
-optional = false
-python-versions = ">=2"
-files = [
-    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
-    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
+    {file = "typing_extensions-4.4.0-py3-none-any.whl", hash = "sha256:16fa4864408f655d35ec496218b85f79b3437c829e93320c7c9215ccfd92489e"},
+    {file = "typing_extensions-4.4.0.tar.gz", hash = "sha256:1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa"},
 ]
 
-[[package]]
-name = "uri-template"
-version = "1.2.0"
-description = "RFC 6570 URI Template Processor"
-category = "main"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "uri_template-1.2.0-py3-none-any.whl", hash = "sha256:f1699c77b73b925cf4937eae31ab282a86dc885c333f2e942513f08f691fc7db"},
-    {file = "uri_template-1.2.0.tar.gz", hash = "sha256:934e4d09d108b70eb8a24410af8615294d09d279ce0e7cbcdaef1bd21f932b06"},
-]
-
-[package.extras]
-dev = ["flake8 (<4.0.0)", "flake8-annotations", "flake8-bugbear", "flake8-commas", "flake8-comprehensions", "flake8-continuation", "flake8-datetimez", "flake8-docstrings", "flake8-import-order", "flake8-literal", "flake8-noqa", "flake8-requirements", "flake8-type-annotations", "flake8-use-fstring", "mypy", "pep8-naming"]
-
 [[package]]
 name = "urllib3"
-version = "1.26.16"
+version = "1.26.13"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
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 [[package]]
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 [package.extras]
@@ -4462,54 +4010,26 @@ watchmedo = ["PyYAML (>=3.10)"]
 
 [[package]]
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+version = "0.2.5"
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 python-versions = "*"
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 [[package]]
 name = "websocket-client"
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 description = "WebSocket client for Python with low level API options"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.extras]
@@ -4530,106 +4050,95 @@ files = [
 
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 category = "main"
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 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
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 ]
 
 [[package]]
 name = "zipp"
-version = "3.15.0"
+version = "3.11.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
-    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
+    {file = "zipp-3.11.0-py3-none-any.whl", hash = "sha256:83a28fcb75844b5c0cdaf5aa4003c2d728c77e05f5aeabe8e95e56727005fbaa"},
+    {file = "zipp-3.11.0.tar.gz", hash = "sha256:a7a22e05929290a67401440b39690ae6563279bced5f314609d9d03798f56766"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.8"
-content-hash = "2eecee77243f09c4003a0c8d3f88cc5606813bfa36068072a047b929f41919d2"
+content-hash = "73342679bbbcad09591bfe6895b5cf0b47ab36676a5346e8420e67fe0af00ec8"
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index b9a89275..57738ee5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,7 @@ wget = "^3.2"
 ensmallen = "0.8.35"
 environments-utils = "^1.0.9"
 py-cpuinfo = "^9.0.0"
-bioregistry = "^0.6.45"
+bioregistry = "^0.9.66"
 downloaders = "^1.0.15"
 dict-hash = "^1.1.29"
 userinput = "^1.0.20"