From 9862ec0e7664bfe91aec61dbad5965d19976c56e Mon Sep 17 00:00:00 2001
From: Harshad <hrshdhgd@users.noreply.github.com>
Date: Tue, 5 Dec 2023 15:53:16 -0600
Subject: [PATCH] OAK dependency tuning (#686)

* OAK dependency tuning

* changed semsimian version window
---
 poetry.lock    | 3317 ++++++++++++++++++++++--------------------------
 pyproject.toml |    8 +-
 tox.ini        |    1 +
 3 files changed, 1491 insertions(+), 1835 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 7717f58c1..3d343101c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,10 +1,9 @@
-# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "adeft"
 version = "0.11.2"
 description = "Acromine based Disambiguation of Entities From Text"
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -23,118 +22,104 @@ test = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "aiohttp"
-version = "3.8.6"
+version = "3.9.1"
 description = "Async http client/server framework (asyncio)"
-category = "main"
 optional = true
-python-versions = ">=3.6"
+python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
 aiosignal = ">=1.1.2"
-async-timeout = ">=4.0.0a3,<5.0"
+async-timeout = {version = ">=4.0,<5.0", markers = "python_version < \"3.11\""}
 attrs = ">=17.3.0"
-charset-normalizer = ">=2.0,<4.0"
 frozenlist = ">=1.1.1"
 multidict = ">=4.5,<7.0"
 yarl = ">=1.0,<2.0"
 
 [package.extras]
-speedups = ["Brotli", "aiodns", "cchardet"]
+speedups = ["Brotli", "aiodns", "brotlicffi"]
 
 [[package]]
 name = "aiosignal"
 version = "1.3.1"
 description = "aiosignal: a list of registered asynchronous callbacks"
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -149,7 +134,6 @@ frozenlist = ">=1.1.0"
 name = "airium"
 version = "0.2.6"
 description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. Serves pure pythonic library with no dependencies."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -165,7 +149,6 @@ parse = ["beautifulsoup4 (>=4.10.0,<5.0)", "requests (>=2.12.0,<3)"]
 name = "alabaster"
 version = "0.7.13"
 description = "A configurable sidebar-enabled Sphinx theme"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -177,7 +160,6 @@ files = [
 name = "aniso8601"
 version = "9.0.1"
 description = "A library for parsing ISO 8601 strings."
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -188,11 +170,21 @@ files = [
 [package.extras]
 dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"]
 
+[[package]]
+name = "annotated-types"
+version = "0.6.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"},
+    {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"},
+]
+
 [[package]]
 name = "antlr4-python3-runtime"
 version = "4.9.3"
 description = "ANTLR 4.9.3 runtime for Python 3.7"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -201,14 +193,13 @@ files = [
 
 [[package]]
 name = "anyio"
-version = "4.0.0"
+version = "4.1.0"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "anyio-4.0.0-py3-none-any.whl", hash = "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f"},
-    {file = "anyio-4.0.0.tar.gz", hash = "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a"},
+    {file = "anyio-4.1.0-py3-none-any.whl", hash = "sha256:56a415fbc462291813a94528a779597226619c8e78af7de0507333f700011e5f"},
+    {file = "anyio-4.1.0.tar.gz", hash = "sha256:5a0bec7085176715be77df87fc66d6c9d70626bd752fcc85f57cdbee5b3760da"},
 ]
 
 [package.dependencies]
@@ -217,15 +208,14 @@ idna = ">=2.8"
 sniffio = ">=1.1"
 
 [package.extras]
-doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"]
-test = ["anyio[trio]", "coverage[toml] (>=7)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
-trio = ["trio (>=0.22)"]
+doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
+trio = ["trio (>=0.23)"]
 
 [[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 = [
@@ -237,7 +227,6 @@ files = [
 name = "appnope"
 version = "0.1.3"
 description = "Disable App Nap on macOS >= 10.9"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -249,7 +238,6 @@ files = [
 name = "argon2-cffi"
 version = "23.1.0"
 description = "Argon2 for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -270,7 +258,6 @@ typing = ["mypy"]
 name = "argon2-cffi-bindings"
 version = "21.2.0"
 description = "Low-level CFFI bindings for Argon2"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -308,7 +295,6 @@ tests = ["pytest"]
 name = "arrow"
 version = "1.3.0"
 description = "Better dates & times for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -322,31 +308,30 @@ types-python-dateutil = ">=2.8.10"
 
 [package.extras]
 doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
-test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"]
+test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
 
 [[package]]
 name = "asttokens"
-version = "2.4.0"
+version = "2.4.1"
 description = "Annotate AST trees with source code positions"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
-    {file = "asttokens-2.4.0-py2.py3-none-any.whl", hash = "sha256:cf8fc9e61a86461aa9fb161a14a0841a03c405fa829ac6b202670b3495d2ce69"},
-    {file = "asttokens-2.4.0.tar.gz", hash = "sha256:2e0171b991b2c959acc6c49318049236844a5da1d65ba2672c4880c1c894834e"},
+    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
+    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
 ]
 
 [package.dependencies]
 six = ">=1.12.0"
 
 [package.extras]
-test = ["astroid", "pytest"]
+astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
+test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 
 [[package]]
 name = "async-lru"
 version = "2.0.4"
 description = "Simple LRU cache for asyncio"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -361,7 +346,6 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 name = "async-timeout"
 version = "4.0.3"
 description = "Timeout context manager for asyncio programs"
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -373,7 +357,6 @@ files = [
 name = "attrs"
 version = "23.1.0"
 description = "Classes Without Boilerplate"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -390,36 +373,25 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
 
 [[package]]
 name = "babel"
-version = "2.13.0"
+version = "2.13.1"
 description = "Internationalization utilities"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.13.0-py3-none-any.whl", hash = "sha256:fbfcae1575ff78e26c7449136f1abbefc3c13ce542eeb13d43d50d8b047216ec"},
-    {file = "Babel-2.13.0.tar.gz", hash = "sha256:04c3e2d28d2b7681644508f836be388ae49e0cfe91465095340395b60d00f210"},
+    {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"},
+    {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"},
 ]
 
+[package.dependencies]
+setuptools = {version = "*", markers = "python_version >= \"3.12\""}
+
 [package.extras]
 dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
-[[package]]
-name = "backcall"
-version = "0.2.0"
-description = "Specifications for callback functions passed in to an API"
-category = "dev"
-optional = false
-python-versions = "*"
-files = [
-    {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
-    {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
-]
-
 [[package]]
 name = "bcp47"
 version = "0.0.4"
 description = "Language tags made easy"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -431,7 +403,6 @@ files = [
 name = "beautifulsoup4"
 version = "4.12.2"
 description = "Screen-scraping library"
-category = "main"
 optional = false
 python-versions = ">=3.6.0"
 files = [
@@ -450,7 +421,6 @@ lxml = ["lxml"]
 name = "bleach"
 version = "6.1.0"
 description = "An easy safelist-based HTML-sanitizing tool."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -467,34 +437,32 @@ css = ["tinycss2 (>=1.1.0,<1.3)"]
 
 [[package]]
 name = "boto3"
-version = "1.28.63"
+version = "1.33.8"
 description = "The AWS SDK for Python"
-category = "main"
 optional = true
 python-versions = ">= 3.7"
 files = [
-    {file = "boto3-1.28.63-py3-none-any.whl", hash = "sha256:65d052ec13197460586ee385aa2d6bba0e7378d2d2c7f3e93c044c43ae1ca782"},
-    {file = "boto3-1.28.63.tar.gz", hash = "sha256:94218aba2feb5b404b665b8d76c172dc654f79b4c5fa0e9e92459c098da87bf4"},
+    {file = "boto3-1.33.8-py3-none-any.whl", hash = "sha256:b8c818125489fc0371ef28d806d36d8f1dcb71734fcb0d96b3201563e3e86f22"},
+    {file = "boto3-1.33.8.tar.gz", hash = "sha256:d02a084b25aa8d46ef917b128e90877efab1ba45f9d1ba3a11f336930378e350"},
 ]
 
 [package.dependencies]
-botocore = ">=1.31.63,<1.32.0"
+botocore = ">=1.33.8,<1.34.0"
 jmespath = ">=0.7.1,<2.0.0"
-s3transfer = ">=0.7.0,<0.8.0"
+s3transfer = ">=0.8.2,<0.9.0"
 
 [package.extras]
 crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.31.63"
+version = "1.33.8"
 description = "Low-level, data-driven core of boto 3."
-category = "main"
 optional = true
 python-versions = ">= 3.7"
 files = [
-    {file = "botocore-1.31.63-py3-none-any.whl", hash = "sha256:cb9db5db5af865b1fc2e1405b967db5d78dd0f4d84e5dc1974e082733c1034b7"},
-    {file = "botocore-1.31.63.tar.gz", hash = "sha256:6e582c811ea74f25bdb490ac372b2645de4a60286b42ddd8c69f3b6df82b6b12"},
+    {file = "botocore-1.33.8-py3-none-any.whl", hash = "sha256:90236e6e69d7e80875d7f9d39383630706edbc1298026698c6c70d9b6a65576e"},
+    {file = "botocore-1.33.8.tar.gz", hash = "sha256:e6970bf89cbe2624399aeffce52c253917d8e5a1c671de4054557603ab56c922"},
 ]
 
 [package.dependencies]
@@ -506,63 +474,59 @@ urllib3 = [
 ]
 
 [package.extras]
-crt = ["awscrt (==0.16.26)"]
+crt = ["awscrt (==0.19.17)"]
 
 [[package]]
 name = "cachetools"
-version = "5.3.1"
+version = "5.3.2"
 description = "Extensible memoizing collections and decorators"
-category = "main"
 optional = false
 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-5.3.2-py3-none-any.whl", hash = "sha256:861f35a13a451f94e301ce2bec7cac63e881232ccce7ed67fab9b5df4d3beaa1"},
+    {file = "cachetools-5.3.2.tar.gz", hash = "sha256:086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2"},
 ]
 
 [[package]]
 name = "cattrs"
-version = "23.1.2"
+version = "23.2.3"
 description = "Composable complex class support for attrs and dataclasses."
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "cattrs-23.1.2-py3-none-any.whl", hash = "sha256:b2bb14311ac17bed0d58785e5a60f022e5431aca3932e3fc5cc8ed8639de50a4"},
-    {file = "cattrs-23.1.2.tar.gz", hash = "sha256:db1c821b8c537382b2c7c66678c3790091ca0275ac486c76f3c8f3920e83c657"},
+    {file = "cattrs-23.2.3-py3-none-any.whl", hash = "sha256:0341994d94971052e9ee70662542699a3162ea1e0c62f7ce1b4a57f563685108"},
+    {file = "cattrs-23.2.3.tar.gz", hash = "sha256:a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f"},
 ]
 
 [package.dependencies]
-attrs = ">=20"
-exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
-typing_extensions = {version = ">=4.1.0", markers = "python_version < \"3.11\""}
+attrs = ">=23.1.0"
+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\""}
 
 [package.extras]
-bson = ["pymongo (>=4.2.0,<5.0.0)"]
-cbor2 = ["cbor2 (>=5.4.6,<6.0.0)"]
-msgpack = ["msgpack (>=1.0.2,<2.0.0)"]
-orjson = ["orjson (>=3.5.2,<4.0.0)"]
-pyyaml = ["PyYAML (>=6.0,<7.0)"]
-tomlkit = ["tomlkit (>=0.11.4,<0.12.0)"]
-ujson = ["ujson (>=5.4.0,<6.0.0)"]
+bson = ["pymongo (>=4.4.0)"]
+cbor2 = ["cbor2 (>=5.4.6)"]
+msgpack = ["msgpack (>=1.0.5)"]
+orjson = ["orjson (>=3.9.2)"]
+pyyaml = ["pyyaml (>=6.0)"]
+tomlkit = ["tomlkit (>=0.11.8)"]
+ujson = ["ujson (>=5.7.0)"]
 
 [[package]]
 name = "certifi"
-version = "2023.7.22"
+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
-    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
+    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
+    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
 ]
 
 [[package]]
 name = "cffi"
 version = "1.16.0"
 description = "Foreign Function Interface for Python calling C code."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -627,7 +591,6 @@ pycparser = "*"
 name = "cfgraph"
 version = "0.2.1"
 description = "rdflib collections flattening graph"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -641,7 +604,6 @@ rdflib = ">=0.4.2"
 name = "chardet"
 version = "5.2.0"
 description = "Universal encoding detector for Python 3"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -651,109 +613,107 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.0"
+version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "charset-normalizer-3.3.0.tar.gz", hash = "sha256:63563193aec44bce707e0c5ca64ff69fa72ed7cf34ce6e11d5127555756fd2f6"},
-    {file = "charset_normalizer-3.3.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:effe5406c9bd748a871dbcaf3ac69167c38d72db8c9baf3ff954c344f31c4cbe"},
-    {file = "charset_normalizer-3.3.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:4162918ef3098851fcd8a628bf9b6a98d10c380725df9e04caf5ca6dd48c847a"},
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@@ -780,7 +740,6 @@ torch-geometric = ["torch", "torch-geometric", "torch-sparse"]
 name = "click"
 version = "8.1.7"
 description = "Composable command line interface toolkit"
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@@ -795,7 +754,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "click-default-group"
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 description = "click_default_group"
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@@ -813,7 +771,6 @@ test = ["pytest"]
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@@ -823,164 +780,88 @@ files = [
 
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+    {file = "contourpy-1.2.0.tar.gz", hash = "sha256:171f311cb758de7da13fc53af221ae47a5877be5a0843a9fe150818c51ed276a"},
+]
+
+[package.dependencies]
+numpy = ">=1.20,<2.0"
 
 [package.extras]
 bokeh = ["bokeh", "selenium"]
 docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
-mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.4.1)", "types-Pillow"]
+mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.6.1)", "types-Pillow"]
 test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
-test-no-images = ["pytest", "pytest-cov", "wurlitzer"]
+test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "coverage"
 version = "6.5.0"
 description = "Code coverage measurement for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1041,14 +922,13 @@ toml = ["tomli"]
 
 [[package]]
 name = "curies"
-version = "0.6.6"
+version = "0.7.4"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "curies-0.6.6-py3-none-any.whl", hash = "sha256:a4d13a82881a4ed8fb65f9bafa41e3154c249affb39accf4bcc5cb875db18a16"},
-    {file = "curies-0.6.6.tar.gz", hash = "sha256:f0ae232060dd31b4adfcbe35aa16e490d09e33f0051dcf58a6c56fa9895cfecd"},
+    {file = "curies-0.7.4-py3-none-any.whl", hash = "sha256:478f1818345988933d8bc6060f80a985401331f856ff8cf9bd98fa00d178ad39"},
+    {file = "curies-0.7.4.tar.gz", hash = "sha256:d3aaf16644b26ac2605ff83c565ec7df0ba0b5f7425516047666e609ec5fb718"},
 ]
 
 [package.dependencies]
@@ -1068,7 +948,6 @@ tests = ["coverage", "pytest"]
 name = "cycler"
 version = "0.12.1"
 description = "Composable style cycles"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1084,7 +963,6 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 name = "debugpy"
 version = "1.8.0"
 description = "An implementation of the Debug Adapter Protocol for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1112,7 +990,6 @@ files = [
 name = "decorator"
 version = "5.1.1"
 description = "Decorators for Humans"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1124,7 +1001,6 @@ files = [
 name = "defusedxml"
 version = "0.7.1"
 description = "XML bomb protection for Python stdlib modules"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -1136,7 +1012,6 @@ files = [
 name = "deprecated"
 version = "1.2.14"
 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 = [
@@ -1154,7 +1029,6 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 name = "deprecation"
 version = "2.1.0"
 description = "A library to handle automated deprecations"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1169,7 +1043,6 @@ packaging = "*"
 name = "distlib"
 version = "0.3.7"
 description = "Distribution utilities"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1181,7 +1054,6 @@ files = [
 name = "docutils"
 version = "0.18.1"
 description = "Docutils -- Python Documentation Utilities"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -1191,21 +1063,19 @@ files = [
 
 [[package]]
 name = "dominate"
-version = "2.8.0"
+version = "2.9.0"
 description = "Dominate is a Python library for creating and manipulating HTML documents using an elegant DOM API."
-category = "main"
 optional = true
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.4"
 files = [
-    {file = "dominate-2.8.0-py2.py3-none-any.whl", hash = "sha256:1a916479c45b95fedba0d077b081d77c2d2e0f0f484ac827105087af23661d73"},
-    {file = "dominate-2.8.0.tar.gz", hash = "sha256:4c90c3befaf88e612b71f4b39af7bcbef8977acfa855cec957225a8fbf504007"},
+    {file = "dominate-2.9.0-py2.py3-none-any.whl", hash = "sha256:2346cc27dc0fd9d279abd004b29da80ee294782619d1ca1aaccf4fb02439e6f8"},
+    {file = "dominate-2.9.0.tar.gz", hash = "sha256:b15791ebea432218543a1702d76ae45d2ff95ff994e52014b8686a69dad772fd"},
 ]
 
 [[package]]
 name = "editorconfig"
 version = "0.12.3"
 description = "EditorConfig File Locator and Interpreter for Python"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1217,7 +1087,6 @@ files = [
 name = "et-xmlfile"
 version = "1.1.0"
 description = "An implementation of lxml.xmlfile for the standard library"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1229,7 +1098,6 @@ files = [
 name = "eutils"
 version = "0.6.0"
 description = "\"Python interface to NCBI's eutilities API\""
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1247,14 +1115,13 @@ dev = ["flake8", "ipython", "mock", "pytest", "pytest-cov", "restview", "setupto
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.3"
+version = "1.2.0"
 description = "Backport of PEP 654 (exception groups)"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.1.3-py3-none-any.whl", hash = "sha256:343280667a4585d195ca1cf9cef84a4e178c4b6cf2274caef9859782b567d5e3"},
-    {file = "exceptiongroup-1.1.3.tar.gz", hash = "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9"},
+    {file = "exceptiongroup-1.2.0-py3-none-any.whl", hash = "sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14"},
+    {file = "exceptiongroup-1.2.0.tar.gz", hash = "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68"},
 ]
 
 [package.extras]
@@ -1262,14 +1129,13 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "executing"
-version = "2.0.0"
+version = "2.0.1"
 description = "Get the currently executing AST node of a frame, and other information"
-category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
 files = [
-    {file = "executing-2.0.0-py2.py3-none-any.whl", hash = "sha256:06df6183df67389625f4e763921c6cf978944721abf3e714000200aab95b0657"},
-    {file = "executing-2.0.0.tar.gz", hash = "sha256:0ff053696fdeef426cda5bd18eacd94f82c91f49823a2e9090124212ceea9b08"},
+    {file = "executing-2.0.1-py2.py3-none-any.whl", hash = "sha256:eac49ca94516ccc753f9fb5ce82603156e590b27525a8bc32cce8ae302eb61bc"},
+    {file = "executing-2.0.1.tar.gz", hash = "sha256:35afe2ce3affba8ee97f2d69927fa823b08b472b7b994e36a52a964b93d16147"},
 ]
 
 [package.extras]
@@ -1277,14 +1143,13 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
 name = "fastjsonschema"
-version = "2.18.1"
+version = "2.19.0"
 description = "Fastest Python implementation of JSON schema"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
-    {file = "fastjsonschema-2.18.1-py3-none-any.whl", hash = "sha256:aec6a19e9f66e9810ab371cc913ad5f4e9e479b63a7072a2cd060a9369e329a8"},
-    {file = "fastjsonschema-2.18.1.tar.gz", hash = "sha256:06dc8680d937628e993fa0cd278f196d20449a1adc087640710846b324d422ea"},
+    {file = "fastjsonschema-2.19.0-py3-none-any.whl", hash = "sha256:b9fd1a2dd6971dbc7fee280a95bd199ae0dd9ce22beb91cc75e9c1c528a5170e"},
+    {file = "fastjsonschema-2.19.0.tar.gz", hash = "sha256:e25df6647e1bc4a26070b700897b07b542ec898dd4f1f6ea013e7f6a88417225"},
 ]
 
 [package.extras]
@@ -1294,7 +1159,6 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 name = "fastobo"
 version = "0.12.2"
 description = "Faultless AST for Open Biomedical Ontologies in Python."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1339,26 +1203,24 @@ files = [
 
 [[package]]
 name = "filelock"
-version = "3.12.4"
+version = "3.13.1"
 description = "A platform independent file lock."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.12.4-py3-none-any.whl", hash = "sha256:08c21d87ded6e2b9da6728c3dff51baf1dcecf973b768ef35bcbc3447edb9ad4"},
-    {file = "filelock-3.12.4.tar.gz", hash = "sha256:2e6f249f1f3654291606e046b09f1fd5eac39b360664c27f5aad072012f8bcbd"},
+    {file = "filelock-3.13.1-py3-none-any.whl", hash = "sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c"},
+    {file = "filelock-3.13.1.tar.gz", hash = "sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.7.26)", "sphinx (>=7.1.2)", "sphinx-autodoc-typehints (>=1.24)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)"]
-typing = ["typing-extensions (>=4.7.1)"]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
+typing = ["typing-extensions (>=4.8)"]
 
 [[package]]
 name = "flask"
 version = "2.1.3"
 description = "A simple framework for building complex web applications."
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -1381,7 +1243,6 @@ dotenv = ["python-dotenv"]
 name = "flask-bootstrap"
 version = "3.3.7.1"
 description = "An extension that includes Bootstrap in your project, without any boilerplate code."
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -1397,7 +1258,6 @@ visitor = "*"
 name = "flask-restx"
 version = "1.1.0"
 description = "Fully featured framework for fast, easy and documented API development with Flask"
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -1421,7 +1281,6 @@ test = ["Faker (==2.0.0)", "blinker", "invoke (==2.0.0)", "mock (==3.0.5)", "pyt
 name = "flask-wtf"
 version = "1.2.1"
 description = "Form rendering, validation, and CSRF protection for Flask with WTForms."
-category = "main"
 optional = true
 python-versions = ">=3.8"
 files = [
@@ -1439,58 +1298,57 @@ email = ["email-validator"]
 
 [[package]]
 name = "fonttools"
-version = "4.43.1"
+version = "4.46.0"
 description = "Tools to manipulate font files"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "fonttools-4.43.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:10b3922875ffcba636674f406f9ab9a559564fdbaa253d66222019d569db869c"},
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+    {file = "greenlet-3.0.1.tar.gz", hash = "sha256:816bd9488a94cba78d93e1abb58000e8266fa9cc2aa9ccdd6eb0696acb24005b"},
 ]
 
 [package.extras]
@@ -1751,7 +1597,6 @@ test = ["objgraph", "psutil"]
 name = "hbreader"
 version = "0.9.1"
 description = "Honey Badger reader - a generic file/url/string open and read tool"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1761,21 +1606,19 @@ files = [
 
 [[package]]
 name = "idna"
-version = "3.4"
+version = "3.6"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "idna-3.4-py3-none-any.whl", hash = "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"},
-    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
+    {file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"},
+    {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
 ]
 
 [[package]]
 name = "ijson"
 version = "3.2.3"
 description = "Iterative JSON parser with standard Python iterator interfaces"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1874,7 +1717,6 @@ files = [
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1884,34 +1726,32 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.8.0"
+version = "7.0.0"
 description = "Read metadata from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-6.8.0-py3-none-any.whl", hash = "sha256:3ebb78df84a805d7698245025b975d9d67053cd94c79245ba4b3eb694abe68bb"},
-    {file = "importlib_metadata-6.8.0.tar.gz", hash = "sha256:dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743"},
+    {file = "importlib_metadata-7.0.0-py3-none-any.whl", hash = "sha256:d97503976bb81f40a193d41ee6570868479c69d5068651eb039c40d850c59d67"},
+    {file = "importlib_metadata-7.0.0.tar.gz", hash = "sha256:7fc841f8b8332803464e5dc1c63a2e59121f46ca186c0e2e182e80bf8c1319f7"},
 ]
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
 testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
 [[package]]
 name = "importlib-resources"
-version = "6.1.0"
+version = "6.1.1"
 description = "Read resources from Python packages"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-6.1.0-py3-none-any.whl", hash = "sha256:aa50258bbfa56d4e33fbd8aa3ef48ded10d1735f11532b8df95388cc6bdb7e83"},
-    {file = "importlib_resources-6.1.0.tar.gz", hash = "sha256:9d48dcccc213325e810fd723e7fbb45ccb39f6cf5c31f00cf2b965f5f10f3cb9"},
+    {file = "importlib_resources-6.1.1-py3-none-any.whl", hash = "sha256:e8bf90d8213b486f428c9c39714b920041cb02c184686a3dee24905aaa8105d6"},
+    {file = "importlib_resources-6.1.1.tar.gz", hash = "sha256:3893a00122eafde6894c59914446a512f728a0c1a45f9bb9b63721b6bacf0b4a"},
 ]
 
 [package.dependencies]
@@ -1925,7 +1765,6 @@ testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)",
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1935,14 +1774,13 @@ files = [
 
 [[package]]
 name = "ipykernel"
-version = "6.25.2"
+version = "6.27.1"
 description = "IPython Kernel for Jupyter"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipykernel-6.25.2-py3-none-any.whl", hash = "sha256:2e2ee359baba19f10251b99415bb39de1e97d04e1fab385646f24f0596510b77"},
-    {file = "ipykernel-6.25.2.tar.gz", hash = "sha256:f468ddd1f17acb48c8ce67fcfa49ba6d46d4f9ac0438c1f441be7c3d1372230b"},
+    {file = "ipykernel-6.27.1-py3-none-any.whl", hash = "sha256:dab88b47f112f9f7df62236511023c9bdeef67abc73af7c652e4ce4441601686"},
+    {file = "ipykernel-6.27.1.tar.gz", hash = "sha256:7d5d594b6690654b4d299edba5e872dc17bb7396a8d0609c97cb7b8a1c605de6"},
 ]
 
 [package.dependencies]
@@ -1951,7 +1789,7 @@ comm = ">=0.1.1"
 debugpy = ">=1.6.5"
 ipython = ">=7.23.1"
 jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 matplotlib-inline = ">=0.1"
 nest-asyncio = "*"
 packaging = "*"
@@ -1969,62 +1807,45 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio"
 
 [[package]]
 name = "ipython"
-version = "8.16.1"
+version = "8.18.1"
 description = "IPython: Productive Interactive Computing"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "ipython-8.16.1-py3-none-any.whl", hash = "sha256:0852469d4d579d9cd613c220af7bf0c9cc251813e12be647cb9d463939db9b1e"},
-    {file = "ipython-8.16.1.tar.gz", hash = "sha256:ad52f58fca8f9f848e256c629eff888efc0528c12fe0f8ec14f33205f23ef938"},
+    {file = "ipython-8.18.1-py3-none-any.whl", hash = "sha256:e8267419d72d81955ec1177f8a29aaa90ac80ad647499201119e2f05e99aa397"},
+    {file = "ipython-8.18.1.tar.gz", hash = "sha256:ca6f079bb33457c66e233e4580ebfc4128855b4cf6370dddd73842a9563e8a27"},
 ]
 
 [package.dependencies]
-appnope = {version = "*", markers = "sys_platform == \"darwin\""}
-backcall = "*"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 decorator = "*"
 exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
 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 = ">=3.0.41,<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", "exceptiongroup", "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", "exceptiongroup", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
 black = ["black"]
-doc = ["docrepr", "exceptiongroup", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
+doc = ["docrepr", "exceptiongroup", "ipykernel", "matplotlib", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
 nbformat = ["nbformat"]
 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"]
-
-[[package]]
-name = "ipython-genutils"
-version = "0.2.0"
-description = "Vestigial utilities from IPython"
-category = "dev"
-optional = false
-python-versions = "*"
-files = [
-    {file = "ipython_genutils-0.2.0-py2.py3-none-any.whl", hash = "sha256:72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8"},
-    {file = "ipython_genutils-0.2.0.tar.gz", hash = "sha256:eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8"},
-]
+test = ["pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath"]
+test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath", "trio"]
 
 [[package]]
 name = "ipywidgets"
 version = "8.1.1"
 description = "Jupyter interactive widgets"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2046,7 +1867,6 @@ test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
 name = "isodate"
 version = "0.6.1"
 description = "An ISO 8601 date/time/duration parser and formatter"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2061,7 +1881,6 @@ six = "*"
 name = "isoduration"
 version = "20.11.0"
 description = "Operations with ISO 8601 durations"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2076,7 +1895,6 @@ arrow = ">=0.15.0"
 name = "itsdangerous"
 version = "2.1.2"
 description = "Safely pass data to untrusted environments and back."
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -2088,7 +1906,6 @@ files = [
 name = "jedi"
 version = "0.19.1"
 description = "An autocompletion tool for Python that can be used for text editors."
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2108,7 +1925,6 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 name = "jinja2"
 version = "3.1.2"
 description = "A very fast and expressive template engine."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2126,7 +1942,6 @@ i18n = ["Babel (>=2.7)"]
 name = "jmespath"
 version = "1.0.1"
 description = "JSON Matching Expressions"
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -2138,7 +1953,6 @@ files = [
 name = "joblib"
 version = "1.3.2"
 description = "Lightweight pipelining with Python functions"
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -2148,13 +1962,12 @@ files = [
 
 [[package]]
 name = "jsbeautifier"
-version = "1.14.9"
+version = "1.14.11"
 description = "JavaScript unobfuscator and beautifier."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "jsbeautifier-1.14.9.tar.gz", hash = "sha256:c738ebc36b47bd94e4ca6dd17a9004c3cc74edad582ca1d60e0e5d5945a63cb9"},
+    {file = "jsbeautifier-1.14.11.tar.gz", hash = "sha256:6b632581ea60dd1c133cd25a48ad187b4b91f526623c4b0fb5443ef805250505"},
 ]
 
 [package.dependencies]
@@ -2165,7 +1978,6 @@ six = ">=1.13.0"
 name = "json-flattener"
 version = "0.1.9"
 description = "Python library for denormalizing nested dicts or json objects to tables and back"
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -2181,7 +1993,6 @@ pyyaml = "*"
 name = "json5"
 version = "0.9.14"
 description = "A Python implementation of the JSON5 data format."
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -2196,7 +2007,6 @@ dev = ["hypothesis"]
 name = "jsonasobj"
 version = "1.3.1"
 description = "JSON as python objects"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2208,7 +2018,6 @@ files = [
 name = "jsonasobj2"
 version = "1.0.4"
 description = "JSON as python objects - version 2"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2223,7 +2032,6 @@ hbreader = "*"
 name = "jsonpatch"
 version = "1.33"
 description = "Apply JSON-Patches (RFC 6902)"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
@@ -2238,7 +2046,6 @@ jsonpointer = ">=1.9"
 name = "jsonpath-ng"
 version = "1.6.0"
 description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -2253,7 +2060,6 @@ ply = "*"
 name = "jsonpointer"
 version = "2.4"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
@@ -2263,30 +2069,29 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.19.1"
+version = "4.20.0"
 description = "An implementation of JSON Schema validation for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.19.1-py3-none-any.whl", hash = "sha256:cd5f1f9ed9444e554b38ba003af06c0a8c2868131e56bfbef0550fb450c0330e"},
-    {file = "jsonschema-4.19.1.tar.gz", hash = "sha256:ec84cc37cfa703ef7cd4928db24f9cb31428a5d0fa77747b8b51a847458e0bbf"},
+    {file = "jsonschema-4.20.0-py3-none-any.whl", hash = "sha256:ed6231f0429ecf966f5bc8dfef245998220549cbbcf140f913b7464c52c3b6b3"},
+    {file = "jsonschema-4.20.0.tar.gz", hash = "sha256:4f614fd46d8d61258610998997743ec5492a648b33cf478c1ddc23ed4598a5fa"},
 ]
 
 [package.dependencies]
 attrs = ">=22.2.0"
-fqdn = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
-idna = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
-isoduration = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
-jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""}
+fqdn = {version = "*", optional = true, markers = "extra == \"format\""}
+idna = {version = "*", optional = true, markers = "extra == \"format\""}
+isoduration = {version = "*", optional = true, markers = "extra == \"format\""}
+jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format\""}
 jsonschema-specifications = ">=2023.03.6"
 referencing = ">=0.28.4"
-rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
+rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format\""}
 rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
 rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
 rpds-py = ">=0.7.1"
-uri-template = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
-webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-nongpl\""}
+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)"]
@@ -2294,24 +2099,22 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.7.1"
+version = "2023.11.2"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema_specifications-2023.7.1-py3-none-any.whl", hash = "sha256:05adf340b659828a004220a9613be00fa3f223f2b82002e273dee62fd50524b1"},
-    {file = "jsonschema_specifications-2023.7.1.tar.gz", hash = "sha256:c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb"},
+    {file = "jsonschema_specifications-2023.11.2-py3-none-any.whl", hash = "sha256:e74ba7c0a65e8cb49dc26837d6cfe576557084a8b423ed16a420984228104f93"},
+    {file = "jsonschema_specifications-2023.11.2.tar.gz", hash = "sha256:9472fc4fea474cd74bea4a2b190daeccb5a9e4db2ea80efcf7a1b582fc9a81b8"},
 ]
 
 [package.dependencies]
-referencing = ">=0.28.0"
+referencing = ">=0.31.0"
 
 [[package]]
 name = "jupyter"
 version = "1.0.0"
 description = "Jupyter metapackage. Install all the Jupyter components in one go."
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -2330,19 +2133,18 @@ qtconsole = "*"
 
 [[package]]
 name = "jupyter-client"
-version = "8.4.0"
+version = "8.6.0"
 description = "Jupyter protocol implementation and client libraries"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_client-8.4.0-py3-none-any.whl", hash = "sha256:6a2a950ec23a8f62f9e4c66acec7f0ea6c7d1f80ba0992e747b10c56ce2e6dbe"},
-    {file = "jupyter_client-8.4.0.tar.gz", hash = "sha256:dc1b857d5d7d76ac101766c6e9b646bf18742721126e72e5d484c75a993cada2"},
+    {file = "jupyter_client-8.6.0-py3-none-any.whl", hash = "sha256:909c474dbe62582ae62b758bca86d6518c85234bdee2d908c778db6d72f39d99"},
+    {file = "jupyter_client-8.6.0.tar.gz", hash = "sha256:0642244bb83b4764ae60d07e010e15f0e2d275ec4e918a8f7b80fbbef3ca60c7"},
 ]
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 python-dateutil = ">=2.8.2"
 pyzmq = ">=23.0"
 tornado = ">=6.2"
@@ -2356,7 +2158,6 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 name = "jupyter-console"
 version = "6.6.3"
 description = "Jupyter terminal console"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2368,7 +2169,7 @@ files = [
 ipykernel = ">=6.14"
 ipython = "*"
 jupyter-client = ">=7.0.0"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 prompt-toolkit = ">=3.0.30"
 pygments = "*"
 pyzmq = ">=17"
@@ -2379,14 +2180,13 @@ test = ["flaky", "pexpect", "pytest"]
 
 [[package]]
 name = "jupyter-core"
-version = "5.4.0"
+version = "5.5.0"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_core-5.4.0-py3-none-any.whl", hash = "sha256:66e252f675ac04dcf2feb6ed4afb3cd7f68cf92f483607522dc251f32d471571"},
-    {file = "jupyter_core-5.4.0.tar.gz", hash = "sha256:e4b98344bb94ee2e3e6c4519a97d001656009f9cb2b7f2baf15b3c205770011d"},
+    {file = "jupyter_core-5.5.0-py3-none-any.whl", hash = "sha256:e11e02cd8ae0a9de5c6c44abf5727df9f2581055afe00b22183f621ba3585805"},
+    {file = "jupyter_core-5.5.0.tar.gz", hash = "sha256:880b86053bf298a8724994f95e99b99130659022a4f7f45f563084b6223861d3"},
 ]
 
 [package.dependencies]
@@ -2395,19 +2195,18 @@ pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_
 traitlets = ">=5.3"
 
 [package.extras]
-docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
 test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-events"
-version = "0.7.0"
+version = "0.9.0"
 description = "Jupyter Event System library"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_events-0.7.0-py3-none-any.whl", hash = "sha256:4753da434c13a37c3f3c89b500afa0c0a6241633441421f6adafe2fb2e2b924e"},
-    {file = "jupyter_events-0.7.0.tar.gz", hash = "sha256:7be27f54b8388c03eefea123a4f79247c5b9381c49fb1cd48615ee191eb12615"},
+    {file = "jupyter_events-0.9.0-py3-none-any.whl", hash = "sha256:d853b3c10273ff9bc8bb8b30076d65e2c9685579db736873de6c2232dde148bf"},
+    {file = "jupyter_events-0.9.0.tar.gz", hash = "sha256:81ad2e4bc710881ec274d31c6c50669d71bbaa5dd9d01e600b56faa85700d399"},
 ]
 
 [package.dependencies]
@@ -2426,14 +2225,13 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p
 
 [[package]]
 name = "jupyter-lsp"
-version = "2.2.0"
+version = "2.2.1"
 description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter-lsp-2.2.0.tar.gz", hash = "sha256:8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1"},
-    {file = "jupyter_lsp-2.2.0-py3-none-any.whl", hash = "sha256:9e06b8b4f7dd50300b70dd1a78c0c3b0c3d8fa68e0f2d8a5d1fbab62072aca3f"},
+    {file = "jupyter-lsp-2.2.1.tar.gz", hash = "sha256:b17fab6d70fe83c8896b0cff59237640038247c196056b43684a0902b6a9e0fb"},
+    {file = "jupyter_lsp-2.2.1-py3-none-any.whl", hash = "sha256:17a689910c5e4ae5e7d334b02f31d08ffbe98108f6f658fb05e4304b4345368b"},
 ]
 
 [package.dependencies]
@@ -2442,14 +2240,13 @@ jupyter-server = ">=1.1.2"
 
 [[package]]
 name = "jupyter-server"
-version = "2.7.3"
+version = "2.11.2"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_server-2.7.3-py3-none-any.whl", hash = "sha256:8e4b90380b59d7a1e31086c4692231f2a2ea4cb269f5516e60aba72ce8317fc9"},
-    {file = "jupyter_server-2.7.3.tar.gz", hash = "sha256:d4916c8581c4ebbc534cebdaa8eca2478d9f3bfdd88eae29fcab0120eac57649"},
+    {file = "jupyter_server-2.11.2-py3-none-any.whl", hash = "sha256:0c548151b54bcb516ca466ec628f7f021545be137d01b5467877e87f6fff4374"},
+    {file = "jupyter_server-2.11.2.tar.gz", hash = "sha256:0c99f9367b0f24141e527544522430176613f9249849be80504c6d2b955004bb"},
 ]
 
 [package.dependencies]
@@ -2457,8 +2254,8 @@ anyio = ">=3.1.0"
 argon2-cffi = "*"
 jinja2 = "*"
 jupyter-client = ">=7.4.4"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
-jupyter-events = ">=0.6.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+jupyter-events = ">=0.9.0"
 jupyter-server-terminals = "*"
 nbconvert = ">=6.4.4"
 nbformat = ">=5.3.0"
@@ -2481,7 +2278,6 @@ test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-sc
 name = "jupyter-server-terminals"
 version = "0.4.4"
 description = "A Jupyter Server Extension Providing Terminals."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2499,14 +2295,13 @@ test = ["coverage", "jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-cov",
 
 [[package]]
 name = "jupyterlab"
-version = "4.0.7"
+version = "4.0.9"
 description = "JupyterLab computational environment"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyterlab-4.0.7-py3-none-any.whl", hash = "sha256:08683045117cc495531fdb39c22ababb9aaac6977a45e67cfad20046564c9c7c"},
-    {file = "jupyterlab-4.0.7.tar.gz", hash = "sha256:48792efd9f962b2bcda1f87d72168ff122c288b1d97d32109e4a11b33dc862be"},
+    {file = "jupyterlab-4.0.9-py3-none-any.whl", hash = "sha256:9f6f8e36d543fdbcc3df961a1d6a3f524b4a4001be0327a398f68fa4e534107c"},
+    {file = "jupyterlab-4.0.9.tar.gz", hash = "sha256:9ebada41d52651f623c0c9f069ddb8a21d6848e4c887d8e5ddc0613166ed5c0b"},
 ]
 
 [package.dependencies]
@@ -2525,33 +2320,31 @@ tornado = ">=6.2.0"
 traitlets = "*"
 
 [package.extras]
-dev = ["black[jupyter] (==23.7.0)", "build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.0.286)"]
+dev = ["black[jupyter] (==23.10.1)", "build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.1.4)"]
 docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-tornasync", "sphinx (>=1.8,<7.2.0)", "sphinx-copybutton"]
 docs-screenshots = ["altair (==5.0.1)", "ipython (==8.14.0)", "ipywidgets (==8.0.6)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.0.post0)", "matplotlib (==3.7.1)", "nbconvert (>=7.0.0)", "pandas (==2.0.2)", "scipy (==1.10.1)", "vega-datasets (==0.9.0)"]
 test = ["coverage", "pytest (>=7.0)", "pytest-check-links (>=0.7)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter (>=0.5.3)", "pytest-timeout", "pytest-tornasync", "requests", "requests-cache", "virtualenv"]
 
 [[package]]
 name = "jupyterlab-pygments"
-version = "0.2.2"
+version = "0.3.0"
 description = "Pygments theme using JupyterLab CSS variables"
-category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "jupyterlab_pygments-0.2.2-py2.py3-none-any.whl", hash = "sha256:2405800db07c9f770863bcf8049a529c3dd4d3e28536638bd7c1c01d2748309f"},
-    {file = "jupyterlab_pygments-0.2.2.tar.gz", hash = "sha256:7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d"},
+    {file = "jupyterlab_pygments-0.3.0-py3-none-any.whl", hash = "sha256:841a89020971da1d8693f1a99997aefc5dc424bb1b251fd6322462a1b8842780"},
+    {file = "jupyterlab_pygments-0.3.0.tar.gz", hash = "sha256:721aca4d9029252b11cfa9d185e5b5af4d54772bb8072f9b7036f4170054d35d"},
 ]
 
 [[package]]
 name = "jupyterlab-server"
-version = "2.25.0"
+version = "2.25.2"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyterlab_server-2.25.0-py3-none-any.whl", hash = "sha256:c9f67a98b295c5dee87f41551b0558374e45d449f3edca153dd722140630dcb2"},
-    {file = "jupyterlab_server-2.25.0.tar.gz", hash = "sha256:77c2f1f282d610f95e496e20d5bf1d2a7706826dfb7b18f3378ae2870d272fb7"},
+    {file = "jupyterlab_server-2.25.2-py3-none-any.whl", hash = "sha256:5b1798c9cc6a44f65c757de9f97fc06fc3d42535afbf47d2ace5e964ab447aaf"},
+    {file = "jupyterlab_server-2.25.2.tar.gz", hash = "sha256:bd0ec7a99ebcedc8bcff939ef86e52c378e44c2707e053fcd81d046ce979ee63"},
 ]
 
 [package.dependencies]
@@ -2567,13 +2360,12 @@ requests = ">=2.31"
 [package.extras]
 docs = ["autodoc-traits", "jinja2 (<3.2.0)", "mistune (<4)", "myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinxcontrib-openapi (>0.8)"]
 openapi = ["openapi-core (>=0.18.0,<0.19.0)", "ruamel-yaml"]
-test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-validator (>=0.6.0,<0.7.0)", "pytest (>=7.0)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter[server] (>=0.6.2)", "pytest-timeout", "requests-mock", "ruamel-yaml", "sphinxcontrib-spelling", "strict-rfc3339", "werkzeug"]
+test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-validator (>=0.6.0,<0.8.0)", "pytest (>=7.0)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter[server] (>=0.6.2)", "pytest-timeout", "requests-mock", "ruamel-yaml", "sphinxcontrib-spelling", "strict-rfc3339", "werkzeug"]
 
 [[package]]
 name = "jupyterlab-widgets"
 version = "3.0.9"
 description = "Jupyter interactive widgets for JupyterLab"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2585,7 +2377,6 @@ files = [
 name = "kgcl-rdflib"
 version = "0.5.0"
 description = "Schema for the KGCL project."
-category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -2599,27 +2390,25 @@ linkml-runtime = ">=1.1.24"
 
 [[package]]
 name = "kgcl-schema"
-version = "0.6.0"
+version = "0.6.2"
 description = "Schema for the KGCL project."
-category = "main"
 optional = false
-python-versions = ">=3.8,<4.0"
+python-versions = ">=3.9,<4.0"
 files = [
-    {file = "kgcl_schema-0.6.0-py3-none-any.whl", hash = "sha256:c212d459cf98f977c537f025331713c5ecfc9e9065e5cc189b3494beb836036f"},
-    {file = "kgcl_schema-0.6.0.tar.gz", hash = "sha256:382c6cf7d4f6136374f1cc53fbd301af64e872c0ef1f775efb2ae4a789e120fb"},
+    {file = "kgcl_schema-0.6.2-py3-none-any.whl", hash = "sha256:e18b6e763c91db07f3cb6a444658590f43a873332dd2c0c595f379070cbd82e5"},
+    {file = "kgcl_schema-0.6.2.tar.gz", hash = "sha256:a96a7c97f809434d8e27c4b1078ec634fdf72f153355afa40fceeb361cd53d7b"},
 ]
 
 [package.dependencies]
-curies = ">=0.6.0,<0.7.0"
+curies = ">=0.6.0"
 lark = ">=1.1.2"
 linkml-runtime = ">=1.1.24"
-prefixmaps = ">=0.1.5,<0.2.0"
+prefixmaps = ">=0.2.0,<0.3.0"
 
 [[package]]
 name = "kiwisolver"
 version = "1.4.5"
 description = "A fast implementation of the Cassowary constraint solver"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2731,14 +2520,13 @@ files = [
 
 [[package]]
 name = "lark"
-version = "1.1.7"
+version = "1.1.8"
 description = "a modern parsing library"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "lark-1.1.7-py3-none-any.whl", hash = "sha256:9e5dc5bbf93fa1840083707285262514a0ef8a6613874af7ea1cec60468d6e92"},
-    {file = "lark-1.1.7.tar.gz", hash = "sha256:be7437bf1f37ab08b355f29ff2571d77d777113d0a8c4352b0c513dced6c5a1e"},
+    {file = "lark-1.1.8-py3-none-any.whl", hash = "sha256:7d2c221a66a8165f3f81aacb958d26033d40d972fdb70213ab0a2e0627e29c86"},
+    {file = "lark-1.1.8.tar.gz", hash = "sha256:7ef424db57f59c1ffd6f0d4c2b705119927f566b68c0fe1942dddcc0e44391a5"},
 ]
 
 [package.extras]
@@ -2749,14 +2537,13 @@ regex = ["regex"]
 
 [[package]]
 name = "linkml"
-version = "1.6.1"
+version = "1.6.3"
 description = "Linked Open Data Modeling Language"
-category = "dev"
 optional = false
-python-versions = ">=3.8,<4.0"
+python-versions = ">=3.8.1,<4.0.0"
 files = [
-    {file = "linkml-1.6.1-py3-none-any.whl", hash = "sha256:7501cb9c7b2c13ca78fc7121ae8b5457fb5771138714da31cc11f971062070ee"},
-    {file = "linkml-1.6.1.tar.gz", hash = "sha256:65f73cf29a77518972238e71e91e012c081cf2e43d71d8965ca414c78c11e08e"},
+    {file = "linkml-1.6.3-py3-none-any.whl", hash = "sha256:2bcfa9e35b3e0d868f396fa48ede1b9e3c6016df956dd5ca92d70ff621ffc77e"},
+    {file = "linkml-1.6.3.tar.gz", hash = "sha256:2692243c9fb1c262ea83b725c70d6f537844ae7a9405101c94bccf65def6d952"},
 ]
 
 [package.dependencies]
@@ -2774,7 +2561,7 @@ openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
 prefixmaps = ">=0.1.3"
-pydantic = "*"
+pydantic = ">=1.0.0,<3.0.0"
 pyjsg = ">=0.11.6"
 pyshex = ">=0.7.20"
 pyshexc = ">=0.8.3"
@@ -2789,7 +2576,6 @@ watchdog = ">=0.9.0"
 name = "linkml-dataops"
 version = "0.1.0"
 description = "LinkML Data Operations API"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2808,7 +2594,6 @@ linkml-runtime = ">=1.1.6"
 name = "linkml-renderer"
 version = "0.3.0"
 description = "linkml-renderer"
-category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -2824,14 +2609,13 @@ pydantic = "*"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.6.0"
+version = "1.6.2"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
-category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
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+    {file = "linkml_runtime-1.6.2-py3-none-any.whl", hash = "sha256:d9a915faf0ee8c8749f42d38394a06d37f016e155e077ff9cb5c5a21f24e19d6"},
+    {file = "linkml_runtime-1.6.2.tar.gz", hash = "sha256:bcbeff96d24433276755db85375e3dff0c9af0fd04f8a05f7ccd8a669a9e9877"},
 ]
 
 [package.dependencies]
@@ -2851,20 +2635,19 @@ requests = "*"
 
 [[package]]
 name = "llm"
-version = "0.11"
+version = "0.12"
 description = "A CLI utility and Python library for interacting with Large Language Models, including OpenAI, PaLM and local models installed on your own machine."
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
 click = "*"
 click-default-group = ">=1.2.3"
-openai = "*"
+openai = "<1.0"
 pip = "*"
 pluggy = "*"
 pydantic = ">=1.10.2"
@@ -2881,7 +2664,6 @@ test = ["black", "cogapp", "mypy", "numpy", "pytest", "requests-mock", "ruff", "
 name = "lxml"
 version = "4.9.3"
 description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
 files = [
@@ -2987,14 +2769,13 @@ source = ["Cython (>=0.29.35)"]
 
 [[package]]
 name = "markdown"
-version = "3.5"
+version = "3.5.1"
 description = "Python implementation of John Gruber's Markdown."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "Markdown-3.5.1.tar.gz", hash = "sha256:b65d7beb248dc22f2e8a31fb706d93798093c308dc1aba295aedeb9d41a813bd"},
 ]
 
 [package.dependencies]
@@ -3008,7 +2789,6 @@ testing = ["coverage", "pyyaml"]
 name = "markdown-it-py"
 version = "3.0.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3033,7 +2813,6 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 name = "markupsafe"
 version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3101,40 +2880,39 @@ files = [
 
 [[package]]
 name = "matplotlib"
-version = "3.8.0"
+version = "3.8.2"
 description = "Python plotting package"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
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+    {file = "matplotlib-3.8.2.tar.gz", hash = "sha256:01a978b871b881ee76017152f1f1a0cbf6bd5f7b8ff8c96df0df1bd57d8755a1"},
 ]
 
 [package.dependencies]
@@ -3142,19 +2920,17 @@ contourpy = ">=1.0.1"
 cycler = ">=0.10"
 fonttools = ">=4.22.0"
 importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
-kiwisolver = ">=1.0.1"
+kiwisolver = ">=1.3.1"
 numpy = ">=1.21,<2"
 packaging = ">=20.0"
-pillow = ">=6.2.0"
+pillow = ">=8"
 pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
-setuptools_scm = ">=7"
 
 [[package]]
 name = "matplotlib-inline"
 version = "0.1.6"
 description = "Inline Matplotlib backend for Jupyter"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -3169,7 +2945,6 @@ traitlets = "*"
 name = "mdit-py-plugins"
 version = "0.4.0"
 description = "Collection of plugins for markdown-it-py"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3189,7 +2964,6 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 name = "mdurl"
 version = "0.1.2"
 description = "Markdown URL utilities"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3201,7 +2975,6 @@ files = [
 name = "mergedeep"
 version = "1.3.4"
 description = "A deep merge function for 🐍."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -3213,7 +2986,6 @@ files = [
 name = "mistune"
 version = "3.0.2"
 description = "A sane and fast Markdown parser with useful plugins and renderers"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3225,7 +2997,6 @@ files = [
 name = "mkdocs"
 version = "1.5.3"
 description = "Project documentation with Markdown."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3255,14 +3026,13 @@ min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-imp
 
 [[package]]
 name = "mkdocs-material"
-version = "9.4.5"
+version = "9.4.14"
 description = "Documentation that simply works"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -3271,7 +3041,7 @@ colorama = ">=0.4,<1.0"
 jinja2 = ">=3.0,<4.0"
 markdown = ">=3.2,<4.0"
 mkdocs = ">=1.5.3,<2.0"
-mkdocs-material-extensions = ">=1.2,<2.0"
+mkdocs-material-extensions = ">=1.3,<2.0"
 paginate = ">=0.5,<1.0"
 pygments = ">=2.16,<3.0"
 pymdown-extensions = ">=10.2,<11.0"
@@ -3285,21 +3055,19 @@ recommended = ["mkdocs-minify-plugin (>=0.7,<1.0)", "mkdocs-redirects (>=1.2,<2.
 
 [[package]]
 name = "mkdocs-material-extensions"
-version = "1.2"
+version = "1.3.1"
 description = "Extension pack for Python Markdown and MkDocs Material."
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 [[package]]
 name = "mkdocs-mermaid2-plugin"
 version = "0.6.0"
 description = "A MkDocs plugin for including mermaid graphs in markdown sources"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -3321,7 +3089,6 @@ setuptools = ">=18.5"
 name = "more-click"
 version = "0.1.2"
 description = "More click."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3339,7 +3106,6 @@ tests = ["coverage", "pytest"]
 name = "multidict"
 version = "6.0.4"
 description = "multidict implementation"
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -3423,7 +3189,6 @@ files = [
 name = "myst-parser"
 version = "2.0.0"
 description = "An extended [CommonMark](https://spec.commonmark.org/) compliant parser,"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3448,19 +3213,18 @@ testing-docutils = ["pygments", "pytest (>=7,<8)", "pytest-param-files (>=0.3.4,
 
 [[package]]
 name = "nbclient"
-version = "0.8.0"
+version = "0.9.0"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
-category = "dev"
 optional = false
 python-versions = ">=3.8.0"
 files = [
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 [package.dependencies]
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-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 nbformat = ">=5.1"
 traitlets = ">=5.4"
 
@@ -3471,14 +3235,13 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=
 
 [[package]]
 name = "nbconvert"
-version = "7.9.2"
+version = "7.12.0"
 description = "Converting Jupyter Notebooks"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -3505,14 +3268,13 @@ docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sp
 qtpdf = ["nbconvert[qtpng]"]
 qtpng = ["pyqtwebengine (>=5.15)"]
 serve = ["tornado (>=6.1)"]
-test = ["flaky", "ipykernel", "ipywidgets (>=7)", "pytest", "pytest-dependency"]
+test = ["flaky", "ipykernel", "ipywidgets (>=7)", "pytest"]
 webpdf = ["playwright"]
 
 [[package]]
 name = "nbformat"
 version = "5.9.2"
 description = "The Jupyter Notebook format"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3532,14 +3294,13 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
 
 [[package]]
 name = "ndex2"
-version = "3.5.1"
+version = "3.6.0"
 description = "Nice CX Python includes a client and a data model."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
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 [package.dependencies]
@@ -3556,7 +3317,6 @@ urllib3 = ">=1.16"
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 version = "1.5.8"
 description = "Patch asyncio to allow nested event loops"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -3566,28 +3326,26 @@ files = [
 
 [[package]]
 name = "networkx"
-version = "3.1"
+version = "3.2.1"
 description = "Python package for creating and manipulating graphs and networks"
-category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
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 [package.extras]
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-developer = ["mypy (>=1.1)", "pre-commit (>=3.2)"]
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-test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
+default = ["matplotlib (>=3.5)", "numpy (>=1.22)", "pandas (>=1.4)", "scipy (>=1.9,!=1.11.0,!=1.11.1)"]
+developer = ["changelist (==0.4)", "mypy (>=1.1)", "pre-commit (>=3.2)", "rtoml"]
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+extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.11)", "sympy (>=1.10)"]
+test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "nltk"
 version = "3.8.1"
 description = "Natural Language Toolkit"
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -3611,14 +3369,13 @@ twitter = ["twython"]
 
 [[package]]
 name = "notebook"
-version = "7.0.5"
+version = "7.0.6"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
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 python-versions = ">=3.8"
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 [package.dependencies]
@@ -3637,7 +3394,6 @@ test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4
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 version = "0.2.3"
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-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3653,44 +3409,53 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync"
 
 [[package]]
 name = "numpy"
-version = "1.25.2"
+version = "1.26.2"
 description = "Fundamental package for array computing in Python"
-category = "main"
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@@ -3713,7 +3478,6 @@ tests = ["coverage", "pytest"]
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 numpy = [
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-    {version = ">=1.23.2", markers = "python_version == \"3.11\""},
+    {version = ">=1.22.4,<2", markers = "python_version < \"3.11\""},
+    {version = ">=1.23.2,<2", markers = "python_version == \"3.11\""},
+    {version = ">=1.26.0,<2", markers = "python_version >= \"3.12\""},
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 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
 tzdata = ">=2022.1"
 
 [package.extras]
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 clipboard = ["PyQt5 (>=5.15.6)", "qtpy (>=2.2.0)"]
 compression = ["zstandard (>=0.17.0)"]
@@ -3926,14 +3626,13 @@ plot = ["matplotlib (>=3.6.1)"]
 postgresql = ["SQLAlchemy (>=1.4.36)", "psycopg2 (>=2.9.3)"]
 spss = ["pyreadstat (>=1.1.5)"]
 sql-other = ["SQLAlchemy (>=1.4.36)"]
-test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)"]
+test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)"]
 xml = ["lxml (>=4.8.0)"]
 
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-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -3945,7 +3644,6 @@ files = [
 name = "pansql"
 version = "0.0.1"
 description = "sqldf for pandas"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3960,21 +3658,19 @@ sqlalchemy = "*"
 
 [[package]]
 name = "parse"
-version = "1.19.1"
+version = "1.20.0"
 description = "parse() is the opposite of format()"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
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 version = "0.8.3"
 description = "A Python Parser"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -3990,7 +3686,6 @@ testing = ["docopt", "pytest (<6.0.0)"]
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 version = "0.11.2"
 description = "Utility library for gitignore style pattern matching of file paths."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4000,93 +3695,79 @@ files = [
 
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 python-versions = "*"
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 ]
 
 [package.extras]
@@ -4095,26 +3776,24 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
 
 [[package]]
 name = "pip"
-version = "23.2.1"
+version = "23.3.1"
 description = "The PyPA recommended tool for installing Python packages."
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
 name = "platformdirs"
-version = "3.11.0"
+version = "4.1.0"
 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"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -4125,7 +3804,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co
 name = "pluggy"
 version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4141,7 +3819,6 @@ testing = ["pytest", "pytest-benchmark"]
 name = "ply"
 version = "3.11"
 description = "Python Lex & Yacc"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -4153,7 +3830,6 @@ files = [
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 version = "0.1.12"
 description = "A python API for working with ID prefixes"
-category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
@@ -4169,37 +3845,35 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.1.6"
+version = "0.2.0"
 description = "A python library for retrieving semantic prefix maps"
-category = "main"
 optional = false
-python-versions = ">=3.8.0,<4.0.0"
+python-versions = ">=3.9,<4.0"
 files = [
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 ]
 
 [package.dependencies]
 click = ">=8.1.3"
 curies = ">=0.5.3"
-pydantic = ">=1.8.2,<2.0.0"
+pydantic = ">=2.5,<3.0"
 pyyaml = ">=5.3.1"
 tox = ">=4.11.3,<5.0.0"
 
 [package.extras]
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+docs = ["Sphinx[docs] (>=7.2.6,<8.0.0)", "myst-parser[docs] (>=2.0.0,<3.0.0)", "sphinx-autodoc-typehints[docs] (>=1.23.4,<2.0.0)", "sphinx-click[docs] (>=4.3.0,<5.0.0)", "sphinx-rtd-theme[docs] (>=1.0.0,<2.0.0)"]
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 [[package]]
 name = "prometheus-client"
-version = "0.17.1"
+version = "0.19.0"
 description = "Python client for the Prometheus monitoring system."
-category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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+    {file = "prometheus_client-0.19.0-py3-none-any.whl", hash = "sha256:c88b1e6ecf6b41cd8fb5731c7ae919bf66df6ec6fafa555cd6c0e16ca169ae92"},
+    {file = "prometheus_client-0.19.0.tar.gz", hash = "sha256:4585b0d1223148c27a225b10dbec5ae9bc4c81a99a3fa80774fa6209935324e1"},
 ]
 
 [package.extras]
@@ -4207,14 +3881,13 @@ twisted = ["twisted"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.39"
+version = "3.0.41"
 description = "Library for building powerful interactive command lines in Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7.0"
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+
+[package.dependencies]
+typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
 
 [[package]]
 name = "pygments"
-version = "2.16.1"
+version = "2.17.2"
 description = "Pygments is a syntax highlighting package written in Python."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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-    {file = "Pygments-2.16.1.tar.gz", hash = "sha256:1daff0494820c69bc8941e407aa20f577374ee88364ee10a98fdbe0aece96e29"},
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 ]
 
 [package.extras]
 plugins = ["importlib-metadata"]
+windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pyjsg"
 version = "0.11.10"
 description = "Python JSON Schema Grammar interpreter"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4390,18 +4142,17 @@ jsonasobj = ">=1.2.1"
 
 [[package]]
 name = "pymdown-extensions"
-version = "10.3"
+version = "10.5"
 description = "Extension pack for Python Markdown."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-markdown = ">=3.2"
+markdown = ">=3.5"
 pyyaml = "*"
 
 [package.extras]
@@ -4411,7 +4162,6 @@ extra = ["pygments (>=2.12)"]
 name = "pyparsing"
 version = "3.1.1"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-category = "main"
 optional = false
 python-versions = ">=3.6.8"
 files = [
@@ -4426,7 +4176,6 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "pyproject-api"
 version = "1.6.1"
 description = "API to interact with the python pyproject.toml based projects"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4446,7 +4195,6 @@ testing = ["covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytes
 name = "pyshex"
 version = "0.8.1"
 description = "Python ShEx Implementation"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -4469,7 +4217,6 @@ urllib3 = "*"
 name = "pyshexc"
 version = "0.9.1"
 description = "PyShExC - Python ShEx compiler"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4489,7 +4236,6 @@ shexjsg = ">=0.8.1"
 name = "pysolr"
 version = "3.9.0"
 description = "Lightweight Python client for Apache Solr"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4504,14 +4250,13 @@ solrcloud = ["kazoo (>=2.5.0)"]
 
 [[package]]
 name = "pystow"
-version = "0.5.0"
+version = "0.5.2"
 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]
@@ -4529,14 +4274,13 @@ xml = ["lxml"]
 
 [[package]]
 name = "pytest"
-version = "7.4.2"
+version = "7.4.3"
 description = "pytest: simple powerful testing with Python"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -4554,7 +4298,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no
 name = "pytest-logging"
 version = "2015.11.4"
 description = "Configures logging and allows tweaking the log level with a py.test flag"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4568,7 +4311,6 @@ pytest = ">=2.8.1"
 name = "python-dateutil"
 version = "2.8.2"
 description = "Extensions to the standard Python datetime module"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -4583,7 +4325,6 @@ six = ">=1.5"
 name = "python-json-logger"
 version = "2.0.7"
 description = "A python library adding a json log formatter"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -4595,7 +4336,6 @@ files = [
 name = "python-ulid"
 version = "2.2.0"
 description = "Universally unique lexicographically sortable identifier"
-category = "main"
 optional = true
 python-versions = ">=3.9"
 files = [
@@ -4607,7 +4347,6 @@ files = [
 name = "pytrie"
 version = "0.4.0"
 description = "A pure Python implementation of the trie data structure."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4621,7 +4360,6 @@ sortedcontainers = "*"
 name = "pytz"
 version = "2023.3.post1"
 description = "World timezone definitions, modern and historical"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4633,7 +4371,6 @@ files = [
 name = "pywin32"
 version = "306"
 description = "Python for Window Extensions"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -4657,7 +4394,6 @@ files = [
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 version = "2.0.12"
 description = "Pseudo terminal support for Windows from Python."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
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@@ -4673,7 +4409,6 @@ files = [
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 version = "6.0.1"
 description = "YAML parser and emitter for Python"
-category = "main"
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 python-versions = ">=3.6"
 files = [
@@ -4733,7 +4468,6 @@ files = [
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 version = "0.1"
 description = "A custom YAML tag for referencing environment variables in YAML files. "
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -4746,105 +4480,104 @@ pyyaml = "*"
 
 [[package]]
 name = "pyzmq"
-version = "25.1.1"
+version = "25.1.2"
 description = "Python bindings for 0MQ"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
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 ]
 
 [package.dependencies]
@@ -4852,19 +4585,17 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""}
 
 [[package]]
 name = "qtconsole"
-version = "5.4.4"
+version = "5.5.1"
 description = "Jupyter Qt console"
-category = "dev"
 optional = false
-python-versions = ">= 3.7"
+python-versions = ">= 3.8"
 files = [
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 [package.dependencies]
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-ipython-genutils = "*"
 jupyter-client = ">=4.1"
 jupyter-core = "*"
 packaging = "*"
@@ -4879,14 +4610,13 @@ test = ["flaky", "pytest", "pytest-qt"]
 
 [[package]]
 name = "qtpy"
-version = "2.4.0"
+version = "2.4.1"
 description = "Provides an abstraction layer on top of the various Qt bindings (PyQt5/6 and PySide2/6)."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -4899,7 +4629,6 @@ test = ["pytest (>=6,!=7.0.0,!=7.0.1)", "pytest-cov (>=3.0.0)", "pytest-qt"]
 name = "ratelimit"
 version = "2.2.1"
 description = "API rate limit decorator"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4910,7 +4639,6 @@ files = [
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-category = "main"
 optional = false
 python-versions = ">=3.8.1,<4.0.0"
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@@ -4932,7 +4660,6 @@ networkx = ["networkx (>=2.0.0,<3.0.0)"]
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 description = "rdflib extension adding JSON-LD parser and serializer"
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 optional = false
 python-versions = "*"
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 version = "1.0.3"
 description = "Shim for rdflib 5 and 6 incompatibilities"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4961,14 +4687,13 @@ rdflib-jsonld = "0.6.1"
 
 [[package]]
 name = "referencing"
-version = "0.30.2"
+version = "0.31.1"
 description = "JSON Referencing + Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -4979,7 +4704,6 @@ rpds-py = ">=0.7.0"
 name = "regex"
 version = "2023.10.3"
 description = "Alternative regular expression module, to replace re."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -5077,7 +4801,6 @@ files = [
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 version = "2.31.0"
 description = "Python HTTP for Humans."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -5097,14 +4820,13 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "requests-cache"
-version = "1.1.0"
+version = "1.1.1"
 description = "A persistent cache for python requests"
-category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
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 ]
 
 [package.dependencies]
@@ -5130,7 +4852,6 @@ yaml = ["pyyaml (>=5.4)"]
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 version = "1.0.0"
 description = "A utility belt for advanced users of python-requests"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -5145,7 +4866,6 @@ requests = ">=2.0.1,<3.0.0"
 name = "rfc3339-validator"
 version = "0.1.4"
 description = "A pure python RFC3339 validator"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -5160,7 +4880,6 @@ six = "*"
 name = "rfc3986-validator"
 version = "0.1.1"
 description = "Pure python rfc3986 validator"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -5172,7 +4891,6 @@ files = [
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 version = "1.3.8"
 description = "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -5182,173 +4900,184 @@ files = [
 
 [[package]]
 name = "rpds-py"
-version = "0.10.6"
+version = "0.13.2"
 description = "Python bindings to Rust's persistent data structures (rpds)"
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 python-versions = ">=3.8"
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 ]
 
 [[package]]
 name = "ruamel-yaml"
-version = "0.17.35"
+version = "0.18.5"
 description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
-category = "dev"
 optional = false
-python-versions = ">=3"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
 "ruamel.yaml.clib" = {version = ">=0.2.7", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.13\""}
 
 [package.extras]
-docs = ["ryd"]
+docs = ["mercurial (>5.7)", "ryd"]
 jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"]
 
 [[package]]
 name = "ruamel-yaml-clib"
 version = "0.2.8"
 description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml"
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@@ -5356,56 +5085,54 @@ files = [
 
 [[package]]
 name = "s3transfer"
-version = "0.7.0"
+version = "0.8.2"
 description = "An Amazon S3 Transfer Manager"
-category = "main"
 optional = true
 python-versions = ">= 3.7"
 files = [
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+    {file = "s3transfer-0.8.2.tar.gz", hash = "sha256:368ac6876a9e9ed91f6bc86581e319be08188dc60d50e0d56308ed5765446283"},
 ]
 
 [package.dependencies]
-botocore = ">=1.12.36,<2.0a.0"
+botocore = ">=1.33.2,<2.0a.0"
 
 [package.extras]
-crt = ["botocore[crt] (>=1.20.29,<2.0a.0)"]
+crt = ["botocore[crt] (>=1.33.2,<2.0a.0)"]
 
 [[package]]
 name = "scikit-learn"
-version = "1.3.1"
+version = "1.3.2"
 description = "A set of python modules for machine learning and data mining"
-category = "main"
 optional = true
 python-versions = ">=3.8"
 files = [
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 optional = false
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 [[package]]
 name = "semsql"
-version = "0.3.2"
+version = "0.3.3"
 description = ""
-category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -5547,7 +5274,6 @@ SQLAlchemy-Utils = ">=0.38.2,<0.39.0"
 name = "send2trash"
 version = "1.8.2"
 description = "Send file to trash natively under Mac OS X, Windows and Linux"
-category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 files = [
@@ -5562,49 +5288,24 @@ win32 = ["pywin32"]
 
 [[package]]
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 description = "Easily download, build, install, upgrade, and uninstall Python packages"
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 python-versions = ">=3.8"
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 ]
 
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-category = "dev"
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-
-[package.extras]
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-rich = ["rich"]
-test = ["build", "pytest", "rich", "wheel"]
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 description = "ShExJSG - Astract Syntax Tree for the ShEx 2.0 language"
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@@ -5619,7 +5320,6 @@ pyjsg = ">=0.11.10"
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 version = "1.3.0"
 description = "Sniff out which async library your code is running under"
-category = "dev"
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@@ -5643,7 +5342,6 @@ files = [
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 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
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+    {file = "SQLAlchemy-2.0.23.tar.gz", hash = "sha256:c1bda93cbbe4aa2aa0aa8655c5aeda505cd219ff3e8da91d1d329e143e4aff69"},
 ]
 
 [package.dependencies]
@@ -6007,6 +5688,7 @@ typing-extensions = ">=4.2.0"
 
 [package.extras]
 aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
+aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
 aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
 asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
@@ -6017,7 +5699,7 @@ mssql-pyodbc = ["pyodbc"]
 mypy = ["mypy (>=0.910)"]
 mysql = ["mysqlclient (>=1.4.0)"]
 mysql-connector = ["mysql-connector-python"]
-oracle = ["cx-oracle (>=7)"]
+oracle = ["cx-oracle (>=8)"]
 oracle-oracledb = ["oracledb (>=1.0.1)"]
 postgresql = ["psycopg2 (>=2.7)"]
 postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
@@ -6033,7 +5715,6 @@ sqlcipher = ["sqlcipher3-binary"]
 name = "sqlalchemy-utils"
 version = "0.38.3"
 description = "Various utility functions for SQLAlchemy."
-category = "main"
 optional = false
 python-versions = "~=3.6"
 files = [
@@ -6062,7 +5743,6 @@ url = ["furl (>=0.4.1)"]
 name = "sqlite-fts4"
 version = "1.0.3"
 description = "Python functions for working with SQLite FTS4 search"
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -6075,14 +5755,13 @@ test = ["pytest"]
 
 [[package]]
 name = "sqlite-migrate"
-version = "0.1a2"
+version = "0.1b0"
 description = "A simple database migration system for SQLite, based on sqlite-utils"
-category = "main"
 optional = true
 python-versions = "*"
 files = [
-    {file = "sqlite-migrate-0.1a2.tar.gz", hash = "sha256:c33b40a9edd35b4490e095f55cf59e03828d25c8b97377cd8a1f7b72694fc111"},
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+    {file = "sqlite-migrate-0.1b0.tar.gz", hash = "sha256:8d502b3ca4b9c45e56012bd35c03d23235f0823c976d4ce940cbb40e33087ded"},
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 ]
 
 [package.dependencies]
@@ -6093,14 +5772,13 @@ test = ["black", "mypy", "pytest", "ruff"]
 
 [[package]]
 name = "sqlite-utils"
-version = "3.35.1"
+version = "3.35.2"
 description = "CLI tool and Python library for manipulating SQLite databases"
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
-    {file = "sqlite-utils-3.35.1.tar.gz", hash = "sha256:e0f03e6976b05bdb7a5c56454971a0e980fc16dbfd3512bbd3bdcac4f0e4370e"},
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+    {file = "sqlite-utils-3.35.2.tar.gz", hash = "sha256:590b14ad277914cb3fc7d5e254764847facdaaa23c7bafd85ec93874f6f42143"},
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 ]
 
 [package.dependencies]
@@ -6122,7 +5800,6 @@ tui = ["trogon"]
 name = "sssom"
 version = "0.3.41"
 description = "Operations on SSSOM mapping tables"
-category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -6150,7 +5827,6 @@ validators = ">=0.20.0"
 name = "sssom-schema"
 version = "0.15.0"
 description = "SSSOM is a Simple Standard for Sharing Ontology Mappings."
-category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
@@ -6166,7 +5842,6 @@ mkdocs-mermaid2-plugin = ">=0.6.0,<0.7.0"
 name = "stack-data"
 version = "0.6.3"
 description = "Extract data from python stack frames and tracebacks for informative displays"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -6186,7 +5861,6 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 name = "tabulate"
 version = "0.9.0"
 description = "Pretty-print tabular data"
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -6199,14 +5873,13 @@ widechars = ["wcwidth"]
 
 [[package]]
 name = "terminado"
-version = "0.17.1"
+version = "0.18.0"
 description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
-category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -6217,12 +5890,12 @@ tornado = ">=6.1.0"
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
 test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"]
+typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"]
 
 [[package]]
 name = "threadpoolctl"
 version = "3.2.0"
 description = "threadpoolctl"
-category = "main"
 optional = true
 python-versions = ">=3.8"
 files = [
@@ -6234,7 +5907,6 @@ files = [
 name = "tinycss2"
 version = "1.2.1"
 description = "A tiny CSS parser"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -6253,7 +5925,6 @@ test = ["flake8", "isort", "pytest"]
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -6263,35 +5934,33 @@ files = [
 
 [[package]]
 name = "tornado"
-version = "6.3.3"
+version = "6.4"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
-category = "dev"
 optional = false
 python-versions = ">= 3.8"
 files = [
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+    {file = "tornado-6.4.tar.gz", hash = "sha256:72291fa6e6bc84e626589f1c29d90a5a6d593ef5ae68052ee2ef000dfd273dee"},
 ]
 
 [[package]]
 name = "tox"
-version = "4.11.3"
+version = "4.11.4"
 description = "tox is a generic virtualenv management and test command line tool"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tox-4.11.3-py3-none-any.whl", hash = "sha256:599af5e5bb0cad0148ac1558a0b66f8fff219ef88363483b8d92a81e4246f28f"},
-    {file = "tox-4.11.3.tar.gz", hash = "sha256:5039f68276461fae6a9452a3b2c7295798f00a0e92edcd9a3b78ba1a73577951"},
+    {file = "tox-4.11.4-py3-none-any.whl", hash = "sha256:2adb83d68f27116812b69aa36676a8d6a52249cb0d173649de0e7d0c2e3e7229"},
+    {file = "tox-4.11.4.tar.gz", hash = "sha256:73a7240778fabf305aeb05ab8ea26e575e042ab5a18d71d0ed13e343a51d6ce1"},
 ]
 
 [package.dependencies]
@@ -6314,7 +5983,6 @@ testing = ["build[virtualenv] (>=0.10)", "covdefaults (>=2.3)", "detect-test-pol
 name = "tqdm"
 version = "4.66.1"
 description = "Fast, Extensible Progress Meter"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -6333,25 +6001,23 @@ telegram = ["requests"]
 
 [[package]]
 name = "traitlets"
-version = "5.11.2"
+version = "5.14.0"
 description = "Traitlets Python configuration system"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
-test = ["argcomplete (>=3.0.3)", "mypy (>=1.5.1)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"]
+test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"]
 
 [[package]]
 name = "types-python-dateutil"
 version = "2.8.19.14"
 description = "Typing stubs for python-dateutil"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -6363,7 +6029,6 @@ files = [
 name = "typing-extensions"
 version = "4.8.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -6375,7 +6040,6 @@ files = [
 name = "tzdata"
 version = "2023.3"
 description = "Provider of IANA time zone data"
-category = "main"
 optional = false
 python-versions = ">=2"
 files = [
@@ -6387,7 +6051,6 @@ files = [
 name = "unidecode"
 version = "1.3.7"
 description = "ASCII transliterations of Unicode text"
-category = "main"
 optional = true
 python-versions = ">=3.5"
 files = [
@@ -6399,7 +6062,6 @@ files = [
 name = "uri-template"
 version = "1.3.0"
 description = "RFC 6570 URI Template Processor"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -6414,7 +6076,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 name = "url-normalize"
 version = "1.4.3"
 description = "URL normalization for Python"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
@@ -6427,14 +6088,13 @@ six = "*"
 
 [[package]]
 name = "urllib3"
-version = "1.26.17"
+version = "1.26.18"
 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.*"
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 [package.extras]
@@ -6446,7 +6106,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 name = "validators"
 version = "0.22.0"
 description = "Python Data Validation for Humans™"
-category = "main"
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 python-versions = ">=3.8"
 files = [
@@ -6467,20 +6126,19 @@ tooling-extras = ["pyaml (>=23.7.0)", "pypandoc-binary (>=1.11)", "pytest (>=7.4
 
 [[package]]
 name = "virtualenv"
-version = "20.24.5"
+version = "20.25.0"
 description = "Virtual Python Environment builder"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
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 filelock = ">=3.12.2,<4"
-platformdirs = ">=3.9.1,<4"
+platformdirs = ">=3.9.1,<5"
 
 [package.extras]
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@@ -6490,7 +6148,6 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
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 version = "0.1.3"
 description = "A tiny pythonic visitor implementation."
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -6501,7 +6158,6 @@ files = [
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 version = "3.0.0"
 description = "Filesystem events monitoring"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -6539,21 +6195,19 @@ watchmedo = ["PyYAML (>=3.10)"]
 
 [[package]]
 name = "wcwidth"
-version = "0.2.8"
+version = "0.2.12"
 description = "Measures the displayed width of unicode strings in a terminal"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
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 python-versions = ">=3.7"
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@@ -6569,7 +6223,6 @@ tests = ["pytest", "pytest-cov"]
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 description = "Character encoding aliases for legacy web content"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -6579,14 +6232,13 @@ files = [
 
 [[package]]
 name = "websocket-client"
-version = "1.6.4"
+version = "1.7.0"
 description = "WebSocket client for Python with low level API options"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
@@ -6598,7 +6250,6 @@ test = ["websockets"]
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-category = "main"
 optional = true
 python-versions = ">=3.7"
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@@ -6613,7 +6264,6 @@ watchdog = ["watchdog"]
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 description = "Jupyter interactive widgets for Jupyter Notebook"
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 optional = false
 python-versions = ">=3.7"
 files = [
@@ -6623,99 +6273,92 @@ files = [
 
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-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
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 [[package]]
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 optional = true
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 [package.dependencies]
@@ -6726,86 +6369,101 @@ email = ["email-validator"]
 
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+    {file = "yarl-1.9.3-py3-none-any.whl", hash = "sha256:271d63396460b6607b588555ea27a1a02b717ca2e3f2cf53bdde4013d7790929"},
+    {file = "yarl-1.9.3.tar.gz", hash = "sha256:4a14907b597ec55740f63e52d7fee0e9ee09d5b9d57a4f399a7423268e457b57"},
 ]
 
 [package.dependencies]
@@ -6816,7 +6474,6 @@ multidict = ">=4.0"
 name = "zipp"
 version = "3.17.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -6837,4 +6494,4 @@ seaborn = []
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<4.0.0"
-content-hash = "a8be432057df96aaab2e846a99a302d4ad4e14f907685d7390a68862cdebcc7d"
+content-hash = "23021dac286f286371309df5c6cdb17003bc77ff95187d25f9dbcb038801b0f9"
diff --git a/pyproject.toml b/pyproject.toml
index 3ad489866..a82a0ac4d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,13 +15,11 @@ SQLAlchemy = ">=1.4.32"
 linkml-runtime = ">=1.5.3"
 linkml-renderer = ">=0.3.0"
 networkx = ">=2.7.1"
-sssom-schema = ">=0.11.0"
-sssom = ">=0.3.38"
+sssom = "<0.4.0"
 ratelimit = ">=2.2.1"
 appdirs = ">=1.4.4"
 semsql = ">=0.3.1"
-lark = ">=1.1.2"
-kgcl-schema = "0.6.0"
+kgcl-schema = ">=0.6.0"
 funowl = ">=0.2.0"
 gilda = {version = ">=1.0.0", optional = true}
 kgcl-rdflib = "0.5.0"
@@ -37,7 +35,7 @@ pysolr = "^3.9.0"
 eutils = ">=0.6.0"
 requests-cache = "^1.0.1"
 click = "*"
-semsimian = "0.2.1"
+semsimian = "^0.2.1"
 urllib3 = {version = "< 2", optional = true}
 pydantic = "*"
 
diff --git a/tox.ini b/tox.ini
index 0af606fe0..aac36e7b5 100644
--- a/tox.ini
+++ b/tox.ini
@@ -26,6 +26,7 @@ deps =
     coverage
     semsimian
     gilda
+    linkml
 
 [testenv:lint]
 deps =