diff --git a/constraints.txt b/constraints.txt
index 2e62598c..a69446e3 100644
--- a/constraints.txt
+++ b/constraints.txt
@@ -18,21 +18,21 @@ beautifulsoup4==4.12.3
 bidict==0.23.1
 bleach==6.1.0
 bmt==1.4.4
-cachetools==5.4.0
-cattrs==23.2.3
-certifi==2024.7.4
-cffi==1.17.0
+cachetools==5.5.0
+cattrs==24.1.1
+certifi==2024.8.30
+cffi==1.17.1
 CFGraph==0.2.1
 chardet==5.2.0
 charset-normalizer==3.3.2
-class_resolver==0.4.3
+class_resolver==0.5.0
 click==8.1.7
 click-default-group==1.2.4
 colorama==0.4.6
 comm==0.2.2
 commonmark==0.9.1
-contourpy==1.2.1
-cryptography==43.0.0
+contourpy==1.3.0
+cryptography==43.0.1
 curies==0.7.10
 cycler==0.12.1
 dacite==1.8.1
@@ -55,44 +55,44 @@ EditorConfig==0.12.4
 et-xmlfile==1.1.0
 eutils==0.6.0
 exceptiongroup==1.2.2
-executing==2.0.1
+executing==2.1.0
 fastjsonschema==2.20.0
 fastobo==0.12.3
-filelock==3.15.4
+filelock==3.16.0
 fonttools==4.53.1
 fqdn==1.5.1
 funowl==0.2.3
 ghp-import==2.1.0
 google==3.0.0
-google-api-core==2.19.1
-google-api-python-client==2.140.0
-google-auth==2.33.0
+google-api-core==2.19.2
+google-api-python-client==2.145.0
+google-auth==2.34.0
 google-auth-httplib2==0.2.0
 google-auth-oauthlib==1.2.1
-googleapis-common-protos==1.63.2
+googleapis-common-protos==1.65.0
 graphviz==0.20.3
-greenlet==3.0.3
+greenlet==3.1.0
 gspread==6.1.2
 gspread-formatting==1.2.0
 h11==0.14.0
 hbreader==0.9.1
 httpcore==1.0.5
 httplib2==0.22.0
-httpx==0.27.0
-idna==3.7
+httpx==0.27.2
+idna==3.10
 ijson==3.3.0
 imagesize==1.4.1
-importlib_metadata==8.2.0
-importlib_resources==6.4.0
+importlib_metadata==8.5.0
+importlib_resources==6.4.5
 inflection==0.5.1
 iniconfig==2.0.0
 ipykernel==6.29.5
-ipython==8.26.0
-ipywidgets==8.1.3
+ipython==8.27.0
+ipywidgets==8.1.5
 isodate==0.6.1
 isoduration==20.11.0
 jaraco.classes==3.4.0
-jaraco.context==5.3.0
+jaraco.context==6.0.1
 jaraco.functools==4.0.2
 jedi==0.19.1
 jeepney==0.8.0
@@ -110,13 +110,13 @@ jsonlines==4.0.0
 jsonpatch==1.33
 jsonpath-ng==1.6.1
 jsonpath-rw==1.4.0
-jsonpickle==3.2.2
+jsonpickle==3.3.0
 jsonpointer==3.0.0
 jsonschema==4.23.0
 jsonschema-specifications==2023.12.1
 jsonschema2md==1.3.0
 jsonstreams==0.6.0
-jupyter==1.0.0
+jupyter==1.1.1
 jupyter-console==6.6.3
 jupyter-events==0.10.0
 jupyter-lsp==2.2.5
@@ -124,67 +124,67 @@ jupyter_client==8.6.2
 jupyter_core==5.7.2
 jupyter_server==2.14.2
 jupyter_server_terminals==0.5.3
-jupyterlab==4.2.4
+jupyterlab==4.2.5
 jupyterlab_pygments==0.3.0
 jupyterlab_server==2.27.3
-jupyterlab_widgets==3.0.11
+jupyterlab_widgets==3.0.13
 keyring==25.3.0
 kgcl-rdflib==0.5.0
-kgcl_schema==0.6.8
+kgcl_schema==0.6.9
 kgx==2.4.2
-kiwisolver==1.4.5
-lark==1.1.9
+kiwisolver==1.4.7
+lark==1.2.2
 lightrdf==0.4.0
-linkml==1.8.2
+linkml==1.8.3
 linkml-dataops==0.1.0
 linkml-renderer==0.3.1
-linkml-runtime==1.8.1
+linkml-runtime==1.8.2
 llm==0.13.1
 lxml==5.3.0
-Markdown==3.6
+Markdown==3.7
 markdown-it-py==3.0.0
 MarkupSafe==2.1.5
-marshmallow==3.21.3
-matplotlib==3.9.1.post1
+marshmallow==3.22.0
+matplotlib==3.9.2
 matplotlib-inline==0.1.7
 matplotlib-venn==1.1.1
 mdurl==0.1.2
 mergedeep==1.3.4
 mistune==3.0.2
-mkdocs==1.6.0
+mkdocs==1.6.1
 mkdocs-get-deps==0.2.0
-mkdocs-material==9.5.31
+mkdocs-material==9.5.34
 mkdocs-material-extensions==1.3.1
 mkdocs-mermaid2-plugin==1.1.1
-mkdocs-table-reader-plugin==2.2.2
+mkdocs-table-reader-plugin==3.1.0
 more-click==0.1.2
-more-itertools==10.4.0
-mypy==1.11.1
+more-itertools==10.5.0
+mypy==1.11.2
 mypy-extensions==1.0.0
 nbclient==0.10.0
 nbconvert==7.16.4
 nbformat==5.10.4
 ndex2==3.9.0
-neo4j==5.23.1
+neo4j==5.24.0
 nest-asyncio==1.6.0
 networkx==3.3
 nh3==0.2.18
-notebook==7.2.1
+notebook==7.2.2
 notebook_shim==0.2.4
 numpy==1.26.4
-oaklib==0.6.14
+oaklib==0.6.16
 oauthlib==3.2.2
 ols-client==0.1.4
-ontobio==2.9.3
+ontobio==2.9.10
 ontodev-cogs==0.3.3
 ontodev-gizmos==0.3.2
 ontoportal-client==0.0.4
-openai==1.40.3
+openai==1.45.0
 openpyxl==3.1.5
 ordered-set==4.1.0
 overrides==7.7.0
 packaging==24.1
-paginate==0.5.6
+paginate==0.5.7
 pandas==2.2.2
 pandocfilters==1.5.1
 pansql==0.0.1
@@ -194,8 +194,8 @@ pathspec==0.12.1
 pexpect==4.9.0
 pillow==10.4.0
 pkginfo==1.10.0
-platformdirs==4.2.2
-plotly==5.23.0
+platformdirs==4.3.3
+plotly==5.24.1
 pluggy==1.5.0
 ply==3.11
 prefixcommons==0.1.12
@@ -203,20 +203,20 @@ prefixmaps==0.2.5
 prologterms==0.0.6
 prometheus_client==0.20.0
 prompt_toolkit==3.0.47
-pronto==2.5.7
+pronto==2.5.8
 proto-plus==1.24.0
-protobuf==5.27.3
+protobuf==5.28.1
 psutil==6.0.0
 ptyprocess==0.7.0
 pure_eval==0.2.3
 pyarrow==15.0.2
-pyasn1==0.6.0
-pyasn1_modules==0.4.0
+pyasn1==0.6.1
+pyasn1_modules==0.4.1
 pycparser==2.22
-pydantic==2.8.2
-pydantic_core==2.20.1
+pydantic==2.9.1
+pydantic_core==2.23.3
 pydotplus==2.0.2
-PyGithub==2.3.0
+PyGithub==2.4.0
 Pygments==2.18.0
 PyJSG==0.11.10
 PyJWT==2.9.0
@@ -228,20 +228,18 @@ PyShEx==0.8.1
 PyShExC==0.9.1
 pysolr==3.9.0
 pyspellchecker==0.8.1
-pystow==0.5.4
-pytest==8.3.2
+pystow==0.5.5
+pytest==8.3.3
 pytest-logging==2015.11.4
 python-dateutil==2.9.0.post0
 python-dotenv==1.0.1
 python-json-logger==2.0.7
 python-ulid==2.7.0
 PyTrie==0.4.0
-pytz==2024.1
+pytz==2024.2
 PyYAML==6.0.2
 pyyaml_env_tag==0.1
-pyzmq==26.1.0
-qtconsole==5.5.2
-QtPy==2.4.1
+pyzmq==26.2.0
 ratelimit==2.2.1
 rdflib==7.0.0
 rdflib-jsonld==0.6.1
@@ -249,7 +247,7 @@ rdflib-shim==1.0.3
 readme_renderer==44.0
 recommonmark==0.7.1
 referencing==0.35.1
-regex==2024.7.24
+regex==2024.9.11
 requests==2.32.3
 requests-cache==1.2.1
 requests-oauthlib==2.0.0
@@ -258,15 +256,15 @@ rfc3339-validator==0.1.4
 rfc3986==2.0.0
 rfc3986-validator==0.1.1
 rfc3987==1.3.8
-rich==13.7.1
+rich==13.8.1
 rpds-py==0.20.0
 rsa==4.9
 ruamel.yaml==0.18.6
 ruamel.yaml.clib==0.2.8
-scipy==1.14.0
+scipy==1.14.1
 seaborn==0.13.2
 SecretStorage==3.3.3
-semsimian==0.2.18
+semsimian==0.2.19
 semsql==0.3.3
 Send2Trash==1.8.3
 ShExJSG==0.8.2
@@ -274,7 +272,7 @@ six==1.16.0
 sniffio==1.3.1
 snowballstemmer==2.2.0
 sortedcontainers==2.4.0
-soupsieve==2.5
+soupsieve==2.6
 sparqlslurper==0.5.1
 SPARQLWrapper==2.0.0
 Sphinx==8.0.2
@@ -284,7 +282,7 @@ sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
-SQLAlchemy==2.0.32
+SQLAlchemy==2.0.34
 SQLAlchemy-Utils==0.38.3
 sqlite-fts4==1.0.3
 sqlite-migrate==0.1b0
@@ -301,12 +299,12 @@ terminaltables==3.1.10
 tinycss2==1.3.0
 tomli==2.0.1
 tornado==6.4.1
-tox==4.17.1
+tox==4.18.1
 tqdm==4.66.5
 traitlets==5.14.3
 tsvalid==0.0.3
 twine==5.1.1
-types-python-dateutil==2.9.0.20240316
+types-python-dateutil==2.9.0.20240906
 typing-inspect==0.9.0
 typing_extensions==4.12.2
 tzdata==2024.1
@@ -314,16 +312,16 @@ UpSetPlot==0.9.0
 uri-template==1.3.0
 uritemplate==4.1.1
 url-normalize==1.4.3
-urllib3==2.2.2
+urllib3==2.2.3
 validators==0.20.0
-virtualenv==20.26.3
-watchdog==4.0.2
+virtualenv==20.26.4
+watchdog==5.0.2
 wcwidth==0.2.13
 webcolors==24.8.0
 webencodings==0.5.1
 websocket-client==1.8.0
-widgetsnbextension==4.0.11
+widgetsnbextension==4.0.13
 wrapt==1.16.0
 xmltodict==0.13.0
 yamldown==0.1.8
-zipp==3.19.2
+zipp==3.20.2