diff --git a/constraints.txt b/constraints.txt
index 580c9ee3..189a6209 100644
--- a/constraints.txt
+++ b/constraints.txt
@@ -7,32 +7,30 @@ appdirs==1.4.4
 argon2-cffi==23.1.0
 argon2-cffi-bindings==21.2.0
 arrow==1.3.0
-asttokens==2.4.0
+asttokens==2.4.1
 async-lru==2.0.4
 attrs==23.1.0
-Babel==2.13.0
-backcall==0.2.0
+Babel==2.13.1
 bcp47==0.0.4
 beautifulsoup4==4.12.2
 bidict==0.22.1
-black==21.12b0
 bleach==6.1.0
 bmt==1.1.2
-cachetools==5.3.1
+cachetools==5.3.2
 cattrs==23.1.2
 certifi==2023.7.22
 cffi==1.16.0
 CFGraph==0.2.1
 chardet==5.2.0
-charset-normalizer==3.3.0
+charset-normalizer==3.3.2
 class-resolver==0.4.2
 click==8.1.7
 colorama==0.4.6
-comm==0.1.4
+comm==0.2.0
 commonmark==0.9.1
-contourpy==1.1.1
-cryptography==41.0.4
-curies==0.6.6
+contourpy==1.2.0
+cryptography==41.0.5
+curies==0.6.7
 cycler==0.12.1
 dacite==1.8.1
 daff==1.3.46
@@ -47,31 +45,30 @@ deprecation==2.1.0
 diskcache==5.6.3
 distlib==0.3.7
 docker==6.1.3
-docutils==0.16
+docutils==0.18.1
 dosdp==0.1.10.dev1
 EditorConfig==0.12.3
 et-xmlfile==1.1.0
 eutils==0.6.0
 exceptiongroup==1.1.3
-executing==2.0.0
+executing==2.0.1
 fastjsonschema==2.18.1
 fastobo==0.12.2
-filelock==3.12.4
-flake8==6.1.0
-fonttools==4.43.1
+filelock==3.13.1
+fonttools==4.44.0
 fqdn==1.5.1
 funowl==0.2.3
 ghp-import==2.1.0
 google==3.0.0
 google-api-core==2.12.0
-google-api-python-client==2.103.0
-google-auth==2.23.3
+google-api-python-client==2.106.0
+google-auth==2.23.4
 google-auth-httplib2==0.1.1
 google-auth-oauthlib==1.1.0
 googleapis-common-protos==1.61.0
 graphviz==0.20.1
 greenlet==2.0.1
-gspread==5.11.3
+gspread==5.12.0
 gspread-formatting==1.1.2
 hbreader==0.9.1
 httplib2==0.22.0
@@ -79,10 +76,10 @@ idna==3.4
 ijson==3.2.3
 imagesize==1.4.1
 importlib-metadata==6.8.0
+inflection==0.5.1
 iniconfig==2.0.0
-ipykernel==6.25.2
-ipython==8.16.1
-ipython-genutils==0.2.0
+ipykernel==6.26.0
+ipython==8.17.2
 ipywidgets==8.1.1
 isodate==0.6.1
 isoduration==20.11.0
@@ -97,75 +94,74 @@ json-flattener==0.1.9
 json5==0.9.14
 jsonasobj==1.3.1
 jsonasobj2==1.0.4
-jsonlines==4.0.0
+jsonlines==3.1.0
 jsonpatch==1.33
 jsonpath-ng==1.6.0
 jsonpath-rw==1.4.0
 jsonpickle==3.0.2
 jsonpointer==2.4
-jsonschema==4.19.1
+jsonschema==4.19.2
 jsonschema-specifications==2023.7.1
 jsonschema2md==1.0.0
 jsonstreams==0.6.0
 jupyter==1.0.0
 jupyter-console==6.6.3
-jupyter-events==0.8.0
+jupyter-events==0.9.0
 jupyter-lsp==2.2.0
-jupyter_client==8.4.0
-jupyter_core==5.4.0
-jupyter_server==2.8.0
+jupyter_client==8.6.0
+jupyter_core==5.5.0
+jupyter_server==2.9.1
 jupyter_server_terminals==0.4.4
-jupyterlab==4.0.7
+jupyterlab==4.0.8
 jupyterlab-pygments==0.2.2
 jupyterlab-widgets==3.0.9
 jupyterlab_server==2.25.0
 keyring==24.2.0
 kgcl-rdflib==0.5.0
 kgcl-schema==0.6.0
-kgx==1.7.2
+kgx==2.2.3
 kiwisolver==1.4.5
-lark==1.1.7
+lark==1.1.8
 lightrdf==0.4.0
-linkml==1.6.1
+linkml==1.6.2
 linkml-dataops==0.1.0
 linkml-renderer==0.3.0
 linkml-runtime==1.6.0
 lxml==4.9.3
-Markdown==3.5
+Markdown==3.5.1
 markdown-it-py==3.0.0
 MarkupSafe==2.1.3
 marshmallow==3.20.1
-matplotlib==3.8.0
+matplotlib==3.8.1
 matplotlib-inline==0.1.6
 matplotlib-venn==0.11.9
-mccabe==0.7.0
 mdurl==0.1.2
 mergedeep==1.3.4
 mistune==3.0.2
 mkdocs==1.5.3
-mkdocs-material==9.4.6
-mkdocs-material-extensions==1.2
+mkdocs-material==9.4.8
+mkdocs-material-extensions==1.3
 mkdocs-mermaid2-plugin==0.6.0
 mkdocs-table-reader-plugin==2.0.3
 more-click==0.1.2
 more-itertools==10.1.0
-mypy==1.6.0
+mypy==1.6.1
 mypy-extensions==1.0.0
 nbclient==0.8.0
-nbconvert==7.9.2
+nbconvert==7.11.0
 nbformat==5.9.2
 ndex2==3.5.1
-neo4j==4.3.0
+neo4j==4.4.11
 nest-asyncio==1.5.8
-networkx==3.1
+networkx==3.2.1
 nh3==0.2.14
-notebook==7.0.5
+notebook==7.0.6
 notebook_shim==0.2.3
 numpy==1.26.1
-oaklib==0.5.20
+oaklib==0.5.21
 oauthlib==3.2.2
 ols-client==0.1.4
-ontobio==2.8.16
+ontobio==2.8.17
 ontodev-cogs==0.3.3
 ontodev-gizmos==0.3.2
 ontoportal-client==0.0.4
@@ -174,44 +170,41 @@ ordered-set==4.1.0
 overrides==7.4.0
 packaging==23.2
 paginate==0.5.6
-pandas==2.1.1
+pandas==2.1.2
 pandocfilters==1.5.0
 pansql==0.0.1
 parse==1.19.1
 parso==0.8.3
 pathspec==0.11.2
 pexpect==4.8.0
-pickleshare==0.7.5
 Pillow==10.1.0
 pkginfo==1.9.6
 platformdirs==3.11.0
-plotly==5.17.0
+plotly==5.18.0
 pluggy==1.3.0
 ply==3.11
 prefixcommons==0.1.12
 prefixmaps==0.1.5
 prologterms==0.0.6
-prometheus-client==0.17.1
+prometheus-client==0.18.0
 prompt-toolkit==3.0.39
 pronto==2.5.5
-protobuf==4.24.4
+protobuf==4.25.0
 psutil==5.9.6
 ptyprocess==0.7.0
 pure-eval==0.2.2
 py==1.11.0
 pyasn1==0.5.0
 pyasn1-modules==0.3.0
-pycodestyle==2.11.1
 pycparser==2.21
 pydantic==2.4.2
 pydantic_core==2.10.1
 pydotplus==2.0.2
-pyflakes==3.1.0
 PyGithub==2.1.1
 Pygments==2.16.1
 PyJSG==0.11.10
 PyJWT==2.8.0
-pymdown-extensions==10.3
+pymdown-extensions==10.3.1
 PyNaCl==1.5.0
 pyparsing==2.4.7
 PyShEx==0.8.1
@@ -219,7 +212,7 @@ PyShExC==0.9.1
 pysolr==3.9.0
 pyspellchecker==0.7.2
 pystow==0.5.0
-pytest==7.4.2
+pytest==7.4.3
 pytest-logging==2015.11.4
 python-dateutil==2.8.2
 python-json-logger==2.0.7
@@ -228,8 +221,8 @@ pytz==2023.3.post1
 PyYAML==6.0.1
 pyyaml_env_tag==0.1
 pyzmq==25.1.1
-qtconsole==5.4.4
-QtPy==2.4.0
+qtconsole==5.5.0
+QtPy==2.4.1
 ratelimit==2.2.1
 rdflib==7.0.0
 rdflib-jsonld==0.6.1
@@ -247,9 +240,9 @@ rfc3986==2.0.0
 rfc3986-validator==0.1.1
 rfc3987==1.3.8
 rich==13.6.0
-rpds-py==0.10.6
+rpds-py==0.12.0
 rsa==4.9
-ruamel.yaml==0.17.35
+ruamel.yaml==0.18.5
 ruamel.yaml.clib==0.2.8
 scipy==1.11.3
 seaborn==0.13.0
@@ -265,17 +258,14 @@ sortedcontainers==2.4.0
 soupsieve==2.5
 sparqlslurper==0.5.1
 SPARQLWrapper==2.0.0
-Sphinx==5.3.0
-sphinx-click==5.0.1
-sphinx-rtd-theme==1.3.0
+Sphinx==7.2.6
 sphinxcontrib-applehelp==1.0.7
 sphinxcontrib-devhelp==1.0.5
 sphinxcontrib-htmlhelp==2.0.4
-sphinxcontrib-jquery==4.1
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.6
 sphinxcontrib-serializinghtml==1.1.9
-SQLAlchemy==2.0.22
+SQLAlchemy==2.0.23
 SQLAlchemy-Utils==0.38.3
 sssom==0.3.41
 sssom-schema==0.15.0
@@ -287,13 +277,11 @@ termcolor==2.3.0
 terminado==0.17.1
 terminaltables==3.1.10
 tinycss2==1.2.1
-toml==0.10.2
-tomli==1.2.3
+tomli==2.0.1
 tornado==6.3.3
-tox==3.25.1
-tox-docker==4.1.0
+tox==3.28.0
 tqdm==4.66.1
-traitlets==5.11.2
+traitlets==5.13.0
 tsvalid==0.0.3
 twine==4.0.2
 types-python-dateutil==2.8.19.14
@@ -304,11 +292,11 @@ UpSetPlot==0.8.0
 uri-template==1.3.0
 uritemplate==4.1.1
 url-normalize==1.4.3
-urllib3==2.0.6
-validators==0.22.0
-virtualenv==20.24.5
+urllib3==2.0.7
+validators==0.20.0
+virtualenv==20.24.6
 watchdog==3.0.0
-wcwidth==0.2.8
+wcwidth==0.2.9
 webcolors==1.13
 webencodings==0.5.1
 websocket-client==1.6.4