diff --git a/CHANGELOG.md b/CHANGELOG.md
index 48bef4fc..61235622 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@
 - KGCL plugin for ROBOT updated to version 0.4.0
 - SSSOM command-line tool and plugin for ROBOT updated to version 0.7.7
 - Several Python packages updated, including:
-    - `oaklib` (OAK) 0.6.5
+    - `oaklib` (OAK) 0.6.6
     - `sssom` 0.4.8 and `sssom-schema` 0.15.2
 - Bufgixes:
     - Added back `class-count-by-prefix.sparql` ([https://github.com/INCATools/ontology-development-kit/issues/1030](#1030))
diff --git a/constraints.txt b/constraints.txt
index c3a91fee..c2e725ef 100644
--- a/constraints.txt
+++ b/constraints.txt
@@ -1,8 +1,8 @@
 airium==0.2.6
 alabaster==0.7.16
-annotated-types==0.6.0
+annotated-types==0.7.0
 antlr4-python3-runtime==4.9.3
-anyio==4.3.0
+anyio==4.4.0
 appdirs==1.4.4
 argon2-cffi==23.1.0
 argon2-cffi-bindings==21.2.0
@@ -10,14 +10,14 @@ arrow==1.3.0
 asttokens==2.4.1
 async-lru==2.0.4
 attrs==23.2.0
-Babel==2.14.0
+Babel==2.15.0
 babelon==0.2.9
 backports.tarfile==1.1.1
-bcp47==0.0.4
+bcp47==0.1.0
 beautifulsoup4==4.12.3
 bidict==0.23.1
 bleach==6.1.0
-bmt==1.4.0
+bmt==1.4.1
 cachetools==5.3.3
 cattrs==23.2.3
 certifi==2024.2.2
@@ -32,13 +32,13 @@ colorama==0.4.6
 comm==0.2.2
 commonmark==0.9.1
 contourpy==1.2.1
-cryptography==42.0.5
+cryptography==42.0.7
 curies==0.7.9
 cycler==0.12.1
 dacite==1.8.1
 daff==1.3.46
 dataclasses==0.6
-dataclasses-json==0.6.5
+dataclasses-json==0.6.6
 dataclasses-jsonschema==2.16.0
 debugpy==1.8.1
 decorator==5.1.1
@@ -59,20 +59,20 @@ executing==2.0.1
 fastjsonschema==2.19.1
 fastobo==0.12.3
 filelock==3.14.0
-fonttools==4.51.0
+fonttools==4.52.1
 fqdn==1.5.1
 funowl==0.2.3
 ghp-import==2.1.0
 google==3.0.0
-google-api-core==2.18.0
-google-api-python-client==2.127.0
+google-api-core==2.19.0
+google-api-python-client==2.130.0
 google-auth==2.29.0
 google-auth-httplib2==0.2.0
 google-auth-oauthlib==1.2.0
 googleapis-common-protos==1.63.0
 graphviz==0.20.3
 greenlet==3.0.3
-gspread==6.1.0
+gspread==6.1.2
 gspread-formatting==1.1.2
 h11==0.14.0
 hbreader==0.9.1
@@ -97,7 +97,7 @@ jaraco.context==5.3.0
 jaraco.functools==4.0.1
 jedi==0.19.1
 jeepney==0.8.0
-Jinja2==3.1.3
+Jinja2==3.1.4
 jsbeautifier==1.15.1
 jsobject==0.10.2
 json-flattener==0.1.9
@@ -110,7 +110,7 @@ jsonpath-ng==1.6.1
 jsonpath-rw==1.4.0
 jsonpickle==3.0.4
 jsonpointer==2.4
-jsonschema==4.21.1
+jsonschema==4.22.0
 jsonschema-specifications==2023.12.1
 jsonschema2md==1.1.0
 jsonstreams==0.6.0
@@ -118,32 +118,32 @@ jupyter==1.0.0
 jupyter-console==6.6.3
 jupyter-events==0.10.0
 jupyter-lsp==2.2.5
-jupyter_client==8.6.1
+jupyter_client==8.6.2
 jupyter_core==5.7.2
 jupyter_server==2.14.0
 jupyter_server_terminals==0.5.3
-jupyterlab==4.1.8
+jupyterlab==4.2.1
 jupyterlab_pygments==0.3.0
-jupyterlab_server==2.27.1
+jupyterlab_server==2.27.2
 jupyterlab_widgets==3.0.10
-keyring==25.2.0
+keyring==25.2.1
 kgcl-rdflib==0.5.0
 kgcl_schema==0.6.8
 kgx==2.4.0
 kiwisolver==1.4.5
 lark==1.1.9
 lightrdf==0.4.0
-linkml==1.7.8
+linkml==1.7.10
 linkml-dataops==0.1.0
 linkml-renderer==0.3.0
 linkml-runtime==1.7.5
 llm==0.13.1
-lxml==5.2.1
+lxml==5.2.2
 Markdown==3.6
 markdown-it-py==3.0.0
 MarkupSafe==2.1.5
-marshmallow==3.21.1
-matplotlib==3.8.4
+marshmallow==3.21.2
+matplotlib==3.9.0
 matplotlib-inline==0.1.7
 matplotlib-venn==0.11.10
 mdurl==0.1.2
@@ -151,10 +151,10 @@ mergedeep==1.3.4
 mistune==3.0.2
 mkdocs==1.6.0
 mkdocs-get-deps==0.2.0
-mkdocs-material==9.5.20
+mkdocs-material==9.5.25
 mkdocs-material-extensions==1.3.1
 mkdocs-mermaid2-plugin==1.1.1
-mkdocs-table-reader-plugin==2.1.0
+mkdocs-table-reader-plugin==2.2.2
 more-click==0.1.2
 more-itertools==10.2.0
 mypy==1.10.0
@@ -167,17 +167,17 @@ neo4j==4.4.12
 nest-asyncio==1.6.0
 networkx==3.3
 nh3==0.2.17
-notebook==7.1.3
+notebook==7.2.0
 notebook_shim==0.2.4
 numpy==1.26.4
-oaklib==0.6.5
+oaklib==0.6.6
 oauthlib==3.2.2
 ols-client==0.1.4
-ontobio==2.8.24
+ontobio==2.9.0
 ontodev-cogs==0.3.3
 ontodev-gizmos==0.3.2
 ontoportal-client==0.0.4
-openai==1.23.6
+openai==1.30.3
 openpyxl==3.1.2
 ordered-set==4.1.0
 overrides==7.7.0
@@ -192,8 +192,8 @@ pathspec==0.12.1
 pexpect==4.9.0
 pillow==10.3.0
 pkginfo==1.10.0
-platformdirs==4.2.1
-plotly==5.21.0
+platformdirs==4.2.2
+plotly==5.22.0
 pluggy==1.5.0
 ply==3.11
 prefixcommons==0.1.12
@@ -215,7 +215,7 @@ pydantic==2.7.1
 pydantic_core==2.18.2
 pydotplus==2.0.2
 PyGithub==2.3.0
-Pygments==2.17.2
+Pygments==2.18.0
 PyJSG==0.11.10
 PyJWT==2.8.0
 pymdown-extensions==10.8.1
@@ -227,18 +227,18 @@ PyShExC==0.9.1
 pysolr==3.9.0
 pyspellchecker==0.8.1
 pystow==0.5.4
-pytest==8.2.0
+pytest==8.2.1
 pytest-logging==2015.11.4
 python-dateutil==2.9.0.post0
 python-dotenv==1.0.1
 python-json-logger==2.0.7
-python-ulid==2.5.0
+python-ulid==2.6.0
 PyTrie==0.4.0
 pytz==2024.1
 PyYAML==6.0.1
 pyyaml_env_tag==0.1
-pyzmq==26.0.2
-qtconsole==5.5.1
+pyzmq==26.0.3
+qtconsole==5.5.2
 QtPy==2.4.1
 ratelimit==2.2.1
 rdflib==7.0.0
@@ -246,9 +246,9 @@ rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
 readme_renderer==43.0
 recommonmark==0.7.1
-referencing==0.35.0
-regex==2024.4.28
-requests==2.31.0
+referencing==0.35.1
+regex==2024.5.15
+requests==2.32.2
 requests-cache==1.2.0
 requests-oauthlib==2.0.0
 requests-toolbelt==1.0.0
@@ -257,14 +257,14 @@ rfc3986==2.0.0
 rfc3986-validator==0.1.1
 rfc3987==1.3.8
 rich==13.7.1
-rpds-py==0.18.0
+rpds-py==0.18.1
 rsa==4.9
 ruamel.yaml==0.18.6
 ruamel.yaml.clib==0.2.8
-scipy==1.13.0
+scipy==1.13.1
 seaborn==0.13.2
 SecretStorage==3.3.3
-semsimian==0.2.15
+semsimian==0.2.16
 semsql==0.3.3
 Send2Trash==1.8.3
 ShExJSG==0.8.2
@@ -282,18 +282,17 @@ sphinxcontrib-htmlhelp==2.0.5
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.7
 sphinxcontrib-serializinghtml==1.1.10
-SQLAlchemy==2.0.29
+SQLAlchemy==2.0.30
 SQLAlchemy-Utils==0.38.3
 sqlite-fts4==1.0.3
 sqlite-migrate==0.1b0
 sqlite-utils==3.36
-sssom==0.4.8
+sssom==0.4.9
 sssom-schema==0.15.2
 stack-data==0.6.3
-StrEnum==0.4.15
 stringcase==1.2.0
 tabulate==0.9.0
-tenacity==8.2.3
+tenacity==8.3.0
 termcolor==2.4.0
 terminado==0.18.1
 terminaltables==3.1.10
@@ -301,13 +300,13 @@ tinycss2==1.3.0
 tomli==2.0.1
 tornado==6.4
 tox==4.15.0
-tqdm==4.66.2
+tqdm==4.66.4
 traitlets==5.14.3
 tsvalid==0.0.3
-twine==5.0.0
+twine==5.1.0
 types-python-dateutil==2.9.0.20240316
 typing-inspect==0.9.0
-typing_extensions==4.11.0
+typing_extensions==4.12.0
 tzdata==2024.1
 UpSetPlot==0.9.0
 uri-template==1.3.0
@@ -315,8 +314,8 @@ uritemplate==4.1.1
 url-normalize==1.4.3
 urllib3==2.2.1
 validators==0.20.0
-virtualenv==20.26.1
-watchdog==4.0.0
+virtualenv==20.26.2
+watchdog==4.0.1
 wcwidth==0.2.13
 webcolors==1.13
 webencodings==0.5.1
@@ -325,4 +324,4 @@ widgetsnbextension==4.0.10
 wrapt==1.16.0
 xmltodict==0.13.0
 yamldown==0.1.8
-zipp==3.18.1
+zipp==3.19.0