From aef24c83475d924bea9573e64e4478194e17f4a7 Mon Sep 17 00:00:00 2001
From: Harry Caufield <j.harry.caufield@gmail.com>
Date: Thu, 9 May 2024 17:23:44 -0400
Subject: [PATCH] Update to support new semsimian IC map functionality (#755)

* Updating dependencies

* Add IC functions to SemsimianImplementation

* Back to delegating to semsim interface
---
 poetry.lock    | 1354 ++++++++++++++++++++++++------------------------
 pyproject.toml |    2 +-
 2 files changed, 669 insertions(+), 687 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 971c10b10..beaeca0ad 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -22,87 +22,87 @@ test = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "aiohttp"
-version = "3.9.4"
+version = "3.9.5"
 description = "Async http client/server framework (asyncio)"
 optional = true
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -375,13 +375,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p
 
 [[package]]
 name = "babel"
-version = "2.14.0"
+version = "2.15.0"
 description = "Internationalization utilities"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -439,28 +439,28 @@ css = ["tinycss2 (>=1.1.0,<1.3)"]
 
 [[package]]
 name = "blinker"
-version = "1.7.0"
+version = "1.8.2"
 description = "Fast, simple object-to-object and broadcast signaling"
 optional = true
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "boto3"
-version = "1.34.84"
+version = "1.34.100"
 description = "The AWS SDK for Python"
 optional = true
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-botocore = ">=1.34.84,<1.35.0"
+botocore = ">=1.34.100,<1.35.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.10.0,<0.11.0"
 
@@ -469,13 +469,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.34.84"
+version = "1.34.100"
 description = "Low-level, data-driven core of boto 3."
 optional = true
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -487,7 +487,7 @@ urllib3 = [
 ]
 
 [package.extras]
-crt = ["awscrt (==0.19.19)"]
+crt = ["awscrt (==0.20.9)"]
 
 [[package]]
 name = "cachetools"
@@ -1121,13 +1121,13 @@ dev = ["flake8", "ipython", "mock", "pytest", "pytest-cov", "restview", "setupto
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.0"
+version = "1.2.1"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -1218,13 +1218,13 @@ files = [
 
 [[package]]
 name = "filelock"
-version = "3.13.4"
+version = "3.14.0"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -1462,13 +1462,13 @@ rfc3987 = "*"
 
 [[package]]
 name = "gilda"
-version = "1.1.0"
+version = "1.2.0"
 description = "Grounding for biomedical entities with contextual disambiguation"
 optional = true
 python-versions = "*"
 files = [
-    {file = "gilda-1.1.0-py3-none-any.whl", hash = "sha256:e1ff6cf0a25890f6053f161fc9bd9e9f7e2442cc9bab26608f5e898ab9af0264"},
-    {file = "gilda-1.1.0.tar.gz", hash = "sha256:b017509c0da7c08d51643f013d10af526d3fa9c2044147574d0e6fa1856a077f"},
+    {file = "gilda-1.2.0-py3-none-any.whl", hash = "sha256:0ed74847d4f52cea9d48e38aa32c431e787f905676c1a5e111a9f59ae20e9696"},
+    {file = "gilda-1.2.0.tar.gz", hash = "sha256:5ef630d6de7d03704ed57408ce5b8679f1f42e4e72ea3dfc0eaf4c50555686dd"},
 ]
 
 [package.dependencies]
@@ -1941,13 +1941,13 @@ arrow = ">=0.15.0"
 
 [[package]]
 name = "itsdangerous"
-version = "2.1.2"
+version = "2.2.0"
 description = "Safely pass data to untrusted environments and back."
 optional = true
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "itsdangerous-2.1.2-py3-none-any.whl", hash = "sha256:2c2349112351b88699d8d4b6b075022c0808887cb7ad10069318a8b0bc88db44"},
-    {file = "itsdangerous-2.1.2.tar.gz", hash = "sha256:5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a"},
+    {file = "itsdangerous-2.2.0-py3-none-any.whl", hash = "sha256:c6242fc49e35958c8b15141343aa660db5fc54d4f13a1db01a3f5891b98700ef"},
+    {file = "itsdangerous-2.2.0.tar.gz", hash = "sha256:e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173"},
 ]
 
 [[package]]
@@ -1971,13 +1971,13 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
 name = "jinja2"
-version = "3.1.3"
+version = "3.1.4"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"},
-    {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"},
+    {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"},
+    {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"},
 ]
 
 [package.dependencies]
@@ -1999,13 +1999,13 @@ files = [
 
 [[package]]
 name = "joblib"
-version = "1.4.0"
+version = "1.4.2"
 description = "Lightweight pipelining with Python functions"
 optional = true
 python-versions = ">=3.8"
 files = [
-    {file = "joblib-1.4.0-py3-none-any.whl", hash = "sha256:42942470d4062537be4d54c83511186da1fc14ba354961a2114da91efa9a4ed7"},
-    {file = "joblib-1.4.0.tar.gz", hash = "sha256:1eb0dc091919cd384490de890cb5dfd538410a6d4b3b54eef09fb8c50b409b1c"},
+    {file = "joblib-1.4.2-py3-none-any.whl", hash = "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6"},
+    {file = "joblib-1.4.2.tar.gz", hash = "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e"},
 ]
 
 [[package]]
@@ -2114,13 +2114,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.21.1"
+version = "4.22.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.21.1-py3-none-any.whl", hash = "sha256:7996507afae316306f9e2290407761157c6f78002dcf7419acb99822143d1c6f"},
-    {file = "jsonschema-4.21.1.tar.gz", hash = "sha256:85727c00279f5fa6bedbe6238d2aa6403bedd8b4864ab11207d07df3cc1b2ee5"},
+    {file = "jsonschema-4.22.0-py3-none-any.whl", hash = "sha256:ff4cfd6b1367a40e7bc6411caec72effadd3db0bbe5017de188f2d6108335802"},
+    {file = "jsonschema-4.22.0.tar.gz", hash = "sha256:5b22d434a45935119af990552c862e5d6d564e8f6601206b305a61fdf661a2b7"},
 ]
 
 [package.dependencies]
@@ -2340,13 +2340,13 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 
 [[package]]
 name = "jupyterlab"
-version = "4.1.6"
+version = "4.1.8"
 description = "JupyterLab computational environment"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyterlab-4.1.6-py3-none-any.whl", hash = "sha256:cf3e862bc10dbf4331e4eb37438634f813c238cfc62c71c640b3b3b2caa089a8"},
-    {file = "jupyterlab-4.1.6.tar.gz", hash = "sha256:7935f36ba26eb615183a4f5c2bbca5791b5108ce2a00b5505f8cfd100d53648e"},
+    {file = "jupyterlab-4.1.8-py3-none-any.whl", hash = "sha256:c3baf3a2f91f89d110ed5786cd18672b9a357129d4e389d2a0dead15e11a4d2c"},
+    {file = "jupyterlab-4.1.8.tar.gz", hash = "sha256:3384aded8680e7ce504fd63b8bb89a39df21c9c7694d9e7dc4a68742cdb30f9b"},
 ]
 
 [package.dependencies]
@@ -2358,7 +2358,7 @@ jinja2 = ">=3.0.3"
 jupyter-core = "*"
 jupyter-lsp = ">=2.0.0"
 jupyter-server = ">=2.4.0,<3"
-jupyterlab-server = ">=2.19.0,<3"
+jupyterlab-server = ">=2.27.1,<3"
 notebook-shim = ">=0.2"
 packaging = "*"
 tomli = {version = ">=1.2.2", markers = "python_version < \"3.11\""}
@@ -2385,13 +2385,13 @@ files = [
 
 [[package]]
 name = "jupyterlab-server"
-version = "2.26.0"
+version = "2.27.1"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyterlab_server-2.26.0-py3-none-any.whl", hash = "sha256:54622cbd330526a385ee0c1fdccdff3a1e7219bf3e864a335284a1270a1973df"},
-    {file = "jupyterlab_server-2.26.0.tar.gz", hash = "sha256:9b3ba91cf2837f7f124fca36d63f3ca80ace2bed4898a63dd47e6598c1ab006f"},
+    {file = "jupyterlab_server-2.27.1-py3-none-any.whl", hash = "sha256:f5e26156e5258b24d532c84e7c74cc212e203bff93eb856f81c24c16daeecc75"},
+    {file = "jupyterlab_server-2.27.1.tar.gz", hash = "sha256:097b5ac709b676c7284ac9c5e373f11930a561f52cd5a86e4fc7e5a9c8a8631d"},
 ]
 
 [package.dependencies]
@@ -2584,13 +2584,13 @@ regex = ["regex"]
 
 [[package]]
 name = "linkml"
-version = "1.7.8"
+version = "1.7.9"
 description = "Linked Open Data Modeling Language"
 optional = false
 python-versions = "<4.0.0,>=3.8.1"
 files = [
-    {file = "linkml-1.7.8-py3-none-any.whl", hash = "sha256:4b8ebe33b422517b08ca01802dc2899ac133c502a71d811c58fa6f4263130709"},
-    {file = "linkml-1.7.8.tar.gz", hash = "sha256:af48ee1ad6751c8d20de2832dbeefe225da9be5f39a7f8ea7821a691cf7c0148"},
+    {file = "linkml-1.7.9-py3-none-any.whl", hash = "sha256:7712cdd6342f781605ba32d97ad19f256d3dc211491f0196ff82ca43873fc492"},
+    {file = "linkml-1.7.9.tar.gz", hash = "sha256:1fd198057e86a87ec5f79a831fb0475ad56847d7633b5c6dacb0afcaf5a986f8"},
 ]
 
 [package.dependencies]
@@ -3028,13 +3028,13 @@ python-dateutil = ">=2.7"
 
 [[package]]
 name = "matplotlib-inline"
-version = "0.1.6"
+version = "0.1.7"
 description = "Inline Matplotlib backend for Jupyter"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
 files = [
-    {file = "matplotlib-inline-0.1.6.tar.gz", hash = "sha256:f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304"},
-    {file = "matplotlib_inline-0.1.6-py3-none-any.whl", hash = "sha256:f1f41aab5328aa5aaea9b16d083b128102f8712542f819fe7e6a420ff581b311"},
+    {file = "matplotlib_inline-0.1.7-py3-none-any.whl", hash = "sha256:df192d39a4ff8f21b1895d72e6a13f5fcc5099f00fa84384e0ea28c2cc0653ca"},
+    {file = "matplotlib_inline-0.1.7.tar.gz", hash = "sha256:8423b23ec666be3d16e16b60bdd8ac4e86e840ebd1dd11a30b9f117f2fa0ab90"},
 ]
 
 [package.dependencies]
@@ -3199,17 +3199,17 @@ files = [
 
 [[package]]
 name = "myst-parser"
-version = "2.0.0"
+version = "3.0.1"
 description = "An extended [CommonMark](https://spec.commonmark.org/) compliant parser,"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "myst_parser-2.0.0-py3-none-any.whl", hash = "sha256:7c36344ae39c8e740dad7fdabf5aa6fc4897a813083c6cc9990044eb93656b14"},
-    {file = "myst_parser-2.0.0.tar.gz", hash = "sha256:ea929a67a6a0b1683cdbe19b8d2e724cd7643f8aa3e7bb18dd65beac3483bead"},
+    {file = "myst_parser-3.0.1-py3-none-any.whl", hash = "sha256:6457aaa33a5d474aca678b8ead9b3dc298e89c68e67012e73146ea6fd54babf1"},
+    {file = "myst_parser-3.0.1.tar.gz", hash = "sha256:88f0cb406cb363b077d176b51c476f62d60604d68a8dcdf4832e080441301a87"},
 ]
 
 [package.dependencies]
-docutils = ">=0.16,<0.21"
+docutils = ">=0.18,<0.22"
 jinja2 = "*"
 markdown-it-py = ">=3.0,<4.0"
 mdit-py-plugins = ">=0.4,<1.0"
@@ -3219,9 +3219,9 @@ sphinx = ">=6,<8"
 [package.extras]
 code-style = ["pre-commit (>=3.0,<4.0)"]
 linkify = ["linkify-it-py (>=2.0,<3.0)"]
-rtd = ["ipython", "pydata-sphinx-theme (==v0.13.0rc4)", "sphinx-autodoc2 (>=0.4.2,<0.5.0)", "sphinx-book-theme (==1.0.0rc2)", "sphinx-copybutton", "sphinx-design2", "sphinx-pyscript", "sphinx-tippy (>=0.3.1)", "sphinx-togglebutton", "sphinxext-opengraph (>=0.8.2,<0.9.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"]
-testing = ["beautifulsoup4", "coverage[toml]", "pytest (>=7,<8)", "pytest-cov", "pytest-param-files (>=0.3.4,<0.4.0)", "pytest-regressions", "sphinx-pytest"]
-testing-docutils = ["pygments", "pytest (>=7,<8)", "pytest-param-files (>=0.3.4,<0.4.0)"]
+rtd = ["ipython", "sphinx (>=7)", "sphinx-autodoc2 (>=0.5.0,<0.6.0)", "sphinx-book-theme (>=1.1,<2.0)", "sphinx-copybutton", "sphinx-design", "sphinx-pyscript", "sphinx-tippy (>=0.4.3)", "sphinx-togglebutton", "sphinxext-opengraph (>=0.9.0,<0.10.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"]
+testing = ["beautifulsoup4", "coverage[toml]", "defusedxml", "pytest (>=8,<9)", "pytest-cov", "pytest-param-files (>=0.6.0,<0.7.0)", "pytest-regressions", "sphinx-pytest"]
+testing-docutils = ["pygments", "pytest (>=8,<9)", "pytest-param-files (>=0.6.0,<0.7.0)"]
 
 [[package]]
 name = "nbclient"
@@ -3247,13 +3247,13 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=
 
 [[package]]
 name = "nbconvert"
-version = "7.16.3"
+version = "7.16.4"
 description = "Converting Jupyter Notebooks (.ipynb files) to other formats.  Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script.  nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "nbconvert-7.16.3-py3-none-any.whl", hash = "sha256:ddeff14beeeedf3dd0bc506623e41e4507e551736de59df69a91f86700292b3b"},
-    {file = "nbconvert-7.16.3.tar.gz", hash = "sha256:a6733b78ce3d47c3f85e504998495b07e6ea9cf9bf6ec1c98dda63ec6ad19142"},
+    {file = "nbconvert-7.16.4-py3-none-any.whl", hash = "sha256:05873c620fe520b6322bf8a5ad562692343fe3452abda5765c7a34b7d1aa3eb3"},
+    {file = "nbconvert-7.16.4.tar.gz", hash = "sha256:86ca91ba266b0a448dc96fa6c5b9d98affabde2867b363258703536807f9f7f4"},
 ]
 
 [package.dependencies]
@@ -3275,9 +3275,9 @@ tinycss2 = "*"
 traitlets = ">=5.1"
 
 [package.extras]
-all = ["nbconvert[docs,qtpdf,serve,test,webpdf]"]
+all = ["flaky", "ipykernel", "ipython", "ipywidgets (>=7.5)", "myst-parser", "nbsphinx (>=0.2.12)", "playwright", "pydata-sphinx-theme", "pyqtwebengine (>=5.15)", "pytest (>=7)", "sphinx (==5.0.2)", "sphinxcontrib-spelling", "tornado (>=6.1)"]
 docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sphinx-theme", "sphinx (==5.0.2)", "sphinxcontrib-spelling"]
-qtpdf = ["nbconvert[qtpng]"]
+qtpdf = ["pyqtwebengine (>=5.15)"]
 qtpng = ["pyqtwebengine (>=5.15)"]
 serve = ["tornado (>=6.1)"]
 test = ["flaky", "ipykernel", "ipywidgets (>=7.5)", "pytest (>=7)"]
@@ -3381,13 +3381,13 @@ twitter = ["twython"]
 
 [[package]]
 name = "notebook"
-version = "7.1.2"
+version = "7.1.3"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "notebook-7.1.2-py3-none-any.whl", hash = "sha256:fc6c24b9aef18d0cd57157c9c47e95833b9b0bdc599652639acf0bdb61dc7d5f"},
-    {file = "notebook-7.1.2.tar.gz", hash = "sha256:efc2c80043909e0faa17fce9e9b37c059c03af0ec99a4d4db84cb21d9d2e936a"},
+    {file = "notebook-7.1.3-py3-none-any.whl", hash = "sha256:919b911e59f41f6e3857ce93c9d93535ba66bb090059712770e5968c07e1004d"},
+    {file = "notebook-7.1.3.tar.gz", hash = "sha256:41fcebff44cf7bb9377180808bcbae066629b55d8c7722f1ebbe75ca44f9cfc1"},
 ]
 
 [package.dependencies]
@@ -3507,13 +3507,13 @@ tests = ["coverage", "pytest", "unittest-templates"]
 
 [[package]]
 name = "openai"
-version = "1.17.1"
+version = "1.26.0"
 description = "The official Python library for the openai API"
 optional = true
 python-versions = ">=3.7.1"
 files = [
-    {file = "openai-1.17.1-py3-none-any.whl", hash = "sha256:d42e0d7a692c7b78cbae21598df5ded396abecf6c285325635ec62621e6c82f1"},
-    {file = "openai-1.17.1.tar.gz", hash = "sha256:c5a909e70e2b4cd04ef4076b68497c4eb894704cf8ab23d32d6552931fda6e5b"},
+    {file = "openai-1.26.0-py3-none-any.whl", hash = "sha256:884ced523fb0225780f8b0e0ed6f7e014049c32d049a41ad0ac962869f1055d1"},
+    {file = "openai-1.26.0.tar.gz", hash = "sha256:642e857b60855702ee6ff665e8fa80946164f77b92e58fd24e01b545685b8405"},
 ]
 
 [package.dependencies]
@@ -3803,28 +3803,29 @@ files = [
 
 [[package]]
 name = "platformdirs"
-version = "4.2.0"
-description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "4.2.1"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "platformdirs-4.2.0-py3-none-any.whl", hash = "sha256:0614df2a2f37e1a662acbd8e2b25b92ccf8632929bc6d43467e17fe89c75e068"},
-    {file = "platformdirs-4.2.0.tar.gz", hash = "sha256:ef0cc731df711022c174543cb70a9b5bd22e5a9337c8624ef2c2ceb8ddad8768"},
+    {file = "platformdirs-4.2.1-py3-none-any.whl", hash = "sha256:17d5a1161b3fd67b390023cb2d3b026bbd40abde6fdb052dfbd3a29c3ba22ee1"},
+    {file = "platformdirs-4.2.1.tar.gz", hash = "sha256:031cd18d4ec63ec53e82dceaac0417d218a6863f7745dfcc9efe7793b7039bdf"},
 ]
 
 [package.extras]
 docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
 test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
+type = ["mypy (>=1.8)"]
 
 [[package]]
 name = "pluggy"
-version = "1.4.0"
+version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pluggy-1.4.0-py3-none-any.whl", hash = "sha256:7db9f7b503d67d1c5b95f59773ebb58a8c1c288129a88665838012cfb07b8981"},
-    {file = "pluggy-1.4.0.tar.gz", hash = "sha256:8c85c2876142a764e5b7548e7d9a0e0ddb46f5185161049a79b7e974454223be"},
+    {file = "pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"},
+    {file = "pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"},
 ]
 
 [package.extras]
@@ -3861,13 +3862,13 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.2.3"
+version = "0.2.4"
 description = "A python library for retrieving semantic prefix maps"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
-    {file = "prefixmaps-0.2.3-py3-none-any.whl", hash = "sha256:342f13b74c056f5b99bcd55e79710a7cb53a2908a2a424c68d830d8d68bb9491"},
-    {file = "prefixmaps-0.2.3.tar.gz", hash = "sha256:b63df4428672e89dc39a7f02816e47b1e8d74653dd3308a69465d6694fad7618"},
+    {file = "prefixmaps-0.2.4-py3-none-any.whl", hash = "sha256:89bf0e6fb08c276f754f9624c42adf2e87c64ee92a3dde1f7eff01f22d85b512"},
+    {file = "prefixmaps-0.2.4.tar.gz", hash = "sha256:ae86a1b31189d0516d199756d5808f75f44b39e86546c356cc78c0fe8d2078af"},
 ]
 
 [package.dependencies]
@@ -3904,13 +3905,13 @@ wcwidth = "*"
 
 [[package]]
 name = "pronto"
-version = "2.5.6"
+version = "2.5.7"
 description = "Python frontend to ontologies."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pronto-2.5.6-py2.py3-none-any.whl", hash = "sha256:b9043569418c473224c0be3b7955c56a76a99580670ee5647ca7df4d71afaf0c"},
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+    {file = "pronto-2.5.7-py2.py3-none-any.whl", hash = "sha256:d7a053cb1735353ef1c708226e77d051a1a32906b5c77f89f9d99c6ca5b5c985"},
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 [[package]]
@@ -4310,13 +4310,13 @@ files = [
 
 [[package]]
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 optional = false
 python-versions = "*"
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@@ -4447,104 +4446,99 @@ files = [
 
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 [package.dependencies]
@@ -4654,13 +4648,13 @@ rdflib-jsonld = "0.6.1"
 
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 name = "referencing"
-version = "0.34.0"
+version = "0.35.1"
 description = "JSON Referencing + Python"
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 name = "regex"
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 description = "Alternative regular expression module, to replace re."
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 [[package]]
@@ -4872,110 +4852,110 @@ files = [
 
 [[package]]
 name = "rpds-py"
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 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
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 [[package]]
@@ -5255,13 +5235,13 @@ win32 = ["pywin32"]
 
 [[package]]
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-version = "69.5.0"
+version = "69.5.1"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
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 [package.extras]
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 imagesize = ">=1.3"
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 sphinxcontrib-qthelp = "*"
 sphinxcontrib-serializinghtml = ">=1.1.9"
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 [[package]]
 name = "sphinx-click"
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+    {file = "SQLAlchemy-2.0.30-cp39-cp39-win32.whl", hash = "sha256:1f9a727312ff6ad5248a4367358e2cf7e625e98b1028b1d7ab7b806b7d757513"},
+    {file = "SQLAlchemy-2.0.30-cp39-cp39-win_amd64.whl", hash = "sha256:a0ef36b28534f2a5771191be6edb44cc2673c7b2edf6deac6562400288664221"},
+    {file = "SQLAlchemy-2.0.30-py3-none-any.whl", hash = "sha256:7108d569d3990c71e26a42f60474b4c02c8586c4681af5fd67e51a044fdea86a"},
+    {file = "SQLAlchemy-2.0.30.tar.gz", hash = "sha256:2b1708916730f4830bc69d6f49d37f7698b5bd7530aca7f04f785f8849e95255"},
 ]
 
 [package.dependencies]
@@ -5755,13 +5736,13 @@ tui = ["trogon"]
 
 [[package]]
 name = "sssom"
-version = "0.4.7"
+version = "0.4.8"
 description = "Operations on SSSOM mapping tables"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
-    {file = "sssom-0.4.7-py3-none-any.whl", hash = "sha256:93118cafec7f35948f3bdb17f21612cf94162a500c8f569c8a8564de36e3c040"},
-    {file = "sssom-0.4.7.tar.gz", hash = "sha256:c2f8bf418f159f778e4564cdec2a859f2bfae5891a33e0b67b2d8bb56c6221b3"},
+    {file = "sssom-0.4.8-py3-none-any.whl", hash = "sha256:1b41f5aedb61e8fc4c4cef581da3fd64a3b8bbfaec46062a00a0105ab253d93b"},
+    {file = "sssom-0.4.8.tar.gz", hash = "sha256:8a316d836e655f86c8907bbb5916129d59cbf3d189e9dd9c872d0732f80ad89d"},
 ]
 
 [package.dependencies]
@@ -5829,17 +5810,18 @@ widechars = ["wcwidth"]
 
 [[package]]
 name = "tenacity"
-version = "8.2.3"
+version = "8.3.0"
 description = "Retry code until it succeeds"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "tenacity-8.2.3-py3-none-any.whl", hash = "sha256:ce510e327a630c9e1beaf17d42e6ffacc88185044ad85cf74c0a8887c6a0f88c"},
-    {file = "tenacity-8.2.3.tar.gz", hash = "sha256:5398ef0d78e63f40007c1fb4c0bff96e1911394d2fa8d194f77619c05ff6cc8a"},
+    {file = "tenacity-8.3.0-py3-none-any.whl", hash = "sha256:3649f6443dbc0d9b01b9d8020a9c4ec7a1ff5f6f3c6c8a036ef371f573fe9185"},
+    {file = "tenacity-8.3.0.tar.gz", hash = "sha256:953d4e6ad24357bceffbc9707bc74349aca9d245f68eb65419cf0c249a1949a2"},
 ]
 
 [package.extras]
-doc = ["reno", "sphinx", "tornado (>=4.5)"]
+doc = ["reno", "sphinx"]
+test = ["pytest", "tornado (>=4.5)", "typeguard"]
 
 [[package]]
 name = "terminado"
@@ -5864,24 +5846,24 @@ typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"]
 
 [[package]]
 name = "threadpoolctl"
-version = "3.4.0"
+version = "3.5.0"
 description = "threadpoolctl"
 optional = true
 python-versions = ">=3.8"
 files = [
-    {file = "threadpoolctl-3.4.0-py3-none-any.whl", hash = "sha256:8f4c689a65b23e5ed825c8436a92b818aac005e0f3715f6a1664d7c7ee29d262"},
-    {file = "threadpoolctl-3.4.0.tar.gz", hash = "sha256:f11b491a03661d6dd7ef692dd422ab34185d982466c49c8f98c8f716b5c93196"},
+    {file = "threadpoolctl-3.5.0-py3-none-any.whl", hash = "sha256:56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467"},
+    {file = "threadpoolctl-3.5.0.tar.gz", hash = "sha256:082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"},
 ]
 
 [[package]]
 name = "tinycss2"
-version = "1.2.1"
+version = "1.3.0"
 description = "A tiny CSS parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "tinycss2-1.2.1-py3-none-any.whl", hash = "sha256:2b80a96d41e7c3914b8cda8bc7f705a4d9c49275616e886103dd839dfc847847"},
-    {file = "tinycss2-1.2.1.tar.gz", hash = "sha256:8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627"},
+    {file = "tinycss2-1.3.0-py3-none-any.whl", hash = "sha256:54a8dbdffb334d536851be0226030e9505965bb2f30f21a4a82c55fb2a80fae7"},
+    {file = "tinycss2-1.3.0.tar.gz", hash = "sha256:152f9acabd296a8375fbca5b84c961ff95971fcfc32e79550c8df8e29118c54d"},
 ]
 
 [package.dependencies]
@@ -5889,7 +5871,7 @@ webencodings = ">=0.4"
 
 [package.extras]
 doc = ["sphinx", "sphinx_rtd_theme"]
-test = ["flake8", "isort", "pytest"]
+test = ["pytest", "ruff"]
 
 [[package]]
 name = "tomli"
@@ -5924,13 +5906,13 @@ files = [
 
 [[package]]
 name = "tox"
-version = "4.14.2"
+version = "4.15.0"
 description = "tox is a generic virtualenv management and test command line tool"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tox-4.14.2-py3-none-any.whl", hash = "sha256:2900c4eb7b716af4a928a7fdc2ed248ad6575294ed7cfae2ea41203937422847"},
-    {file = "tox-4.14.2.tar.gz", hash = "sha256:0defb44f6dafd911b61788325741cc6b2e12ea71f987ac025ad4d649f1f1a104"},
+    {file = "tox-4.15.0-py3-none-any.whl", hash = "sha256:300055f335d855b2ab1b12c5802de7f62a36d4fd53f30bd2835f6a201dda46ea"},
+    {file = "tox-4.15.0.tar.gz", hash = "sha256:7a0beeef166fbe566f54f795b4906c31b428eddafc0102ac00d20998dd1933f6"},
 ]
 
 [package.dependencies]
@@ -5951,13 +5933,13 @@ testing = ["build[virtualenv] (>=1.0.3)", "covdefaults (>=2.3)", "detect-test-po
 
 [[package]]
 name = "tqdm"
-version = "4.66.2"
+version = "4.66.4"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.2-py3-none-any.whl", hash = "sha256:1ee4f8a893eb9bef51c6e35730cebf234d5d0b6bd112b0271e10ed7c24a02bd9"},
-    {file = "tqdm-4.66.2.tar.gz", hash = "sha256:6cd52cdf0fef0e0f543299cfc96fec90d7b8a7e88745f411ec33eb44d5ed3531"},
+    {file = "tqdm-4.66.4-py3-none-any.whl", hash = "sha256:b75ca56b413b030bc3f00af51fd2c1a1a5eac6a0c1cca83cbb37a5c52abce644"},
+    {file = "tqdm-4.66.4.tar.gz", hash = "sha256:e4d936c9de8727928f3be6079590e97d9abfe8d39a590be678eb5919ffc186bb"},
 ]
 
 [package.dependencies]
@@ -5971,18 +5953,18 @@ telegram = ["requests"]
 
 [[package]]
 name = "traitlets"
-version = "5.14.2"
+version = "5.14.3"
 description = "Traitlets Python configuration system"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "traitlets-5.14.2-py3-none-any.whl", hash = "sha256:fcdf85684a772ddeba87db2f398ce00b40ff550d1528c03c14dbf6a02003cd80"},
-    {file = "traitlets-5.14.2.tar.gz", hash = "sha256:8cdd83c040dab7d1dee822678e5f5d100b514f7b72b01615b26fc5718916fdf9"},
+    {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"},
+    {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"},
 ]
 
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
-test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.1)", "pytest-mock", "pytest-mypy-testing"]
+test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"]
 
 [[package]]
 name = "types-python-dateutil"
@@ -6074,24 +6056,24 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "validators"
-version = "0.28.0"
+version = "0.28.1"
 description = "Python Data Validation for Humans™"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "validators-0.28.0-py3-none-any.whl", hash = "sha256:e0184691dea3ba82b52c161ba81d3ec1d8be8da9609f0137d1430b395b366521"},
-    {file = "validators-0.28.0.tar.gz", hash = "sha256:85bc82511f6ccd0800f4c15d8c0dc546c15e369640c5ea1f24349ba0b3b17815"},
+    {file = "validators-0.28.1-py3-none-any.whl", hash = "sha256:890c98789ad884037f059af6ea915ec2d667129d509180c2c590b8009a4c4219"},
+    {file = "validators-0.28.1.tar.gz", hash = "sha256:5ac88e7916c3405f0ce38ac2ac82a477fcf4d90dbbeddd04c8193171fc17f7dc"},
 ]
 
 [[package]]
 name = "virtualenv"
-version = "20.25.1"
+version = "20.26.1"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.25.1-py3-none-any.whl", hash = "sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a"},
-    {file = "virtualenv-20.25.1.tar.gz", hash = "sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197"},
+    {file = "virtualenv-20.26.1-py3-none-any.whl", hash = "sha256:7aa9982a728ae5892558bff6a2839c00b9ed145523ece2274fad6f414690ae75"},
+    {file = "virtualenv-20.26.1.tar.gz", hash = "sha256:604bfdceaeece392802e6ae48e69cec49168b9c5f4a44e483963f9242eb0e78b"},
 ]
 
 [package.dependencies]
@@ -6100,7 +6082,7 @@ filelock = ">=3.12.2,<4"
 platformdirs = ">=3.9.1,<5"
 
 [package.extras]
-docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
 test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
 [[package]]
@@ -6183,29 +6165,29 @@ files = [
 
 [[package]]
 name = "websocket-client"
-version = "1.7.0"
+version = "1.8.0"
 description = "WebSocket client for Python with low level API options"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "websocket-client-1.7.0.tar.gz", hash = "sha256:10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6"},
-    {file = "websocket_client-1.7.0-py3-none-any.whl", hash = "sha256:f4c3d22fec12a2461427a29957ff07d35098ee2d976d3ba244e688b8b4057588"},
+    {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"},
+    {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"},
 ]
 
 [package.extras]
-docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"]
+docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"]
 optional = ["python-socks", "wsaccel"]
 test = ["websockets"]
 
 [[package]]
 name = "werkzeug"
-version = "3.0.2"
+version = "3.0.3"
 description = "The comprehensive WSGI web application library."
 optional = true
 python-versions = ">=3.8"
 files = [
-    {file = "werkzeug-3.0.2-py3-none-any.whl", hash = "sha256:3aac3f5da756f93030740bc235d3e09449efcf65f2f55e3602e1d851b8f48795"},
-    {file = "werkzeug-3.0.2.tar.gz", hash = "sha256:e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d"},
+    {file = "werkzeug-3.0.3-py3-none-any.whl", hash = "sha256:fc9645dc43e03e4d630d23143a04a7f947a9a3b5727cd535fdfe155a17cc48c8"},
+    {file = "werkzeug-3.0.3.tar.gz", hash = "sha256:097e5bfda9f0aba8da6b8545146def481d06aa7d3266e7448e2cccf67dd8bd18"},
 ]
 
 [package.dependencies]
@@ -6432,4 +6414,4 @@ semsimian = ["semsimian"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<4.0.0"
-content-hash = "cb94df3f00372e9a58007cc2bb2a486e049124f1de9cc858f1e1f48a97f35bf0"
+content-hash = "8fa6de9d76676819eb4939f307d04acd7b20b0e852f88a70f691fe6e376d0cb7"
diff --git a/pyproject.toml b/pyproject.toml
index 564d4d717..c59c8cd83 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@ kgcl-schema = "^0.6.8"
 
 funowl = ">=0.2.0"
 gilda = {version = ">=1.0.0", optional = true}
-semsimian = {version = ">=0.2.15", optional = true}
+semsimian = {version = ">=0.2.16", optional = true}
 kgcl-rdflib = "0.5.0"
 llm = {version = "*", optional = true}
 html2text = {version = "*", optional = true}