Repository: linkml/linkml-owl (language: python)

Issue:
incompatibility with funowl 0.1.13
https://github.com/Harold-Solbrig/funowl/releases/tag/v0.1.13
Bumping funowl to >=0.2.0
I expect this will break due to #32, but oaklib currently requires funowl >=0.2.0.
This attempts to align accordingly.


Discussion / hints:

Fix patch:
diff --git a/linkml_owl/dumpers/owl_dumper.py b/linkml_owl/dumpers/owl_dumper.py
index f650a22..e037c5e 100644
--- a/linkml_owl/dumpers/owl_dumper.py
+++ b/linkml_owl/dumpers/owl_dumper.py
@@ -261,7 +261,12 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
         else:
             for obj_type in [ObjectProperty, DataProperty, AnnotationProperty, NamedIndividual, Class, Datatype]:
                 if obj_type.__name__ in cls_interps:
-                    decl = Declaration(obj_type(subj))
+                    if not subj:
+                        raise ValueError(f"Cannot create {obj_type} without an identifier for {element}")
+                    if not isinstance(subj, URIRef):
+                        raise ValueError(f"Cannot create {obj_type} with non-URI identifier for {element}")
+                    di = obj_type(subj)
+                    decl = Declaration(di)
                     logging.debug(f"Inferred {decl} based on {obj_type.__name__} in {cls_interps}")
                     o.axioms.append(decl)
         logging.info(f"Subject={subj}")
@@ -442,7 +447,7 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
                     elif axiom_type == AnnotationAssertion:
                         axiom = AnnotationAssertion(slot_uri, subj, parent)
                     else:
-                        raise Exception(f'Unknown: {axiom_type}')
+                        raise ValueError(f'Unknown axiom type: {axiom_type}')
                     if axiom is not None:
                         self.add_axiom(axiom, o, axiom_annotations)
                     else:
@@ -558,8 +563,18 @@ def _get_inferred_slot_annotations(self, slot: SlotDefinition, ann_key: str,
         return list(vals)
 
     def _get_inferred_class_annotations(self, cls: ClassDefinition, ann_key: str) -> List[str]:
+        """
+        Retrieve owl annotations for a class, including those inherited from ancestors.
+
+        OWL annotations are specified in LinkML using the annotations slot, where the
+        key is "owl" or something in the owl namespace.
+
+        :param cls: class to query
+        :param ann_key: annotation key to query
+        :return:
+        """
         vals = set()
-        anc_classes = [cls]
+        anc_classes = []
         sv = self.schemaview
         for anc_c in sv.class_ancestors(cls.name, reflexive=True):
             anc_classes.append(sv.get_class(anc_c))
diff --git a/poetry.lock b/poetry.lock
index 44fb98f..6882632 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,17 +1,20 @@
-# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
 
 [[package]]
-name = "alabaster"
-version = "0.7.13"
-description = "A configurable sidebar-enabled Sphinx theme"
+name = "annotated-types"
+version = "0.5.0"
+description = "Reusable constraint types to use with typing.Annotated"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
-    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+    {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"},
+    {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"},
 ]
 
+[package.dependencies]
+typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""}
+
 [[package]]
 name = "antlr4-python3-runtime"
 version = "4.9.3"
@@ -38,50 +41,24 @@ files = [
 [package.dependencies]
 python-dateutil = ">=2.7.0"
 
-[[package]]
-name = "atomicwrites"
-version = "1.4.1"
-description = "Atomic file writes."
-category = "main"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
-]
-
 [[package]]
 name = "attrs"
-version = "22.2.0"
+version = "23.1.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
-    {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
-]
-
-[package.extras]
-cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
-tests = ["attrs[tests-no-zope]", "zope.interface"]
-tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
-
-[[package]]
-name = "babel"
-version = "2.12.1"
-description = "Internationalization utilities"
-category = "main"
-optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
-    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
+    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
 ]
 
-[package.dependencies]
-pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
+[package.extras]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "bcp47"
@@ -97,32 +74,43 @@ files = [
 
 [[package]]
 name = "black"
-version = "22.12.0"
+version = "23.7.0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "black-22.12.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9eedd20838bd5d75b80c9f5487dbcb06836a43833a37846cf1d8c1cc01cef59d"},
-    {file = "black-22.12.0-cp310-cp310-win_amd64.whl", hash = "sha256:159a46a4947f73387b4d83e87ea006dbb2337eab6c879620a3ba52699b1f4351"},
-    {file = "black-22.12.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d30b212bffeb1e252b31dd269dfae69dd17e06d92b87ad26e23890f3efea366f"},
-    {file = "black-22.12.0-cp311-cp311-win_amd64.whl", hash = "sha256:7412e75863aa5c5411886804678b7d083c7c28421210180d67dfd8cf1221e1f4"},
-    {file = "black-22.12.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c116eed0efb9ff870ded8b62fe9f28dd61ef6e9ddd28d83d7d264a38417dcee2"},
-    {file = "black-22.12.0-cp37-cp37m-win_amd64.whl", hash = "sha256:1f58cbe16dfe8c12b7434e50ff889fa479072096d79f0a7f25e4ab8e94cd8350"},
-    {file = "black-22.12.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:77d86c9f3db9b1bf6761244bc0b3572a546f5fe37917a044e02f3166d5aafa7d"},
-    {file = "black-22.12.0-cp38-cp38-win_amd64.whl", hash = "sha256:82d9fe8fee3401e02e79767016b4907820a7dc28d70d137eb397b92ef3cc5bfc"},
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-    {file = "black-22.12.0-py3-none-any.whl", hash = "sha256:436cc9167dd28040ad90d3b404aec22cedf24a6e4d7de221bec2730ec0c97bcf"},
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+    {file = "black-23.7.0-cp310-cp310-macosx_10_16_arm64.whl", hash = "sha256:5c4bc552ab52f6c1c506ccae05681fab58c3f72d59ae6e6639e8885e94fe2587"},
+    {file = "black-23.7.0-cp310-cp310-macosx_10_16_universal2.whl", hash = "sha256:552513d5cd5694590d7ef6f46e1767a4df9af168d449ff767b13b084c020e63f"},
+    {file = "black-23.7.0-cp310-cp310-macosx_10_16_x86_64.whl", hash = "sha256:86cee259349b4448adb4ef9b204bb4467aae74a386bce85d56ba4f5dc0da27be"},
+    {file = "black-23.7.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:501387a9edcb75d7ae8a4412bb8749900386eaef258f1aefab18adddea1936bc"},
+    {file = "black-23.7.0-cp310-cp310-win_amd64.whl", hash = "sha256:fb074d8b213749fa1d077d630db0d5f8cc3b2ae63587ad4116e8a436e9bbe995"},
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+    {file = "black-23.7.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:831d8f54c3a8c8cf55f64d0422ee875eecac26f5f649fb6c1df65316b67c8926"},
+    {file = "black-23.7.0-cp311-cp311-win_amd64.whl", hash = "sha256:7f3bf2dec7d541b4619b8ce526bda74a6b0bffc480a163fed32eb8b3c9aed8ad"},
+    {file = "black-23.7.0-cp38-cp38-macosx_10_16_arm64.whl", hash = "sha256:f9062af71c59c004cd519e2fb8f5d25d39e46d3af011b41ab43b9c74e27e236f"},
+    {file = "black-23.7.0-cp38-cp38-macosx_10_16_universal2.whl", hash = "sha256:01ede61aac8c154b55f35301fac3e730baf0c9cf8120f65a9cd61a81cfb4a0c3"},
+    {file = "black-23.7.0-cp38-cp38-macosx_10_16_x86_64.whl", hash = "sha256:327a8c2550ddc573b51e2c352adb88143464bb9d92c10416feb86b0f5aee5ff6"},
+    {file = "black-23.7.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6d1c6022b86f83b632d06f2b02774134def5d4d4f1dac8bef16d90cda18ba28a"},
+    {file = "black-23.7.0-cp38-cp38-win_amd64.whl", hash = "sha256:27eb7a0c71604d5de083757fbdb245b1a4fae60e9596514c6ec497eb63f95320"},
+    {file = "black-23.7.0-cp39-cp39-macosx_10_16_arm64.whl", hash = "sha256:8417dbd2f57b5701492cd46edcecc4f9208dc75529bcf76c514864e48da867d9"},
+    {file = "black-23.7.0-cp39-cp39-macosx_10_16_universal2.whl", hash = "sha256:47e56d83aad53ca140da0af87678fb38e44fd6bc0af71eebab2d1f59b1acf1d3"},
+    {file = "black-23.7.0-cp39-cp39-macosx_10_16_x86_64.whl", hash = "sha256:25cc308838fe71f7065df53aedd20327969d05671bac95b38fdf37ebe70ac087"},
+    {file = "black-23.7.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:642496b675095d423f9b8448243336f8ec71c9d4d57ec17bf795b67f08132a91"},
+    {file = "black-23.7.0-cp39-cp39-win_amd64.whl", hash = "sha256:ad0014efc7acf0bd745792bd0d8857413652979200ab924fbf239062adc12491"},
+    {file = "black-23.7.0-py3-none-any.whl", hash = "sha256:9fd59d418c60c0348505f2ddf9609c1e1de8e7493eab96198fc89d9f865e7a96"},
+    {file = "black-23.7.0.tar.gz", hash = "sha256:022a582720b0d9480ed82576c920a8c1dde97cc38ff11d8d8859b3bd6ca9eedb"},
 ]
 
 [package.dependencies]
 click = ">=8.0.0"
 mypy-extensions = ">=0.4.3"
+packaging = ">=22.0"
 pathspec = ">=0.9.0"
 platformdirs = ">=2"
-tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""}
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
@@ -131,16 +119,28 @@ d = ["aiohttp (>=3.7.4)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
+[[package]]
+name = "cachetools"
+version = "5.3.1"
+description = "Extensible memoizing collections and decorators"
+category = "dev"
+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"},
+]
+
 [[package]]
 name = "certifi"
-version = "2022.12.7"
+version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"},
-    {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"},
+    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
+    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
 ]
 
 [[package]]
@@ -159,111 +159,111 @@ rdflib = ">=0.4.2"
 
 [[package]]
 name = "chardet"
-version = "5.1.0"
+version = "5.2.0"
 description = "Universal encoding detector for Python 3"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "chardet-5.1.0-py3-none-any.whl", hash = "sha256:362777fb014af596ad31334fde1e8c327dfdb076e1960d1694662d46a6917ab9"},
-    {file = "chardet-5.1.0.tar.gz", hash = "sha256:0d62712b956bc154f85fb0a266e2a3c5913c2967e00348701b32411d6def31e5"},
+    {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"},
+    {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"},
 ]
 
 [[package]]
 name = "charset-normalizer"
-version = "3.1.0"
+version = "3.2.0"
 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-3.1.0.tar.gz", hash = "sha256:34e0a2f9c370eb95597aae63bf85eb5e96826d81e3dcf88b8886012906f509b5"},
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 [package.dependencies]
@@ -350,25 +359,25 @@ toml = ["tomli"]
 
 [[package]]
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+version = "0.6.0"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
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 pytrie = "*"
 requests = "*"
 
 [package.extras]
-bioregistry = ["bioregistry (>=0.5.136)"]
-docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-theme"]
-fastapi = ["fastapi", "httpx"]
-flask = ["flask"]
+docs = ["sphinx", "sphinx-automodapi", "sphinx-rtd-theme"]
+fastapi = ["defusedxml", "fastapi", "httpx", "python-multipart", "uvicorn"]
+flask = ["defusedxml", "flask"]
 pandas = ["pandas"]
 rdflib = ["rdflib"]
 tests = ["coverage", "pytest"]
@@ -387,44 +396,32 @@ files = [
 
 [[package]]
 name = "deprecated"
-version = "1.2.13"
+version = "1.2.14"
 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
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 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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 [package.dependencies]
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 [package.extras]
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+dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 
 [[package]]
 name = "distlib"
-version = "0.3.6"
+version = "0.3.7"
 description = "Distribution utilities"
-category = "main"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
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-
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-name = "docutils"
-version = "0.19"
-description = "Docutils -- Python Documentation Utilities"
-category = "main"
-optional = false
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 ]
 
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@@ -439,21 +436,36 @@ files = [
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 ]
 
+[[package]]
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+version = "1.1.2"
+description = "Backport of PEP 654 (exception groups)"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[package.extras]
+test = ["pytest (>=6)"]
+
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-version = "3.10.0"
+version = "3.12.2"
 description = "A platform independent file lock."
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
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-testing = ["covdefaults (>=2.3)", "coverage (>=7.2.1)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.5.20)", "sphinx (>=7.0.1)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"]
 
 [[package]]
 name = "fqdn"
@@ -469,20 +481,21 @@ files = [
 
 [[package]]
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-version = "0.1.12"
+version = "0.2.3"
 description = "Python rendering of the OWL Functional syntax"
 category = "main"
 optional = false
 python-versions = ">=3.7"
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 [package.dependencies]
 bcp47 = "*"
+jsonasobj = "*"
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-rdflib = ">=5.0.0"
+rdflib = ">=6.2.0,<8"
 rdflib-shim = "*"
 rfc3987 = "*"
 
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+    {file = "greenlet-2.0.1.tar.gz", hash = "sha256:42e602564460da0e8ee67cb6d7236363ee5e131aa15943b6670e44e5c2ed0f67"},
 ]
 
 [package.extras]
 docs = ["Sphinx", "docutils (<0.18)"]
-test = ["objgraph", "psutil"]
+test = ["faulthandler", "objgraph", "psutil"]
 
 [[package]]
 name = "hbreader"
@@ -619,56 +632,44 @@ files = [
     {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
 ]
 
-[[package]]
-name = "imagesize"
-version = "1.4.1"
-description = "Getting image size from png/jpeg/jpeg2000/gif file"
-category = "main"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
-    {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
-]
-
 [[package]]
 name = "importlib-metadata"
-version = "4.13.0"
+version = "6.8.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-4.13.0-py3-none-any.whl", hash = "sha256:8a8a81bcf996e74fee46f0d16bd3eaa382a7eb20fd82445c3ad11f4090334116"},
-    {file = "importlib_metadata-4.13.0.tar.gz", hash = "sha256:dd0173e8f150d6815e098fd354f6414b0f079af4644ddfe90c71e2fc6174346d"},
+    {file = "importlib_metadata-6.8.0-py3-none-any.whl", hash = "sha256:3ebb78df84a805d7698245025b975d9d67053cd94c79245ba4b3eb694abe68bb"},
+    {file = "importlib_metadata-6.8.0.tar.gz", hash = "sha256:dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743"},
 ]
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
+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 = "5.12.0"
+version = "6.0.1"
 description = "Read resources from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-5.12.0-py3-none-any.whl", hash = "sha256:7b1deeebbf351c7578e09bf2f63fa2ce8b5ffec296e0d349139d43cca061a81a"},
-    {file = "importlib_resources-5.12.0.tar.gz", hash = "sha256:4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6"},
+    {file = "importlib_resources-6.0.1-py3-none-any.whl", hash = "sha256:134832a506243891221b88b4ae1213327eea96ceb4e407a00d790bb0626f45cf"},
+    {file = "importlib_resources-6.0.1.tar.gz", hash = "sha256:4359457e42708462b9626a04657c6208ad799ceb41e5c58c57ffa0e6a098a5d4"},
 ]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [[package]]
 name = "iniconfig"
@@ -775,14 +776,14 @@ hbreader = "*"
 
 [[package]]
 name = "jsonpatch"
-version = "1.32"
+version = "1.33"
 description = "Apply JSON-Patches (RFC 6902)"
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
-    {file = "jsonpatch-1.32-py2.py3-none-any.whl", hash = "sha256:26ac385719ac9f54df8a2f0827bb8253aa3ea8ab7b3368457bcdb8c14595a397"},
-    {file = "jsonpatch-1.32.tar.gz", hash = "sha256:b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2"},
+    {file = "jsonpatch-1.33-py2.py3-none-any.whl", hash = "sha256:0ae28c0cd062bbd8b8ecc26d7d164fbbea9652a1a3693f3b956c1eae5145dade"},
+    {file = "jsonpatch-1.33.tar.gz", hash = "sha256:9fcd4009c41e6d12348b4a0ff2563ba56a2923a7dfee731d004e212e1ee5030c"},
 ]
 
 [package.dependencies]
@@ -808,39 +809,41 @@ six = "*"
 
 [[package]]
 name = "jsonpointer"
-version = "2.3"
+version = "2.4"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
-    {file = "jsonpointer-2.3-py2.py3-none-any.whl", hash = "sha256:51801e558539b4e9cd268638c078c6c5746c9ac96bc38152d443400e4f3793e9"},
-    {file = "jsonpointer-2.3.tar.gz", hash = "sha256:97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a"},
+    {file = "jsonpointer-2.4-py2.py3-none-any.whl", hash = "sha256:15d51bba20eea3165644553647711d150376234112651b4f1811022aecad7d7a"},
+    {file = "jsonpointer-2.4.tar.gz", hash = "sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88"},
 ]
 
 [[package]]
 name = "jsonschema"
-version = "4.17.3"
+version = "4.19.0"
 description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.17.3-py3-none-any.whl", hash = "sha256:a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6"},
-    {file = "jsonschema-4.17.3.tar.gz", hash = "sha256:0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d"},
+    {file = "jsonschema-4.19.0-py3-none-any.whl", hash = "sha256:043dc26a3845ff09d20e4420d6012a9c91c9aa8999fa184e7efcfeccb41e32cb"},
+    {file = "jsonschema-4.19.0.tar.gz", hash = "sha256:6e1e7569ac13be8139b2dd2c21a55d350066ee3f80df06c608b398cdc6f30e8f"},
 ]
 
 [package.dependencies]
-attrs = ">=17.4.0"
+attrs = ">=22.2.0"
 fqdn = {version = "*", optional = true, markers = "extra == \"format\""}
 idna = {version = "*", optional = true, markers = "extra == \"format\""}
 importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
 isoduration = {version = "*", optional = true, markers = "extra == \"format\""}
 jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format\""}
+jsonschema-specifications = ">=2023.03.6"
 pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""}
-pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+referencing = ">=0.28.4"
 rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format\""}
 rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
+rpds-py = ">=0.7.1"
 uri-template = {version = "*", optional = true, markers = "extra == \"format\""}
 webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\""}
 
@@ -848,16 +851,32 @@ webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\"
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
 format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
 
+[[package]]
+name = "jsonschema-specifications"
+version = "2023.7.1"
+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"},
+]
+
+[package.dependencies]
+importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+referencing = ">=0.28.0"
+
 [[package]]
 name = "linkml"
-version = "1.4.10"
+version = "1.5.6"
 description = "Linked Open Data Modeling Language"
 category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -870,12 +889,11 @@ jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = {version = ">=4.0.0", extras = ["format"]}
 linkml-dataops = "*"
-linkml-runtime = ">=1,<2"
-myst-parser = "*"
+linkml-runtime = ">=1.5.4"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
-prefixmaps = ">=0.1.3,<0.2.0"
+prefixmaps = ">=0.1.3"
 pydantic = "*"
 pyjsg = ">=0.11.6"
 pyshex = ">=0.7.20"
@@ -884,15 +902,9 @@ python-dateutil = "*"
 pyyaml = "*"
 rdflib = ">=6.0.0"
 requests = ">=2.22"
-sphinx-click = "*"
-sphinx-rtd-theme = "*"
 sqlalchemy = ">=1.4.31"
-tox = ">=3.25.1,<4.0.0"
 watchdog = ">=0.9.0"
 
-[package.extras]
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-
 [[package]]
 name = "linkml-dataops"
 version = "0.1.0"
@@ -914,163 +926,108 @@ linkml-runtime = ">=1.1.6"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.4.9"
+version = "1.5.6"
 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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 ]
 
 [package.dependencies]
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-curies = ">=0.4.0,<0.5.0"
+curies = ">=0.5.4"
 deprecated = "*"
 hbreader = "*"
 json-flattener = ">=0.1.9"
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 jsonschema = ">=3.2.0"
 prefixcommons = ">=0.1.12"
 prefixmaps = ">=0.1.4"
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 pyyaml = "*"
 rdflib = ">=6.0.0"
 requests = "*"
 
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-version = "3.3.7"
-description = "Python implementation of Markdown."
+version = "3.4.4"
+description = "Python implementation of John Gruber's Markdown."
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 importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 
 [package.extras]
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 testing = ["coverage", "pyyaml"]
 
-[[package]]
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-[package.dependencies]
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 ]
 
 [[package]]
@@ -1087,14 +1044,14 @@ files = [
 
 [[package]]
 name = "mkdocs"
-version = "1.4.2"
+version = "1.5.2"
 description = "Project documentation with Markdown."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "mkdocs-1.4.2-py3-none-any.whl", hash = "sha256:c8856a832c1e56702577023cd64cc5f84948280c1c0fcc6af4cd39006ea6aa8c"},
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+    {file = "mkdocs-1.5.2.tar.gz", hash = "sha256:70d0da09c26cff288852471be03c23f0f521fc15cf16ac89c7a3bfb9ae8d24f9"},
 ]
 
 [package.dependencies]
@@ -1103,16 +1060,19 @@ colorama = {version = ">=0.4", markers = "platform_system == \"Windows\""}
 ghp-import = ">=1.0"
 importlib-metadata = {version = ">=4.3", markers = "python_version < \"3.10\""}
 jinja2 = ">=2.11.1"
-markdown = ">=3.2.1,<3.4"
+markdown = ">=3.2.1"
+markupsafe = ">=2.0.1"
 mergedeep = ">=1.3.4"
 packaging = ">=20.5"
+pathspec = ">=0.11.1"
+platformdirs = ">=2.2.0"
 pyyaml = ">=5.1"
 pyyaml-env-tag = ">=0.1"
 watchdog = ">=2.0"
 
 [package.extras]
 i18n = ["babel (>=2.9.0)"]
-min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.3)", "jinja2 (==2.11.1)", "markdown (==3.2.1)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "packaging (==20.5)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "typing-extensions (==3.10)", "watchdog (==2.0)"]
+min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.3)", "jinja2 (==2.11.1)", "markdown (==3.2.1)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "packaging (==20.5)", "pathspec (==0.11.1)", "platformdirs (==2.2.0)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "typing-extensions (==3.10)", "watchdog (==2.0)"]
 
 [[package]]
 name = "mypy-extensions"
@@ -1126,33 +1086,6 @@ files = [
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 ]
 
-[[package]]
-name = "myst-parser"
-version = "1.0.0"
-description = "An extended [CommonMark](https://spec.commonmark.org/) compliant parser,"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
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-]
-
-[package.dependencies]
-docutils = ">=0.15,<0.20"
-jinja2 = "*"
-markdown-it-py = ">=1.0.0,<3.0.0"
-mdit-py-plugins = ">=0.3.4,<0.4.0"
-pyyaml = "*"
-sphinx = ">=5,<7"
-
-[package.extras]
-code-style = ["pre-commit (>=3.0,<4.0)"]
-linkify = ["linkify-it-py (>=1.0,<2.0)"]
-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 (>=0.7.5,<0.8.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"]
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-testing-docutils = ["pygments", "pytest (>=7,<8)", "pytest-param-files (>=0.3.4,<0.4.0)"]
-
 [[package]]
 name = "openpyxl"
 version = "3.1.2"
@@ -1170,37 +1103,38 @@ et-xmlfile = "*"
 
 [[package]]
 name = "packaging"
-version = "23.0"
+version = "23.1"
 description = "Core utilities for Python packages"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "packaging-23.0-py3-none-any.whl", hash = "sha256:714ac14496c3e68c99c29b00845f7a2b85f3bb6f1078fd9f72fd20f0570002b2"},
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+    {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
 ]
 
 [[package]]
 name = "parse"
-version = "1.19.0"
+version = "1.19.1"
 description = "parse() is the opposite of format()"
 category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "parse-1.19.0.tar.gz", hash = "sha256:9ff82852bcb65d139813e2a5197627a94966245c897796760a3a2a8eb66f020b"},
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+    {file = "parse-1.19.1.tar.gz", hash = "sha256:cc3a47236ff05da377617ddefa867b7ba983819c664e1afe46249e5b469be464"},
 ]
 
 [[package]]
 name = "pathspec"
-version = "0.11.1"
+version = "0.11.2"
 description = "Utility library for gitignore style pattern matching of file paths."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pathspec-0.11.1-py3-none-any.whl", hash = "sha256:d8af70af76652554bd134c22b3e8a1cc46ed7d91edcdd721ef1a0c51a84a5293"},
-    {file = "pathspec-0.11.1.tar.gz", hash = "sha256:2798de800fa92780e33acca925945e9a19a133b715067cf165b8866c15a31687"},
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 ]
 
 [[package]]
@@ -1217,30 +1151,30 @@ files = [
 
 [[package]]
 name = "platformdirs"
-version = "3.1.1"
+version = "3.10.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "platformdirs-3.1.1-py3-none-any.whl", hash = "sha256:e5986afb596e4bb5bde29a79ac9061aa955b94fca2399b7aaac4090860920dd8"},
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+    {file = "platformdirs-3.10.0-py3-none-any.whl", hash = "sha256:d7c24979f292f916dc9cbf8648319032f551ea8c49a4c9bf2fb556a02070ec1d"},
+    {file = "platformdirs-3.10.0.tar.gz", hash = "sha256:b45696dab2d7cc691a3226759c0d3b00c47c8b6e293d96f6436f733303f77f6d"},
 ]
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
-test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
 
 [[package]]
 name = "pluggy"
-version = "1.0.0"
+version = "1.2.0"
 description = "plugin and hook calling mechanisms for python"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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-    {file = "pluggy-1.0.0.tar.gz", hash = "sha256:4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159"},
+    {file = "pluggy-1.2.0-py3-none-any.whl", hash = "sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849"},
+    {file = "pluggy-1.2.0.tar.gz", hash = "sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3"},
 ]
 
 [package.extras]
@@ -1279,99 +1213,160 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.1.4"
+version = "0.1.5"
 description = "A python library for retrieving semantic prefix maps"
 category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
-    {file = "prefixmaps-0.1.4-py3-none-any.whl", hash = "sha256:845457a5149e56b676827d002200840ae487052f08879a8d6ca9093aa6b9213e"},
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+    {file = "prefixmaps-0.1.5-py3-none-any.whl", hash = "sha256:afe679efa0fa62ae69939771956a76e2958505743b40755c8bae85732622b5b2"},
+    {file = "prefixmaps-0.1.5.tar.gz", hash = "sha256:0073f69477f7e9e2359409c0e9d2f853c958600825d9ed859c4c6c71134010a1"},
 ]
 
 [package.dependencies]
-importlib-metadata = ">=4.12.0,<5.0.0"
+click = ">=8.1.3,<9.0.0"
+greenlet = "2.0.1"
+importlib-metadata = ">=1.0.0"
 pyyaml = ">=5.3.1"
+typing-extensions = ">=4.4.0,<5.0.0"
 
-[[package]]
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+[package.dependencies]
+packaging = ">=23.1"
+tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+
+[package.extras]
+docs = ["furo (>=2023.5.20)", "sphinx (>=7.0.1)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"]
+testing = ["covdefaults (>=2.3)", "importlib-metadata (>=6.6)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)", "setuptools (>=67.8)", "wheel (>=0.40)"]
+
 [[package]]
 name = "pyshex"
 version = "0.8.1"
@@ -1486,39 +1464,37 @@ shexjsg = ">=0.8.1"
 
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 name = "pytest"
-version = "6.2.5"
+version = "7.4.0"
 description = "pytest: simple powerful testing with Python"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
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 packaging = "*"
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-py = ">=1.8.2"
-toml = "*"
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 [package.extras]
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+version = "4.1.0"
 description = "Pytest plugin for measuring coverage."
 category = "dev"
 optional = false
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+python-versions = ">=3.7"
 files = [
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 [package.dependencies]
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-description = "World timezone definitions, modern and historical"
-category = "main"
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-
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 description = "YAML parser and emitter for Python"
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 python-versions = ">=3.6"
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 ]
 
 [[package]]
@@ -1650,28 +1614,25 @@ pyyaml = "*"
 
 [[package]]
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-version = "6.2.0"
+version = "6.3.2"
 description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.7,<4.0"
 files = [
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-    {file = "rdflib-6.2.0.tar.gz", hash = "sha256:62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942"},
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 [package.dependencies]
-isodate = "*"
-pyparsing = "*"
-setuptools = "*"
+isodate = ">=0.6.0,<0.7.0"
+pyparsing = ">=2.1.0,<4"
 
 [package.extras]
-berkeleydb = ["berkeleydb"]
-dev = ["black (==22.6.0)", "flake8", "flakeheaven", "isort", "mypy", "pep8-naming", "types-setuptools"]
-docs = ["myst-parser", "sphinx (<6)", "sphinx-autodoc-typehints", "sphinxcontrib-apidoc", "sphinxcontrib-kroki"]
-html = ["html5lib"]
-networkx = ["networkx"]
-tests = ["html5lib", "pytest", "pytest-cov"]
+berkeleydb = ["berkeleydb (>=18.1.0,<19.0.0)"]
+html = ["html5lib (>=1.0,<2.0)"]
+lxml = ["lxml (>=4.3.0,<5.0.0)"]
+networkx = ["networkx (>=2.0.0,<3.0.0)"]
 
 [[package]]
 name = "rdflib-jsonld"
@@ -1704,23 +1665,39 @@ files = [
 rdflib = ">=5.0.0"
 rdflib-jsonld = "0.6.1"
 
+[[package]]
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+version = "0.30.2"
+description = "JSON Referencing + Python"
+category = "main"
+optional = false
+python-versions = ">=3.8"
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+rpds-py = ">=0.7.0"
+
 [[package]]
 name = "requests"
-version = "2.28.2"
+version = "2.31.0"
 description = "Python HTTP for Humans."
 category = "main"
 optional = false
-python-versions = ">=3.7, <4"
+python-versions = ">=3.7"
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 certifi = ">=2017.4.17"
 charset-normalizer = ">=2,<4"
 idna = ">=2.5,<4"
-urllib3 = ">=1.21.1,<1.27"
+urllib3 = ">=1.21.1,<3"
 
 [package.extras]
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
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 ]
 
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+optional = false
+python-versions = ">=3.8"
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-
 [[package]]
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@@ -1862,18 +1930,6 @@ files = [
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 [[package]]
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@@ -1924,221 +1980,55 @@ docs = ["sphinx (<5)", "sphinx-rtd-theme"]
 keepalive = ["keepalive (>=0.5)"]
 pandas = ["pandas (>=1.3.5)"]
 
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-test = ["cython", "html5lib", "pytest (>=4.6)"]
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 [package.dependencies]
@@ -2165,21 +2055,10 @@ postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
 postgresql-psycopg = ["psycopg (>=3.0.7)"]
 postgresql-psycopg2binary = ["psycopg2-binary"]
 postgresql-psycopg2cffi = ["psycopg2cffi"]
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 pymysql = ["pymysql"]
 sqlcipher = ["sqlcipher3-binary"]
 
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-category = "main"
-optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-files = [
-    {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
-    {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
-]
-
 [[package]]
 name = "tomli"
 version = "2.0.1"
@@ -2194,94 +2073,97 @@ files = [
 
 [[package]]
 name = "tox"
-version = "3.28.0"
+version = "4.7.0"
 description = "tox is a generic virtualenv management and test command line tool"
-category = "main"
+category = "dev"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+python-versions = ">=3.7"
 files = [
-    {file = "tox-3.28.0-py2.py3-none-any.whl", hash = "sha256:57b5ab7e8bb3074edc3c0c0b4b192a4f3799d3723b2c5b76f1fa9f2d40316eea"},
-    {file = "tox-3.28.0.tar.gz", hash = "sha256:d0d28f3fe6d6d7195c27f8b054c3e99d5451952b54abdae673b71609a581f640"},
+    {file = "tox-4.7.0-py3-none-any.whl", hash = "sha256:79399a3d4641d1fd15eb6bd62c2f35923988038bf0ecf37a688b5e7a767de7d7"},
+    {file = "tox-4.7.0.tar.gz", hash = "sha256:89120e1568c763924301cfde61ba7d4b5c4615eeb1086d5370deb03e9cf63c41"},
 ]
 
 [package.dependencies]
-colorama = {version = ">=0.4.1", markers = "platform_system == \"Windows\""}
-filelock = ">=3.0.0"
-packaging = ">=14"
-pluggy = ">=0.12.0"
-py = ">=1.4.17"
-six = ">=1.14.0"
-tomli = {version = ">=2.0.1", markers = "python_version >= \"3.7\" and python_version < \"3.11\""}
-virtualenv = ">=16.0.0,<20.0.0 || >20.0.0,<20.0.1 || >20.0.1,<20.0.2 || >20.0.2,<20.0.3 || >20.0.3,<20.0.4 || >20.0.4,<20.0.5 || >20.0.5,<20.0.6 || >20.0.6,<20.0.7 || >20.0.7"
+cachetools = ">=5.3.1"
+chardet = ">=5.1"
+colorama = ">=0.4.6"
+filelock = ">=3.12.2"
+packaging = ">=23.1"
+platformdirs = ">=3.9.1"
+pluggy = ">=1.2"
+pyproject-api = ">=1.5.3"
+tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+virtualenv = ">=20.24.1"
 
 [package.extras]
-docs = ["pygments-github-lexers (>=0.0.5)", "sphinx (>=2.0.0)", "sphinxcontrib-autoprogram (>=0.1.5)", "towncrier (>=18.5.0)"]
-testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "pathlib2 (>=2.3.3)", "psutil (>=5.6.1)", "pytest (>=4.0.0)", "pytest-cov (>=2.5.1)", "pytest-mock (>=1.10.0)", "pytest-randomly (>=1.0.0)"]
+docs = ["furo (>=2023.5.20)", "sphinx (>=7.0.1)", "sphinx-argparse-cli (>=1.11.1)", "sphinx-autodoc-typehints (>=1.23.3,!=1.23.4)", "sphinx-copybutton (>=0.5.2)", "sphinx-inline-tabs (>=2023.4.21)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+testing = ["build[virtualenv] (>=0.10)", "covdefaults (>=2.3)", "detect-test-pollution (>=1.1.1)", "devpi-process (>=0.3.1)", "diff-cover (>=7.7)", "distlib (>=0.3.7)", "flaky (>=3.7)", "hatch-vcs (>=0.3)", "hatchling (>=1.17.1)", "psutil (>=5.9.5)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-xdist (>=3.3.1)", "re-assert (>=1.1)", "time-machine (>=2.10)", "wheel (>=0.40)"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.5.0"
+version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"},
-    {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"},
+    {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
+    {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
 ]
 
 [[package]]
 name = "uri-template"
-version = "1.2.0"
+version = "1.3.0"
 description = "RFC 6570 URI Template Processor"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "uri_template-1.2.0-py3-none-any.whl", hash = "sha256:f1699c77b73b925cf4937eae31ab282a86dc885c333f2e942513f08f691fc7db"},
-    {file = "uri_template-1.2.0.tar.gz", hash = "sha256:934e4d09d108b70eb8a24410af8615294d09d279ce0e7cbcdaef1bd21f932b06"},
+    {file = "uri-template-1.3.0.tar.gz", hash = "sha256:0e00f8eb65e18c7de20d595a14336e9f337ead580c70934141624b6d1ffdacc7"},
+    {file = "uri_template-1.3.0-py3-none-any.whl", hash = "sha256:a44a133ea12d44a0c0f06d7d42a52d71282e77e2f937d8abd5655b8d56fc1363"},
 ]
 
 [package.extras]
-dev = ["flake8 (<4.0.0)", "flake8-annotations", "flake8-bugbear", "flake8-commas", "flake8-comprehensions", "flake8-continuation", "flake8-datetimez", "flake8-docstrings", "flake8-import-order", "flake8-literal", "flake8-noqa", "flake8-requirements", "flake8-type-annotations", "flake8-use-fstring", "mypy", "pep8-naming"]
+dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake8-commas", "flake8-comprehensions", "flake8-continuation", "flake8-datetimez", "flake8-docstrings", "flake8-import-order", "flake8-literal", "flake8-modern-annotations", "flake8-noqa", "flake8-pyproject", "flake8-requirements", "flake8-typechecking-import", "flake8-use-fstring", "mypy", "pep8-naming", "types-PyYAML"]
 
 [[package]]
 name = "urllib3"
-version = "1.26.15"
+version = "2.0.4"
 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.*"
+python-versions = ">=3.7"
 files = [
-    {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"},
-    {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"},
+    {file = "urllib3-2.0.4-py3-none-any.whl", hash = "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4"},
+    {file = "urllib3-2.0.4.tar.gz", hash = "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.21.0"
+version = "20.24.2"
 description = "Virtual Python Environment builder"
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.21.0-py3-none-any.whl", hash = "sha256:31712f8f2a17bd06234fa97fdf19609e789dd4e3e4bf108c3da71d710651adbc"},
-    {file = "virtualenv-20.21.0.tar.gz", hash = "sha256:f50e3e60f990a0757c9b68333c9fdaa72d7188caa417f96af9e52407831a3b68"},
+    {file = "virtualenv-20.24.2-py3-none-any.whl", hash = "sha256:43a3052be36080548bdee0b42919c88072037d50d56c28bd3f853cbe92b953ff"},
+    {file = "virtualenv-20.24.2.tar.gz", hash = "sha256:fd8a78f46f6b99a67b7ec5cf73f92357891a7b3a40fd97637c27f854aae3b9e0"},
 ]
 
 [package.dependencies]
-distlib = ">=0.3.6,<1"
-filelock = ">=3.4.1,<4"
-platformdirs = ">=2.4,<4"
+distlib = ">=0.3.7,<1"
+filelock = ">=3.12.2,<4"
+platformdirs = ">=3.9.1,<4"
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
-test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx (>=7.0.1)", "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]]
 name = "watchdog"
@@ -2325,16 +2207,20 @@ watchmedo = ["PyYAML (>=3.10)"]
 
 [[package]]
 name = "webcolors"
-version = "1.12"
-description = "A library for working with color names and color values formats defined by HTML and CSS."
+version = "1.13"
+description = "A library for working with the color formats defined by HTML and CSS."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "webcolors-1.12-py3-none-any.whl", hash = "sha256:d98743d81d498a2d3eaf165196e65481f0d2ea85281463d856b1e51b09f62dce"},
-    {file = "webcolors-1.12.tar.gz", hash = "sha256:16d043d3a08fd6a1b1b7e3e9e62640d09790dce80d2bdd4792a175b35fe794a9"},
+    {file = "webcolors-1.13-py3-none-any.whl", hash = "sha256:29bc7e8752c0a1bd4a1f03c14d6e6a72e93d82193738fa860cbff59d0fcc11bf"},
+    {file = "webcolors-1.13.tar.gz", hash = "sha256:c225b674c83fa923be93d235330ce0300373d02885cef23238813b0d5668304a"},
 ]
 
+[package.extras]
+docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"]
+tests = ["pytest", "pytest-cov"]
+
 [[package]]
 name = "wrapt"
 version = "1.15.0"
@@ -2422,21 +2308,21 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.15.0"
+version = "3.16.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
-    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
+    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
+    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.8"
-content-hash = "e0ea0a8d03495c9518cc714eb24f8606ba13a0cde62ba5ca5fbb20962a1b68b3"
+content-hash = "b86b3c3b9fbee1ec102fef19e208a60f82d2d1ad4ac2aeaa00476d915e7ff062"
diff --git a/pyproject.toml b/pyproject.toml
index 57ff531..1445a07 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,17 +37,17 @@ linkml-data2owl = "linkml_owl.dumpers.owl_dumper:cli"
 python = "^3.8"
 
 click = "*"
-funowl = "0.1.12"
-Jinja2 = "^3.0.3"
-linkml = "^1.3.0"
-linkml-runtime = "^1.3.4"
+funowl = ">=0.2.3"
+Jinja2 = ">=3.0.3"
+linkml = ">=1.3.0"
+linkml-runtime = ">=1.3.4"
 
 [tool.poetry.dev-dependencies]
-tox = "^3.24.5"
-pytest = "^6.2.5"
-pytest-cov = "^3.0.0"
-mkdocs = "^1.2.3"
-black = "^22.10.0"
+tox = ">=3.24.5"
+pytest = ">=6.2.5"
+pytest-cov = ">=3.0.0"
+mkdocs = ">=1.2.3"
+black = ">=22.10.0"
 
 [build-system]
 requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]


Test patch:
diff --git a/tests/inputs/behavior.yaml b/tests/inputs/behavior.yaml
new file mode 100644
index 0000000..452d222
--- /dev/null
+++ b/tests/inputs/behavior.yaml
@@ -0,0 +1,162 @@
+ontology: behavior
+description: Multimodal behavior ontology
+roots:
+  NeuralPathway:
+    aliases:
+      - neural circuit
+    description: a series of connected neuronal activities where neurons send signals from one part of the brain to another.
+    children:
+      DopamineRewardPathway:
+        aliases: [Dopamine Pathway, Reward Pathway]
+        description: A neural pathway that, when activated, causes a reward signal to be sent to the brain, via the release of dopamine.
+      MesolimbicPathway:
+        aliases: [Mesolimbic Pathway, Mesolimbic Reward Pathway]
+        description: A neural pathway that, when activated, causes a reward signal to be sent to the brain, via the release of dopamine.
+      DrosophilaCourtshipNeuralCircuit:
+        references:
+          - PMID:23021897 # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563961/
+  MentalObject:
+    sources:
+      - MF
+    observable: false
+    description: A mental object is an object that exists in the mind.
+    children:
+      Memory:
+        description: A mental object that involves remembering something.
+  MentalState:
+    sources:
+      - MF
+      - MFOEM
+    observable: false
+    description: A mental state is a state of mind that an organism can be in at a given time.
+    children:
+      Perceiving:
+        description: A mental state that involves perceiving something.
+      Aggressive:
+      Hungry:
+  MentalProcess:
+    sources:
+      - MF
+    observable: false
+    description: A mental process is a process that an organism can undergo.
+    children:
+      Daydreaming:
+        description: A mental process that involves daydreaming.
+  Movement:
+    sources:
+      - NBO
+    observable: true
+    aliases:
+      - Kinesthetic Behavior
+    description: "Movement behavior of the body or its parts."
+    exact_mappings:
+      - NBO:0000338
+    children:
+      BodyPartMovement:
+        description: "A change of place or position of part of an organism that does not involve the entire organism [NBO:SMAC]"
+      WholeBodyMovement:
+        description: "A change of place or position of an entire organism"
+      CoordinatedSeriesOfMovements:
+        description: "A series of movements that are coordinated with each other"
+        children:
+          FlappingAppendanges:
+            description: "A coordinated series of movements involving repeated..."
+          Dancing:
+            description: "A coordinated series of movements that are performed in a rhythmic way"
+            defined_subclasses_by:
+              objective:
+                CourtshipDancing:
+                  description: "A coordinated series of movements that are performed in a rhythmic way that is used for courtship"
+                  differentia: Courtship
+          LocomotoryBehavior:
+            children:
+              Walking:
+              Running:
+              Swimming:
+              Flying:
+  BehavioralObjective:
+    sources:
+      - NBO but with rearrangement
+    children:
+      Playing:
+        characteristics:
+          - InvolvesOtherOrganismsOfSameSpecies
+      Communication:
+        #characteristics:
+        #  - InvolvesOtherOrganismsOfSameSpecies
+        children:
+          Gesturing:
+          Vocalizing:
+      Predation:
+        characteristics:
+          - InvolvesOtherOrganisms
+      Escape:
+        characteristics:
+          - InvolvesOtherOrganisms
+      Submission:
+      Cannibalism:
+      Suicide:
+      Grooming:
+        sources:
+          - BCIO
+        children:
+          SelfGrooming:
+            characteristics:
+              - InvolvesSelfOnly
+          GroomingOfOthers:
+            characteristics:
+              - InvolvesOthers
+      Killing:
+        children:
+          KillingOrganismOfSameSpecies:
+            children:
+              KillingOfPersonByPerson:
+                aliases:
+                  - Homicide
+                  - Murder
+      SocialObjective:
+        children:
+          FinancialObjective:
+            children:
+              Payment:
+  Learning:
+    sources:
+      - NBO
+  Memory:
+    sources:
+      - NBO
+  MultiOrganismProcess:
+    children:
+      Predation:
+  BehaviorPattern:
+    children:
+      SmokingPattern:
+  BehavioralCharacteristic:
+    children:
+      InvolvesSelfOnly:
+      InvolvesOthers:
+        children:
+          InvolvesOtherOrganismsOfSameSpecies:
+            children:
+              Interpersonal:
+defined_classes:
+  AddictiveBehavior:
+    type: BehaviorByMentalDisposition
+    genus: Behavior
+    disposition: Addiction
+  DrosophilaCourtshipBehavior:
+    description: >-
+      Drosophila males display a complex repertoire of behaviors that have evolved to achieve reproductive success. 
+      This includes following the female, tapping her with his forelegs, 
+      contacting her genitalia with his mouthparts, 
+      singing a species-specific courtship song, and bending his abdomen to copulate [3]. 
+      It is presumed that Drosophila females assess a courting male by ‘summating’ 
+      sensory cues for species type and fitness before sanctioning mating [3].
+      A virgin female has the ability to be unreceptive to and resist the courtship of 
+      a Drosophila male by exhibiting rejection behaviors, which include extruding her ovipositor, 
+      kicking, or decamping [3–6]. 
+      If she decides to accept the male, she slows down, ceases rejection behaviors and opens her vaginal plate 
+      for copulation [3]. After successful copulation, mated females become temporarily sexually unreceptive
+      to further copulatory attempts, increasing their rate of egg-laying (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563961/)
+    type: BehaviorByNeuralCircuit
+    genus: ...
diff --git a/tests/inputs/expected_ro.ofn b/tests/inputs/expected_ro.ofn
index f64e2b2..77ab071 100644
--- a/tests/inputs/expected_ro.ofn
+++ b/tests/inputs/expected_ro.ofn
@@ -1,8 +1,8 @@
-Prefix( xml: = <http://www.w3.org/XML/1998/namespace> )
+Prefix( owl: = <http://www.w3.org/2002/07/owl#> )
 Prefix( rdf: = <http://www.w3.org/1999/02/22-rdf-syntax-ns#> )
 Prefix( rdfs: = <http://www.w3.org/2000/01/rdf-schema#> )
 Prefix( xsd: = <http://www.w3.org/2001/XMLSchema#> )
-Prefix( owl: = <http://www.w3.org/2002/07/owl#> )
+Prefix( xml: = <http://www.w3.org/XML/1998/namespace> )
 Prefix( linkml: = <https://w3id.org/linkml/> )
 Prefix( rometa: = <http://purl.obolibrary.org/obo/ro/ro-metamodel/> )
 Prefix( biolink: = <https://w3id.org/biolink/vocab/> )
@@ -10,6 +10,7 @@ Prefix( SO: = <http://purl.obolibrary.org/obo/SO_> )
 Prefix( GO: = <http://purl.obolibrary.org/obo/GO_> )
 Prefix( BFO: = <http://purl.obolibrary.org/obo/BFO_> )
 Prefix( IAO: = <http://purl.obolibrary.org/obo/IAO_> )
+Prefix( CARO: = <http://purl.obolibrary.org/obo/CARO_> )
 Prefix( RO: = <http://purl.obolibrary.org/obo/RO_> )
 Prefix( PATO: = <http://purl.obolibrary.org/obo/PATO_> )
 Prefix( NCBITaxon: = <http://purl.obolibrary.org/obo/NCBITaxon_> )
@@ -20,39 +21,39 @@ Prefix( dcterms: = <http://purl.org/dc/terms/> )
 Prefix( orcid: = <https://orcid.org/> )
 
 Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
-    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/BFO_0000051> "Inverse of BFO:0000050 part of" )
+    AnnotationAssertion( IAO:0000115 BFO:0000051 "Inverse of BFO:0000050 part of" )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/BFO_0000050> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/BFO_0000050> "part of" )
     AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/BFO_0000050> "a core relation that holds between a part and its whole" )
-    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/BFO_0000050> rometa:ObjectProperty )
+    AnnotationAssertion( dcterms:conformsTo BFO:0000050 rometa:ObjectProperty )
     SubObjectPropertyOf( <http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/RO_0002131> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/BFO_0000051> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/BFO_0000051> "has part" )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000051> )
     TransitiveObjectProperty( <http://purl.obolibrary.org/obo/BFO_0000050> )
     SubObjectPropertyOf(     ObjectPropertyChain(
-        <http://purl.obolibrary.org/obo/BFO_0000051>
-        <http://purl.obolibrary.org/obo/BFO_0000050>
-    ) <http://purl.obolibrary.org/obo/RO_0002131> )
+        BFO:0000051
+        BFO:0000050
+    ) RO:0002131 )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002131> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002131> "overlaps" )
     AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002131> "a core relation that holds between a part and its whole" )
-    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0002131> rometa:DefinedObjectPropertyByChain )
+    AnnotationAssertion( dcterms:conformsTo RO:0002131 rometa:DefinedObjectPropertyByChain )
     SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0002131> <http://purl.obolibrary.org/obo/RO_0002323> )
     SymmetricObjectProperty( <http://purl.obolibrary.org/obo/RO_0002131> )
     SubObjectPropertyOf(     ObjectPropertyChain(
-        <http://purl.obolibrary.org/obo/RO_0000052>
-        <http://purl.obolibrary.org/obo/BFO_0000050>
-    ) <http://purl.obolibrary.org/obo/RO_0002314> )
+        RO:0000052
+        BFO:0000050
+    ) RO:0002314 )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002314> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002314> "characteristic of part of" )
     AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002314> "A relationship between a characteristic and an entity where the characteristic is of either the entity itself or a part of the entity" )
-    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0002314> rometa:DefinedObjectPropertyByChain )
-    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002203> "Inverse of RO:0002202 develops from" )
+    AnnotationAssertion( dcterms:conformsTo RO:0002314 rometa:DefinedObjectPropertyByChain )
+    AnnotationAssertion( IAO:0000115 RO:0002203 "Inverse of RO:0002202 develops from" )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002202> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002202> "develops from" )
     AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002202> "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" )
-    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0002202> rometa:TransitiveForm )
+    AnnotationAssertion( dcterms:conformsTo RO:0002202 rometa:TransitiveForm )
     SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/RO_0002258> )
     ObjectPropertyDomain( <http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/BFO_0000004> )
     ObjectPropertyRange( <http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/BFO_0000004> )
@@ -60,10 +61,10 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002203> "develops into" )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/RO_0002203> )
     TransitiveObjectProperty( <http://purl.obolibrary.org/obo/RO_0002202> )
-    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_9999998> "Inverse of RO:0002012 occurrent part of" )
+    AnnotationAssertion( IAO:0000115 RO:9999998 "Inverse of RO:0002012 occurrent part of" )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002012> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002012> "occurrent part of" )
-    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0002012> rometa:DefinedObjectPropertyByDomainAndRange )
+    AnnotationAssertion( dcterms:conformsTo RO:0002012 rometa:DefinedObjectPropertyByDomainAndRange )
     SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0002012> <http://purl.obolibrary.org/obo/BFO_0000050> )
     ObjectPropertyDomain( <http://purl.obolibrary.org/obo/RO_0002012> <http://purl.obolibrary.org/obo/BFO_0000003> )
     ObjectPropertyRange( <http://purl.obolibrary.org/obo/RO_0002012> <http://purl.obolibrary.org/obo/BFO_0000003> )
@@ -73,46 +74,46 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002104> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002104> "has plasma membrane part" )
     AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002104> "A part-of relationship between two material entities where there is a plasma membrane intermediate, such that the larger material entity has a plasma membrane as part, and the plasma membrane has the smaller entity as part" )
-    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0002104> rometa:DefinedTransitiveObjectPropertyByIntermediary )
-    ObjectPropertyDomain( <http://purl.obolibrary.org/obo/RO_0002104> CARO:0000006 )
-    ObjectPropertyRange( <http://purl.obolibrary.org/obo/RO_0002104> CARO:0000006 )
-    SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0002481> <http://purl.obolibrary.org/obo/RO_0002564> )
-    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002481> "Helper relation for OWL definition of RO:0002447 phosphorylates" )
+    AnnotationAssertion( dcterms:conformsTo RO:0002104 rometa:DefinedTransitiveObjectPropertyByIntermediary )
+    ObjectPropertyDomain( <http://purl.obolibrary.org/obo/RO_0002104> <http://purl.obolibrary.org/obo/CARO_0000006> )
+    ObjectPropertyRange( <http://purl.obolibrary.org/obo/RO_0002104> <http://purl.obolibrary.org/obo/CARO_0000006> )
+    AnnotationAssertion( IAO:0000115 RO:9999999 "Inverse of RO:0002447 phosphorylates" )
+    SubObjectPropertyOf( RO:0002481 RO:0002564 )
+    AnnotationAssertion( IAO:0000115 RO:0002481 "Helper relation for OWL definition of RO:0002447 phosphorylates" )
     SubObjectPropertyOf(     ObjectPropertyChain(
-        <http://purl.obolibrary.org/obo/RO_0002215>
-        <http://purl.obolibrary.org/obo/RO_0002481>
-        <http://purl.obolibrary.org/obo/RO_0002400>
-    ) <http://purl.obolibrary.org/obo/RO_0002447> )
-    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_9999999> "Inverse of RO:0002447 phosphorylates" )
+        RO:0002215
+        RO:0002481
+        RO:0002400
+    ) RO:0002447 )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002447> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002447> "phosphorylates" )
     AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002447> "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a kinase activity that takes the object as input" )
     AnnotationAssertion( dcterms:contributor <http://purl.obolibrary.org/obo/RO_0002447> orcid:0000-0002-6601-2165 )
-    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0002447> rometa:ObjectPropertyDefinedByInteractionProcess )
+    AnnotationAssertion( dcterms:conformsTo RO:0002447 rometa:ObjectPropertyDefinedByInteractionProcess )
     SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0002447> <http://purl.obolibrary.org/obo/RO_0002436> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_9999999> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_9999999> "phosphorylated by" )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0002447> <http://purl.obolibrary.org/obo/RO_9999999> )
-    SubClassOf( <http://purl.obolibrary.org/obo/GO_0016301>     ObjectHasSelf( <http://purl.obolibrary.org/obo/RO_0002481> ) )
+    SubClassOf( GO:0016301     ObjectHasSelf( RO:0002481 ) )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002481> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002481> "is kinase activity" )
-    SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0018001> <http://purl.obolibrary.org/obo/RO_0002564> )
-    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0018001> "Helper relation for OWL definition of RO:0018002 myristoylates" )
+    AnnotationAssertion( IAO:0000115 RO:0018003 "Inverse of RO:0018002 myristoylates" )
+    SubObjectPropertyOf( RO:0018001 RO:0002564 )
+    AnnotationAssertion( IAO:0000115 RO:0018001 "Helper relation for OWL definition of RO:0018002 myristoylates" )
     SubObjectPropertyOf(     ObjectPropertyChain(
-        <http://purl.obolibrary.org/obo/RO_0002215>
-        <http://purl.obolibrary.org/obo/RO_0018001>
-        <http://purl.obolibrary.org/obo/RO_0002400>
-    ) <http://purl.obolibrary.org/obo/RO_0018002> )
-    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0018003> "Inverse of RO:0018002 myristoylates" )
+        RO:0002215
+        RO:0018001
+        RO:0002400
+    ) RO:0018002 )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0018002> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0018002> "myristoylates" )
     AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0018002> "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" )
-    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0018002> rometa:ObjectPropertyDefinedByInteractionProcess )
+    AnnotationAssertion( dcterms:conformsTo RO:0018002 rometa:ObjectPropertyDefinedByInteractionProcess )
     SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0018002> <http://purl.obolibrary.org/obo/RO_0002436> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0018003> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0018003> "myristoylated by" )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0018002> <http://purl.obolibrary.org/obo/RO_0018003> )
-    SubClassOf( <http://purl.obolibrary.org/obo/GO_0019107>     ObjectHasSelf( <http://purl.obolibrary.org/obo/RO_0018001> ) )
+    SubClassOf( GO:0019107     ObjectHasSelf( RO:0018001 ) )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0018001> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0018001> "is myristoyltransferase activity" )
 )
\ No newline at end of file
diff --git a/tests/inputs/monsters_and_magic.expected.ofn b/tests/inputs/monsters_and_magic.expected.ofn
index a67ebfe..194b75d 100644
--- a/tests/inputs/monsters_and_magic.expected.ofn
+++ b/tests/inputs/monsters_and_magic.expected.ofn
@@ -1,8 +1,8 @@
-Prefix( xml: = <http://www.w3.org/XML/1998/namespace> )
+Prefix( owl: = <http://www.w3.org/2002/07/owl#> )
 Prefix( rdf: = <http://www.w3.org/1999/02/22-rdf-syntax-ns#> )
 Prefix( rdfs: = <http://www.w3.org/2000/01/rdf-schema#> )
 Prefix( xsd: = <http://www.w3.org/2001/XMLSchema#> )
-Prefix( owl: = <http://www.w3.org/2002/07/owl#> )
+Prefix( xml: = <http://www.w3.org/XML/1998/namespace> )
 Prefix( mnm: = <https://w3id.org/cmungall/monsters-and-magic/> )
 Prefix( linkml: = <https://w3id.org/linkml/> )
 Prefix( biolink: = <https://w3id.org/biolink/> )
@@ -10,6 +10,7 @@ Prefix( schema: = <http://schema.org/> )
 Prefix( PATO: = <http://purl.obolibrary.org/obo/PATO_> )
 Prefix( example: = <https://example.org/> )
 Prefix( foaf: = <http://xmlns.com/foaf/0.1/> )
+Prefix( wgs84: = <http://www.w3.org/2003/01/geo/wgs84_pos#> )
 
 Ontology( <https://w3id.org/cmungall/monsters-and-magic>
     Declaration( Class( mnm:Creature ) )
@@ -86,10 +87,12 @@ Ontology( <https://w3id.org/cmungall/monsters-and-magic>
     AnnotationAssertion( schema:description mnm:Zombie "A zombie is a fictional undead creature in the Dungeons & Dragons fantasy role-playing game." )
     SubClassOf( mnm:Zombie mnm:UndeadCreature )
     Declaration( NamedIndividual( mnm:Smaug ) )
+    Declaration( Class( mnm:Smaug ) )
     AnnotationAssertion( schema:description mnm:Smaug "Smaug is a fictional dragon from J. R. R. Tolkien's The Hobbit." )
     ObjectPropertyAssertion( mnm:has_location mnm:Smaug mnm:LonelyMountain )
     ClassAssertion( mnm:RedDragon mnm:Smaug )
     Declaration( NamedIndividual( mnm:TheNightKing ) )
+    Declaration( Class( mnm:TheNightKing ) )
     AnnotationAssertion( schema:description mnm:TheNightKing "The Night King is a fictional character in the HBO fantasy television series Game of Thrones." )
     ObjectPropertyAssertion( mnm:has_location mnm:TheNightKing mnm:Winterfell )
     ClassAssertion( mnm:WhiteWalker mnm:TheNightKing )
@@ -153,57 +156,69 @@ Ontology( <https://w3id.org/cmungall/monsters-and-magic>
     AnnotationAssertion( schema:description mnm:Thief "A thief is a person who steals things." )
     SubClassOf( mnm:Thief mnm:Rogue )
     Declaration( NamedIndividual( mnm:Gandalf ) )
+    Declaration( Class( mnm:Gandalf ) )
     AnnotationAssertion( schema:description mnm:Gandalf "Gandalf is a wizard in Middle-earth." )
     ObjectPropertyAssertion( mnm:alignment mnm:Gandalf mnm:LAWFUL_GOOD )
     ObjectPropertyAssertion( mnm:originates_from mnm:Gandalf mnm:MiddleEarth )
     ClassAssertion( mnm:Wizard mnm:Gandalf )
     Declaration( NamedIndividual( mnm:Aragorn ) )
+    Declaration( Class( mnm:Aragorn ) )
     AnnotationAssertion( schema:description mnm:Aragorn "Aragorn is a ranger in Middle-earth." )
     ObjectPropertyAssertion( mnm:alignment mnm:Aragorn mnm:NEUTRAL_GOOD )
     ObjectPropertyAssertion( mnm:originates_from mnm:Aragorn mnm:MiddleEarth )
     ClassAssertion( mnm:Ranger mnm:Aragorn )
     Declaration( NamedIndividual( mnm:Hawkmoon ) )
+    Declaration( Class( mnm:Hawkmoon ) )
     AnnotationAssertion( schema:description mnm:Hawkmoon "Hawkmoon is a paladin in Middle-earth." )
     ClassAssertion( mnm:Paladin mnm:Hawkmoon )
     Declaration( NamedIndividual( mnm:Elric ) )
+    Declaration( Class( mnm:Elric ) )
     AnnotationAssertion( schema:description mnm:Elric "Elric is a necromancer in Middle-earth." )
     ObjectPropertyAssertion( mnm:alignment mnm:Elric mnm:CHAOTIC_NEUTRAL )
     ClassAssertion( mnm:Necromancer mnm:Elric )
     Declaration( NamedIndividual( mnm:Fafhrd ) )
+    Declaration( Class( mnm:Fafhrd ) )
     AnnotationAssertion( schema:description mnm:Fafhrd "Fafhrd is a thief in Nehwon." )
     ObjectPropertyAssertion( mnm:alignment mnm:Fafhrd mnm:CHAOTIC_GOOD )
     ObjectPropertyAssertion( mnm:originates_from mnm:Fafhrd mnm:DyingEarth )
     ClassAssertion( mnm:Thief mnm:Fafhrd )
     Declaration( NamedIndividual( mnm:TheGreyMouser ) )
+    Declaration( Class( mnm:TheGreyMouser ) )
     AnnotationAssertion( schema:description mnm:TheGreyMouser "The Grey Mouser is a thief in Nehwon." )
     ObjectPropertyAssertion( mnm:alignment mnm:TheGreyMouser mnm:CHAOTIC_GOOD )
     ObjectPropertyAssertion( mnm:originates_from mnm:TheGreyMouser mnm:DyingEarth )
     ClassAssertion( mnm:Thief mnm:TheGreyMouser )
     Declaration( NamedIndividual( mnm:Conan ) )
+    Declaration( Class( mnm:Conan ) )
     AnnotationAssertion( schema:description mnm:Conan "Conan is a barbarian in Cimmeria." )
     ObjectPropertyAssertion( mnm:originates_from mnm:Conan mnm:Cimmeria )
     ClassAssertion( mnm:Barbarian mnm:Conan )
     Declaration( NamedIndividual( mnm:Vecna ) )
+    Declaration( Class( mnm:Vecna ) )
     AnnotationAssertion( schema:description mnm:Vecna "Vecna is a lich in Middle-earth." )
     ObjectPropertyAssertion( mnm:alignment mnm:Vecna mnm:LAWFUL_EVIL )
     ObjectPropertyAssertion( mnm:originates_from mnm:Vecna mnm:MiddleEarth )
     ClassAssertion( mnm:Lich mnm:Vecna )
     Declaration( NamedIndividual( mnm:HarryPotter ) )
+    Declaration( Class( mnm:HarryPotter ) )
     AnnotationAssertion( schema:description mnm:HarryPotter "Harry Potter is a wizard in the Wizarding World." )
     ObjectPropertyAssertion( mnm:alignment mnm:HarryPotter mnm:NEUTRAL_GOOD )
     ObjectPropertyAssertion( mnm:originates_from mnm:HarryPotter mnm:WizardingWorld )
     ClassAssertion( mnm:Wizard mnm:HarryPotter )
     Declaration( NamedIndividual( mnm:Littlefinger ) )
+    Declaration( Class( mnm:Littlefinger ) )
     AnnotationAssertion( schema:description mnm:Littlefinger "Littlefinger is a noble in Westeros." )
     ObjectPropertyAssertion( mnm:alignment mnm:Littlefinger mnm:CHAOTIC_EVIL )
     ObjectPropertyAssertion( mnm:originates_from mnm:Littlefinger mnm:Westeros )
     ClassAssertion( mnm:Noble mnm:Littlefinger )
     Declaration( NamedIndividual( mnm:Severian ) )
+    Declaration( Class( mnm:Severian ) )
     AnnotationAssertion( schema:description mnm:Severian "Severian is a torturer in the Commonwealth." )
     ObjectPropertyAssertion( mnm:alignment mnm:Severian mnm:NEUTRAL_GOOD )
     ObjectPropertyAssertion( mnm:originates_from mnm:Severian mnm:Commonwealth )
     ClassAssertion( mnm:Torturer mnm:Severian )
     Declaration( NamedIndividual( mnm:TheAutarch ) )
+    Declaration( Class( mnm:TheAutarch ) )
     AnnotationAssertion( schema:description mnm:TheAutarch "The Autarch is a Monarch in the Commonwealth." )
     ObjectPropertyAssertion( mnm:originates_from mnm:TheAutarch mnm:Commonwealth )
     ClassAssertion( mnm:Monarch mnm:TheAutarch )
@@ -248,21 +263,30 @@ Ontology( <https://w3id.org/cmungall/monsters-and-magic>
     AnnotationAssertion( schema:description mnm:Throne "A throne is a chair that is used by a king or queen." )
     SubClassOf( mnm:Throne mnm:ManufacturedArtifact )
     Declaration( NamedIndividual( mnm:TheRing ) )
+    Declaration( Class( mnm:TheRing ) )
     AnnotationAssertion( schema:description mnm:TheRing "The Ring is a fictional magical ring that appears in J. R. R. Tolkien's The Lord of the Rings." )
     ObjectPropertyAssertion( mnm:has_location mnm:TheRing mnm:MountDoom )
     ClassAssertion( mnm:Ring mnm:TheRing )
     Declaration( NamedIndividual( mnm:TheIronThrone ) )
+    Declaration( Class( mnm:TheIronThrone ) )
     AnnotationAssertion( schema:description mnm:TheIronThrone "The Iron Throne is a fictional throne that appears in George R. R. Martin's A Song of Ice and Fire." )
     ObjectPropertyAssertion( mnm:has_location mnm:TheIronThrone mnm:KingsLanding )
     ClassAssertion( mnm:Throne mnm:TheIronThrone )
     Declaration( NamedIndividual( mnm:TerminusEst ) )
+    Declaration( Class( mnm:TerminusEst ) )
     AnnotationAssertion( schema:description mnm:TerminusEst "Terminus Est is a fictional sword that appears in Gene Wolfe's The Book of the New Sun." )
     ClassAssertion( mnm:BastardSword mnm:TerminusEst )
+    Declaration( Class( mnm:InvisibilitySpell ) )
     AnnotationAssertion( schema:description mnm:InvisibilitySpell "An invisibility spell makes a character invisible." )
+    Declaration( Class( mnm:FireballSpell ) )
     AnnotationAssertion( schema:description mnm:FireballSpell "A fireball spell causes a fireball to appear and explode." )
+    Declaration( Class( mnm:LightningBoltSpell ) )
     AnnotationAssertion( schema:description mnm:LightningBoltSpell "A lightning bolt spell causes a lightning bolt to appear and strike a target." )
+    Declaration( Class( mnm:PerceptionSkill ) )
     AnnotationAssertion( schema:description mnm:PerceptionSkill "Perception is a measure of a character's ability to notice things." )
+    Declaration( Class( mnm:StealthSkill ) )
     AnnotationAssertion( schema:description mnm:StealthSkill "Stealth is a measure of a character's ability to hide." )
+    Declaration( Class( mnm:AcrobaticsSkill ) )
     AnnotationAssertion( schema:description mnm:AcrobaticsSkill "Acrobatics is a measure of a character's ability to perform acrobatic stunts." )
     Declaration( Class( mnm:Location ) )
     Declaration( Class( mnm:World ) )
@@ -336,77 +360,97 @@ Ontology( <https://w3id.org/cmungall/monsters-and-magic>
     AnnotationAssertion( schema:description mnm:Necropolis "A necropolis is a city of the dead." )
     SubClassOf( mnm:Necropolis mnm:City )
     Declaration( NamedIndividual( mnm:MiddleEarth ) )
+    Declaration( Class( mnm:MiddleEarth ) )
     AnnotationAssertion( schema:description mnm:MiddleEarth "Middle-earth is a fictional setting created by J. R. R. Tolkien." )
     ClassAssertion( mnm:World mnm:MiddleEarth )
     Declaration( NamedIndividual( mnm:Hyboria ) )
+    Declaration( Class( mnm:Hyboria ) )
     AnnotationAssertion( schema:description mnm:Hyboria "Hyboria is a fictional setting created by Robert E. Howard." )
     ClassAssertion( mnm:World mnm:Hyboria )
     Declaration( NamedIndividual( mnm:DyingEarth ) )
+    Declaration( Class( mnm:DyingEarth ) )
     AnnotationAssertion( schema:description mnm:DyingEarth "The Dying Earth is a fictional setting created by Jack Vance." )
     ClassAssertion( mnm:World mnm:DyingEarth )
     Declaration( NamedIndividual( mnm:MinasTirith ) )
+    Declaration( Class( mnm:MinasTirith ) )
     AnnotationAssertion( schema:description mnm:MinasTirith "Minas Tirith is a city in Middle-earth." )
     ObjectPropertyAssertion( mnm:part_of mnm:MinasTirith mnm:Gondor )
     ClassAssertion( mnm:City mnm:MinasTirith )
     Declaration( NamedIndividual( mnm:Gondor ) )
+    Declaration( Class( mnm:Gondor ) )
     AnnotationAssertion( schema:description mnm:Gondor "Gondor is a kingdom in Middle-earth." )
     ObjectPropertyAssertion( mnm:part_of mnm:Gondor mnm:MiddleEarth )
     ClassAssertion( mnm:Country mnm:Gondor )
     Declaration( NamedIndividual( mnm:Rivendell ) )
+    Declaration( Class( mnm:Rivendell ) )
     AnnotationAssertion( schema:description mnm:Rivendell "Rivendell is a city in Middle-earth." )
     ObjectPropertyAssertion( mnm:part_of mnm:Rivendell mnm:MiddleEarth )
     ClassAssertion( mnm:City mnm:Rivendell )
     Declaration( NamedIndividual( mnm:Mirkwood ) )
+    Declaration( Class( mnm:Mirkwood ) )
     AnnotationAssertion( schema:description mnm:Mirkwood "Mirkwood is a forest in Middle-earth." )
     ObjectPropertyAssertion( mnm:part_of mnm:Mirkwood mnm:MiddleEarth )
     ClassAssertion( mnm:Forest mnm:Mirkwood )
     Declaration( NamedIndividual( mnm:Moria ) )
+    Declaration( Class( mnm:Moria ) )
     AnnotationAssertion( schema:description mnm:Moria "Moria is a mine in Middle-earth." )
     ObjectPropertyAssertion( mnm:part_of mnm:Moria mnm:MiddleEarth )
     ClassAssertion( mnm:Mine mnm:Moria )
     Declaration( NamedIndividual( mnm:Lankhmar ) )
+    Declaration( Class( mnm:Lankhmar ) )
     AnnotationAssertion( schema:description mnm:Lankhmar "Lankhmar is a city in Nehwon." )
     ObjectPropertyAssertion( mnm:part_of mnm:Lankhmar mnm:Nehwon )
     ClassAssertion( mnm:City mnm:Lankhmar )
     Declaration( NamedIndividual( mnm:Cimmeria ) )
+    Declaration( Class( mnm:Cimmeria ) )
     AnnotationAssertion( schema:description mnm:Cimmeria "Cimmeria is a country in Hyboria." )
     ObjectPropertyAssertion( mnm:part_of mnm:Cimmeria mnm:Hyboria )
     ClassAssertion( mnm:Country mnm:Cimmeria )
     Declaration( NamedIndividual( mnm:WizardingWorld ) )
+    Declaration( Class( mnm:WizardingWorld ) )
     AnnotationAssertion( schema:description mnm:WizardingWorld "The Wizarding World is a fictional setting created by J. K. Rowling." )
     ClassAssertion( mnm:World mnm:WizardingWorld )
     Declaration( NamedIndividual( mnm:Hogwarts ) )
+    Declaration( Class( mnm:Hogwarts ) )
     AnnotationAssertion( schema:description mnm:Hogwarts "Hogwarts is a school in the Wizarding World." )
     ObjectPropertyAssertion( mnm:part_of mnm:Hogwarts mnm:WizardingWorld )
     ClassAssertion( mnm:School mnm:Hogwarts )
     Declaration( NamedIndividual( mnm:Westeros ) )
+    Declaration( Class( mnm:Westeros ) )
     AnnotationAssertion( schema:description mnm:Westeros "Westeros is a country in the Seven Kingdoms." )
     ObjectPropertyAssertion( mnm:part_of mnm:Westeros mnm:TheSevenKingdoms )
     ClassAssertion( mnm:Country mnm:Westeros )
     Declaration( NamedIndividual( mnm:Winterfell ) )
+    Declaration( Class( mnm:Winterfell ) )
     AnnotationAssertion( schema:description mnm:Winterfell "Winterfell is a castle in Westeros." )
     ObjectPropertyAssertion( mnm:part_of mnm:Winterfell mnm:Westeros )
     ClassAssertion( mnm:Castle mnm:Winterfell )
     Declaration( NamedIndividual( mnm:TheSevenKingdoms ) )
+    Declaration( Class( mnm:TheSevenKingdoms ) )
     AnnotationAssertion( schema:description mnm:TheSevenKingdoms "The Seven Kingdoms is a fictional setting created by George R. R. Martin." )
     ClassAssertion( mnm:World mnm:TheSevenKingdoms )
     Declaration( NamedIndividual( mnm:KingsLanding ) )
+    Declaration( Class( mnm:KingsLanding ) )
     AnnotationAssertion( schema:description mnm:KingsLanding "King's Landing is a city in Westeros." )
     ObjectPropertyAssertion( mnm:part_of mnm:KingsLanding mnm:Westeros )
     ClassAssertion( mnm:City mnm:KingsLanding )
     Declaration( NamedIndividual( mnm:Commonwealth ) )
+    Declaration( Class( mnm:Commonwealth ) )
     AnnotationAssertion( schema:description mnm:Commonwealth "The Commonwealth is a country in the Dying Earth." )
     ObjectPropertyAssertion( mnm:part_of mnm:Commonwealth mnm:DyingEarth )
     ClassAssertion( mnm:Country mnm:Commonwealth )
     Declaration( NamedIndividual( mnm:Ascia ) )
+    Declaration( Class( mnm:Ascia ) )
     AnnotationAssertion( schema:description mnm:Ascia "Ascia is a city in the Commonwealth." )
     ObjectPropertyAssertion( mnm:part_of mnm:Ascia mnm:Commonwealth )
     ClassAssertion( mnm:City mnm:Ascia )
     Declaration( NamedIndividual( mnm:MountDoom ) )
+    Declaration( Class( mnm:MountDoom ) )
     AnnotationAssertion( schema:description mnm:MountDoom "Mount Doom is a mountain in Middle-earth." )
     ObjectPropertyAssertion( mnm:part_of mnm:MountDoom mnm:Mordor )
     ClassAssertion( mnm:Mountain mnm:MountDoom )
     Declaration( NamedIndividual( mnm:Mordor ) )
+    Declaration( Class( mnm:Mordor ) )
     AnnotationAssertion( schema:description mnm:Mordor "Mordor is a country in Middle-earth." )
     ObjectPropertyAssertion( mnm:part_of mnm:Mordor mnm:MiddleEarth )
     ClassAssertion( mnm:Country mnm:Mordor )
diff --git a/tests/inputs/monsters_and_magic.yaml b/tests/inputs/monsters_and_magic.yaml
index 803c0ae..5928ae5 100644
--- a/tests/inputs/monsters_and_magic.yaml
+++ b/tests/inputs/monsters_and_magic.yaml
@@ -15,6 +15,10 @@ prefixes:
   PATO: http://purl.obolibrary.org/obo/PATO_
   example: https://example.org/
   foaf: http://xmlns.com/foaf/0.1/
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
+  rdfs: http://www.w3.org/2000/01/rdf-schema#
+  owl: http://www.w3.org/2002/07/owl#
+  wgs84: http://www.w3.org/2003/01/geo/wgs84_pos#
 default_prefix: mnm
 default_range: string
 
@@ -138,6 +142,8 @@ classes:
       - title
       - type
     class_uri: schema:Thing
+    annotations:
+      owl: Class
 
   Agent:
     class_uri: foaf:Agent
diff --git a/tests/inputs/owl_dumper_test.yaml b/tests/inputs/owl_dumper_test.yaml
index 8e0e1e1..35ed152 100644
--- a/tests/inputs/owl_dumper_test.yaml
+++ b/tests/inputs/owl_dumper_test.yaml
@@ -143,10 +143,10 @@ classes:
     aliases:
       - blank node
     is_a: Thing
-    description: abstract grouping for anonymous expressions
+    description: abstract grouping for anonymous class expressions
     abstract: true
     annotations:
-      owl: Class
+      owl: AnonymousClassExpression
   NamedThingWithMatches:
     is_a: NamedThing
     description: test metaclass illustrating generation of skos annotation axioms
diff --git a/tests/inputs/ro-metamodel.yaml b/tests/inputs/ro-metamodel.yaml
index 07dde06..d85bbae 100644
--- a/tests/inputs/ro-metamodel.yaml
+++ b/tests/inputs/ro-metamodel.yaml
@@ -12,6 +12,7 @@ prefixes:
   GO: http://purl.obolibrary.org/obo/GO_
   BFO: http://purl.obolibrary.org/obo/BFO_
   IAO: http://purl.obolibrary.org/obo/IAO_
+  CARO: http://purl.obolibrary.org/obo/CARO_
   RO: http://purl.obolibrary.org/obo/RO_
   PATO: http://purl.obolibrary.org/obo/PATO_
   NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_
diff --git a/tests/output/chromo.schema.owl.ttl b/tests/output/chromo.schema.owl.ttl
index 851b649..5c17a28 100644
--- a/tests/output/chromo.schema.owl.ttl
+++ b/tests/output/chromo.schema.owl.ttl
@@ -22,20 +22,15 @@
         chromoschema:Genome,
         chromoschema:GenomeBuild,
         chromoschema:OrganismTaxon ;
-    dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
-    linkml:generation_date "2023-04-03T17:22:51" ;
-    linkml:metamodel_version "1.7.0" ;
-    linkml:source_file "chromo.yaml" ;
-    linkml:source_file_date "2022-01-12T21:11:50" ;
-    linkml:source_file_size 8532 .
+    linkml:id "https://w3id.org/biodatamodels/chromoschema" ;
+    linkml:imports "linkml:types" .
 
 chromoschema:download_url a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "download_url" ;
     rdfs:range linkml:Uri .
 
-linkml:SubsetDefinition a owl:Class ;
-    rdfs:label "subset_definition" .
+linkml:SubsetDefinition a owl:Class .
 
 linkml:topValue a owl:DatatypeProperty ;
     rdfs:label "value" .
@@ -47,10 +42,10 @@ chromoschema:ChromosomePartCollection a owl:Class,
             owl:allValuesFrom chromoschema:ChromosomePart ;
             owl:onProperty dcterms:hasPart ],
         [ a owl:Restriction ;
-            owl:allValuesFrom chromoschema:Genome ;
+            owl:allValuesFrom chromoschema:OrganismTaxon ;
             owl:onProperty dcterms:hasPart ],
         [ a owl:Restriction ;
-            owl:allValuesFrom chromoschema:OrganismTaxon ;
+            owl:allValuesFrom chromoschema:Genome ;
             owl:onProperty dcterms:hasPart ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
@@ -66,10 +61,7 @@ chromoschema:band_descriptor a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "band_descriptor" ;
     rdfs:range chromoschema:BandDescriptor ;
-    skos:definition "A string representing a chromosome band, e.g. p31.1. This is local to the chromosome, so the chromosome is not included in the descriptor" ;
-    skos:note "for a chromosome, arm this is a single leter, e.g. p or q",
-        "for a chromosome, this is the empty string",
-        "for common species, the usual structure is the band name followed by dot delimited numbers, e.g. p31.1. However, different species have different systems" .
+    skos:definition "A string representing a chromosome band, e.g. p31.1. This is local to the chromosome, so the chromosome is not included in the descriptor" .
 
 chromoschema:chromosome_name a owl:ObjectProperty,
         linkml:SlotDefinition ;
@@ -146,8 +138,7 @@ GO:0005634 a owl:Class,
 
 GO:0005694 a owl:Class,
         chromoschema:EntityType ;
-    rdfs:label "chromosome" ;
-    rdfs:seeAlso "SO:0000340" .
+    rdfs:label "chromosome" .
 
 GO:0005739 a owl:Class,
         chromoschema:LocationType ;
@@ -159,8 +150,7 @@ GO:0030849 a owl:Class,
 
 GO:0098687 a owl:Class,
         chromoschema:EntityType ;
-    rdfs:label "chromosome_part" ;
-    rdfs:seeAlso "SO:0000830" .
+    rdfs:label "chromosome_part" .
 
 OIO:hasBroadSynonym a owl:ObjectProperty,
         linkml:SlotDefinition ;
@@ -175,8 +165,7 @@ rdf:type a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "type" ;
     rdfs:range chromoschema:EntityType ;
-    skos:exactMatch rdf:type ;
-    skos:note "OWL>> SubClassOf" .
+    skos:exactMatch rdf:type .
 
 skos:exactMatch a owl:ObjectProperty,
         linkml:SlotDefinition ;
@@ -206,24 +195,24 @@ chromoschema:Genome a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "Genome" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:allValuesFrom chromoschema:GenomeBuild ;
-            owl:onProperty chromoschema:previous_builds ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass chromoschema:GenomeBuild ;
+            owl:onProperty biolink:genome_build ],
         [ a owl:Restriction ;
             owl:onClass linkml:String ;
             owl:onProperty chromoschema:id ;
             owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:GenomeBuild ;
+            owl:onProperty chromoschema:previous_builds ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:GenomeBuild ;
-            owl:onProperty biolink:genome_build ],
+            owl:onClass chromoschema:TaxonIdentifier ;
+            owl:onProperty RO:0002162 ],
         [ a owl:Restriction ;
             owl:onClass chromoschema:LabelType ;
             owl:onProperty rdfs:label ;
-            owl:qualifiedCardinality 1 ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:TaxonIdentifier ;
-            owl:onProperty RO:0002162 ] ;
+            owl:qualifiedCardinality 1 ] ;
     skos:definition """Represents a sequenced genome, one per species.
 Each genome can be associated with one or more builds""" .
 
@@ -231,17 +220,17 @@ chromoschema:OrganismTaxon a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "OrganismTaxon" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass chromoschema:LabelType ;
+            owl:onProperty rdfs:label ],
+        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass chromoschema:LabelType ;
             owl:onProperty OIO:hasExactSynonym ],
         [ a owl:Restriction ;
             owl:onClass linkml:String ;
             owl:onProperty chromoschema:id ;
-            owl:qualifiedCardinality 1 ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:LabelType ;
-            owl:onProperty rdfs:label ] ;
+            owl:qualifiedCardinality 1 ] ;
     skos:definition "Represents a species, e.g. Homo sapiens" ;
     skos:exactMatch biolink:OrganismTaxon .
 
@@ -264,8 +253,7 @@ RO:0002162 a owl:ObjectProperty,
     rdfs:label "taxon" ;
     rdfs:range chromoschema:TaxonIdentifier ;
     skos:definition "The taxon to which the chromosome part belongs. Always NCBITaxon." ;
-    skos:exactMatch RO:0002162 ;
-    skos:note "OWL>> ObjectSomeValuesFrom" .
+    skos:exactMatch RO:0002162 .
 
 dcterms:hasPart a owl:ObjectProperty,
         linkml:SlotDefinition .
@@ -309,8 +297,7 @@ chromoschema:id a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "id" ;
     rdfs:range linkml:String ;
-    skos:definition "A unique identifier" ;
-    skos:note "will be of form CHR:...." .
+    skos:definition "A unique identifier" .
 
 rdfs:label a owl:ObjectProperty,
         linkml:SlotDefinition ;
@@ -323,79 +310,74 @@ chromoschema:ChromosomePart a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "ChromosomePart" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:BandDescriptor ;
-            owl:onProperty chromoschema:band_descriptor ],
-        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass chromoschema:ChromosomePart ;
             owl:onProperty BFO:0000050 ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom linkml:String ;
-            owl:onProperty OIO:hasExactSynonym ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass chromoschema:ChromosomeNameType ;
             owl:onProperty chromoschema:chromosome_name ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:ChromosomePart ;
+            owl:onProperty BFO:0000051 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:TaxonIdentifier ;
-            owl:onProperty RO:0002162 ],
+            owl:onClass chromoschema:LocationType ;
+            owl:onProperty BFO:0000050 ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom linkml:String ;
+            owl:onProperty OIO:hasExactSynonym ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass chromoschema:SexChromosomeType ;
             owl:onProperty chromoschema:sex_chromosome_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:EntityType ;
-            owl:onProperty rdf:type ],
+            owl:onClass chromoschema:LabelType ;
+            owl:onProperty rdfs:label ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass chromoschema:AutosomeVsSexChromosome ;
+            owl:onProperty chromoschema:somal_type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass linkml:Integer ;
-            owl:onProperty gff:end ],
+            owl:onProperty gff:start ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:LabelType ;
-            owl:onProperty rdfs:label ],
+            owl:onClass linkml:Integer ;
+            owl:onProperty gff:end ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom linkml:Uriorcurie ;
+            owl:onProperty skos:exactMatch ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass chromoschema:GenomeBuild ;
             owl:onProperty biolink:genome_build ],
         [ a owl:Restriction ;
-            owl:allValuesFrom chromoschema:ChromosomePart ;
-            owl:onProperty BFO:0000051 ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass chromoschema:BandDescriptor ;
+            owl:onProperty chromoschema:band_descriptor ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:AutosomeVsSexChromosome ;
-            owl:onProperty chromoschema:somal_type ],
+            owl:onClass chromoschema:TaxonIdentifier ;
+            owl:onProperty RO:0002162 ],
         [ a owl:Restriction ;
             owl:allValuesFrom linkml:String ;
             owl:onProperty OIO:hasBroadSynonym ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:LocationType ;
-            owl:onProperty BFO:0000050 ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass linkml:Integer ;
-            owl:onProperty gff:start ],
+            owl:onClass chromoschema:EntityType ;
+            owl:onProperty rdf:type ],
         [ a owl:Restriction ;
             owl:onClass linkml:String ;
             owl:onProperty chromoschema:id ;
-            owl:qualifiedCardinality 1 ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom linkml:Uriorcurie ;
-            owl:onProperty skos:exactMatch ] ;
-    skos:definition "A Chromosome or a part of a chromosome (includes whole chromosomes, arms, and bands)" ;
-    skos:note """OWL Notes: when translated to OWL, instances of this class will be treated as
-OWL classes, with the superclass determined by the type field""",
-        "OWL>> Class" .
+            owl:qualifiedCardinality 1 ] ;
+    skos:definition "A Chromosome or a part of a chromosome (includes whole chromosomes, arms, and bands)" .
 
-linkml:ClassDefinition a owl:Class ;
-    rdfs:label "class_definition" .
+linkml:ClassDefinition a owl:Class .
 
-linkml:TypeDefinition a owl:Class ;
-    rdfs:label "type_definition" .
+linkml:TypeDefinition a owl:Class .
 
 chromoschema:GenomeBuild a owl:Class,
         linkml:ClassDefinition ;
@@ -425,7 +407,6 @@ chromoschema:SexChromosomeType a owl:Class,
         GO:0000806,
         GO:0000807 .
 
-linkml:SlotDefinition a owl:Class ;
-    rdfs:label "slot_definition" .
+linkml:SlotDefinition a owl:Class .
 
 
diff --git a/tests/test_examples/test_ro_metamodel.py b/tests/test_examples/test_ro_metamodel.py
index cbc95e2..2c8b78b 100644
--- a/tests/test_examples/test_ro_metamodel.py
+++ b/tests/test_examples/test_ro_metamodel.py
@@ -37,7 +37,7 @@ def test_build_relation_ontology(self):
         #print(f'URI = {domain_slot.slot_uri}')
         assert domain_slot.slot_uri == 'rdfs:domain'
         anns = dumper._get_inferred_slot_annotations(domain_slot, 'owl', 'TransitiveForm')
-        print(f'Anns={anns}')
+        #print(f'Anns={anns}')
         assert 'ObjectPropertyDomain' in anns
 
         test_slot = sv.get_slot('inverse_of')
diff --git a/tests/test_examples/test_rpg.py b/tests/test_examples/test_rpg.py
index 5aca081..b73caf7 100644
--- a/tests/test_examples/test_rpg.py
+++ b/tests/test_examples/test_rpg.py
@@ -20,7 +20,12 @@
 
 
 class TestRolePlayGameExample(unittest.TestCase):
-    """Test case using a fantasy RPG example."""
+    """Test case using a fantasy RPG example.
+
+    Note: the example data here is also an experiment in co-pilot assisted
+    knowledge base generation; the majority of the content was created by
+    LLM-autocomplete.
+    """
 
     def test_build_rpg(self):
         """
@@ -40,6 +45,6 @@ def test_build_rpg(self):
         assert len(axioms) > 5
         # compare with expected output
         doc_expected = to_python(str(EXPECTED))
-        assert len(axioms) == len(doc_expected.ontology.axioms)
+        self.assertEquals(len(axioms), len(doc_expected.ontology.axioms))
         self.assertCountEqual(axioms, doc_expected.ontology.axioms)
 
diff --git a/tests/test_formats/test_from_tsv.py b/tests/test_formats/test_from_tsv.py
index 871ae63..60ec6a4 100644
--- a/tests/test_formats/test_from_tsv.py
+++ b/tests/test_formats/test_from_tsv.py
@@ -18,6 +18,11 @@
 OWL_OUT = os.path.join(OUTPUT_DIR, 'parts.owl.ofn')
 
 
+def _remove_prefixes_hack(s: str) -> str:
+    # with the exception of rdflib 6.2.0, rdflib introduces namespace pollution
+    lines = [line for line in s.split("\n") if not line.startswith("Prefix")]
+    return "\n".join(lines)
+
 class TestFromCSV(unittest.TestCase):
     """Test import from csv."""
 
@@ -34,7 +39,6 @@ def test_from_csv(self):
         dumper = OWLDumper()
         doc = dumper.to_ontology_document(data, schema=sv.schema)
         doc_rt = to_python(str(doc))
-        #print(doc_rt)
         axioms = doc_rt.ontology.axioms
         logging.info(f'AXIOMS={len(axioms)}')
         assert len(axioms) > 5
@@ -44,7 +48,9 @@ def test_from_csv(self):
                                     target_class='EquivGenusAndPartOf', schemaview=sv, delimiter=',', python_module=python_module)
         dumper = OWLDumper()
         doc2 = dumper.to_ontology_document(data, schema=sv.schema)
-        assert doc2 == doc
+        doc = _remove_prefixes_hack(str(doc))
+        doc2 = _remove_prefixes_hack(str(doc2))
+        self.assertEquals(doc2, doc)