From 4269a967786c7da2b544cf8de342f165ad0613a3 Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Thu, 8 Feb 2024 18:08:56 -0800
Subject: [PATCH 1/2] bumped version

---
 Makefile                                 |    3 +-
 poetry.lock                              | 1741 +++++++++++-----------
 pyproject.toml                           |    6 +-
 tests/inputs/expected_ro.ofn             |    7 +
 tests/inputs/monsters_and_magic.yaml     |    2 +-
 tests/output/chromo.schema.owl.ttl       |  518 ++++---
 tests/test_examples/test_ro_metamodel.py |   85 +-
 7 files changed, 1156 insertions(+), 1206 deletions(-)

diff --git a/Makefile b/Makefile
index 5011ee3..3baf583 100644
--- a/Makefile
+++ b/Makefile
@@ -4,8 +4,7 @@ RUN = poetry run
 all: docs/examples.md test
 
 test:
-	$(RUN) python -m unittest discover
-#	$(RUN) pytest
+	$(RUN) pytest tests
 
 tests/model/%.py: tests/model/%.yaml
 	$(RUN) gen-python $< > $@.tmp && mv $@.tmp $@
diff --git a/poetry.lock b/poetry.lock
index 6882632..5e5e558 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,20 +1,5 @@
 # This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
 
-[[package]]
-name = "annotated-types"
-version = "0.5.0"
-description = "Reusable constraint types to use with typing.Annotated"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {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"
@@ -28,37 +13,43 @@ files = [
 
 [[package]]
 name = "arrow"
-version = "1.2.3"
+version = "1.3.0"
 description = "Better dates & times for Python"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"},
-    {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"},
+    {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"},
+    {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"},
 ]
 
 [package.dependencies]
 python-dateutil = ">=2.7.0"
+types-python-dateutil = ">=2.8.10"
+
+[package.extras]
+doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
+test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"]
 
 [[package]]
 name = "attrs"
-version = "23.1.0"
+version = "23.2.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
-    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
+    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
+    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
 ]
 
 [package.extras]
 cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]", "pre-commit"]
+dev = ["attrs[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]"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "bcp47"
@@ -74,34 +65,34 @@ files = [
 
 [[package]]
 name = "black"
-version = "23.7.0"
+version = "24.1.1"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {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-24.1.1-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:7258c27115c1e3b5de9ac6c4f9957e3ee2c02c0b39222a24dc7aa03ba0e986f5"},
+    {file = "black-24.1.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:40657e1b78212d582a0edecafef133cf1dd02e6677f539b669db4746150d38f6"},
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+    {file = "black-24.1.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:854c06fb86fd854140f37fb24dbf10621f5dab9e3b0c29a690ba595e3d543024"},
+    {file = "black-24.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3897ae5a21ca132efa219c029cce5e6bfc9c3d34ed7e892113d199c0b1b444a2"},
+    {file = "black-24.1.1-cp39-cp39-win_amd64.whl", hash = "sha256:ecba2a15dfb2d97105be74bbfe5128bc5e9fa8477d8c46766505c1dda5883aac"},
+    {file = "black-24.1.1-py3-none-any.whl", hash = "sha256:5cdc2e2195212208fbcae579b931407c1fa9997584f0a415421748aeafff1168"},
+    {file = "black-24.1.1.tar.gz", hash = "sha256:48b5760dcbfe5cf97fd4fba23946681f3a81514c6ab8a45b50da67ac8fbc6c7b"},
 ]
 
 [package.dependencies]
@@ -111,36 +102,36 @@ packaging = ">=22.0"
 pathspec = ">=0.9.0"
 platformdirs = ">=2"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
+typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.7.4)"]
+d = ["aiohttp (>=3.7.4)", "aiohttp (>=3.7.4,!=3.9.0)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "cachetools"
-version = "5.3.1"
+version = "5.3.2"
 description = "Extensible memoizing collections and decorators"
-category = "dev"
+category = "main"
 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"},
+    {file = "cachetools-5.3.2-py3-none-any.whl", hash = "sha256:861f35a13a451f94e301ce2bec7cac63e881232ccce7ed67fab9b5df4d3beaa1"},
+    {file = "cachetools-5.3.2.tar.gz", hash = "sha256:086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2"},
 ]
 
 [[package]]
 name = "certifi"
-version = "2023.7.22"
+version = "2024.2.2"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
-    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
+    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
+    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
 ]
 
 [[package]]
@@ -171,99 +162,114 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.2.0"
+version = "3.3.2"
 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-3.2.0.tar.gz", hash = "sha256:3bb3d25a8e6c0aedd251753a79ae98a093c7e7b471faa3aa9a93a81431987ace"},
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 [package.dependencies]
@@ -359,14 +357,14 @@ toml = ["tomli"]
 
 [[package]]
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 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
 category = "main"
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
@@ -382,18 +380,6 @@ pandas = ["pandas"]
 rdflib = ["rdflib"]
 tests = ["coverage", "pytest"]
 
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-name = "decorator"
-version = "5.1.1"
-description = "Decorators for Humans"
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 version = "1.2.14"
@@ -414,14 +400,14 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 
 [[package]]
 name = "distlib"
-version = "0.3.7"
+version = "0.3.8"
 description = "Distribution utilities"
-category = "dev"
+category = "main"
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 python-versions = "*"
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 [[package]]
@@ -438,14 +424,14 @@ files = [
 
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 [[package]]
 name = "fqdn"
@@ -536,77 +523,75 @@ test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>=
 
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 ]
 
 [package.extras]
-docs = ["Sphinx", "docutils (<0.18)"]
-test = ["faulthandler", "objgraph", "psutil"]
+docs = ["Sphinx", "furo"]
+test = ["objgraph", "psutil"]
 
 [[package]]
 name = "hbreader"
@@ -622,54 +607,54 @@ files = [
 
 [[package]]
 name = "idna"
-version = "3.4"
+version = "3.6"
 description = "Internationalized Domain Names in Applications (IDNA)"
 category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
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-    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
+    {file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"},
+    {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
 ]
 
 [[package]]
 name = "importlib-metadata"
-version = "6.8.0"
+version = "7.0.1"
 description = "Read metadata from Python packages"
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
 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 = "6.0.1"
+version = "6.1.1"
 description = "Read resources from Python packages"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "importlib_resources-6.1.1-py3-none-any.whl", hash = "sha256:e8bf90d8213b486f428c9c39714b920041cb02c184686a3dee24905aaa8105d6"},
+    {file = "importlib_resources-6.1.1.tar.gz", hash = "sha256:3893a00122eafde6894c59914446a512f728a0c1a45f9bb9b63721b6bacf0b4a"},
 ]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-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"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "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", "zipp (>=3.17)"]
 
 [[package]]
 name = "iniconfig"
@@ -715,14 +700,14 @@ arrow = ">=0.15.0"
 
 [[package]]
 name = "jinja2"
-version = "3.1.2"
+version = "3.1.3"
 description = "A very fast and expressive template engine."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
-    {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
+    {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"},
+    {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"},
 ]
 
 [package.dependencies]
@@ -791,21 +776,18 @@ jsonpointer = ">=1.9"
 
 [[package]]
 name = "jsonpath-ng"
-version = "1.5.3"
+version = "1.6.1"
 description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
 category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "jsonpath-ng-1.5.3.tar.gz", hash = "sha256:a273b182a82c1256daab86a313b937059261b5c5f8c4fa3fc38b882b344dd567"},
-    {file = "jsonpath_ng-1.5.3-py2-none-any.whl", hash = "sha256:f75b95dbecb8a0f3b86fd2ead21c2b022c3f5770957492b9b6196ecccfeb10aa"},
-    {file = "jsonpath_ng-1.5.3-py3-none-any.whl", hash = "sha256:292a93569d74029ba75ac2dc3d3630fc0e17b2df26119a165fa1d498ca47bf65"},
+    {file = "jsonpath-ng-1.6.1.tar.gz", hash = "sha256:086c37ba4917304850bd837aeab806670224d3f038fe2833ff593a672ef0a5fa"},
+    {file = "jsonpath_ng-1.6.1-py3-none-any.whl", hash = "sha256:8f22cd8273d7772eea9aaa84d922e0841aa36fdb8a2c6b7f6c3791a16a9bc0be"},
 ]
 
 [package.dependencies]
-decorator = "*"
 ply = "*"
-six = "*"
 
 [[package]]
 name = "jsonpointer"
@@ -821,14 +803,14 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.19.0"
+version = "4.21.1"
 description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.19.0-py3-none-any.whl", hash = "sha256:043dc26a3845ff09d20e4420d6012a9c91c9aa8999fa184e7efcfeccb41e32cb"},
-    {file = "jsonschema-4.19.0.tar.gz", hash = "sha256:6e1e7569ac13be8139b2dd2c21a55d350066ee3f80df06c608b398cdc6f30e8f"},
+    {file = "jsonschema-4.21.1-py3-none-any.whl", hash = "sha256:7996507afae316306f9e2290407761157c6f78002dcf7419acb99822143d1c6f"},
+    {file = "jsonschema-4.21.1.tar.gz", hash = "sha256:85727c00279f5fa6bedbe6238d2aa6403bedd8b4864ab11207d07df3cc1b2ee5"},
 ]
 
 [package.dependencies]
@@ -853,30 +835,30 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.7.1"
+version = "2023.12.1"
 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"},
+    {file = "jsonschema_specifications-2023.12.1-py3-none-any.whl", hash = "sha256:87e4fdf3a94858b8a2ba2778d9ba57d8a9cafca7c7489c46ba0d30a8bc6a9c3c"},
+    {file = "jsonschema_specifications-2023.12.1.tar.gz", hash = "sha256:48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc"},
 ]
 
 [package.dependencies]
 importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
-referencing = ">=0.28.0"
+referencing = ">=0.31.0"
 
 [[package]]
 name = "linkml"
-version = "1.5.6"
+version = "1.7.2"
 description = "Linked Open Data Modeling Language"
 category = "main"
 optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = ">=3.8.1,<4.0.0"
 files = [
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-    {file = "linkml-1.5.6.tar.gz", hash = "sha256:54b34ad376c3146eb714e961118ac2a02720ac315d8ab76ca802e5dc479b25fb"},
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 ]
 
 [package.dependencies]
@@ -889,12 +871,12 @@ jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = {version = ">=4.0.0", extras = ["format"]}
 linkml-dataops = "*"
-linkml-runtime = ">=1.5.4"
+linkml-runtime = ">=1.7.0"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
 prefixmaps = ">=0.1.3"
-pydantic = "*"
+pydantic = ">=1.0.0,<3.0.0"
 pyjsg = ">=0.11.6"
 pyshex = ">=0.7.20"
 pyshexc = ">=0.8.3"
@@ -926,14 +908,14 @@ linkml-runtime = ">=1.1.6"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.5.6"
+version = "1.7.0"
 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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+    {file = "linkml_runtime-1.7.0.tar.gz", hash = "sha256:49279407be8941a5ff1aff34aa6660f161cca3611044045835bc660246a57d92"},
 ]
 
 [package.dependencies]
@@ -953,81 +935,91 @@ requests = "*"
 
 [[package]]
 name = "markdown"
-version = "3.4.4"
+version = "3.5.2"
 description = "Python implementation of John Gruber's Markdown."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "Markdown-3.5.2.tar.gz", hash = "sha256:e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8"},
 ]
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.0)", "mkdocs-nature (>=0.4)"]
+docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.5)", "mkdocs-gen-files", "mkdocs-literate-nav", "mkdocs-nature (>=0.6)", "mkdocs-section-index", "mkdocstrings[python]"]
 testing = ["coverage", "pyyaml"]
 
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 name = "markupsafe"
-version = "2.1.3"
+version = "2.1.5"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = false
 python-versions = ">=3.7"
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 [[package]]
@@ -1044,14 +1036,14 @@ files = [
 
 [[package]]
 name = "mkdocs"
-version = "1.5.2"
+version = "1.5.3"
 description = "Project documentation with Markdown."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1103,38 +1095,38 @@ et-xmlfile = "*"
 
 [[package]]
 name = "packaging"
-version = "23.1"
+version = "23.2"
 description = "Core utilities for Python packages"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
 name = "parse"
-version = "1.19.1"
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 description = "parse() is the opposite of format()"
 category = "main"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
 name = "pathspec"
-version = "0.11.2"
+version = "0.12.1"
 description = "Utility library for gitignore style pattern matching of file paths."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -1151,30 +1143,30 @@ files = [
 
 [[package]]
 name = "platformdirs"
-version = "3.10.0"
+version = "4.2.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "dev"
+category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 [package.extras]
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
+docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.4.0"
 description = "plugin and hook calling mechanisms for python"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -1213,160 +1205,79 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.1.5"
+version = "0.1.7"
 description = "A python library for retrieving semantic prefix maps"
 category = "main"
 optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = ">=3.8.0,<4.0.0"
 files = [
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 ]
 
 [package.dependencies]
-click = ">=8.1.3,<9.0.0"
-greenlet = "2.0.1"
-importlib-metadata = ">=1.0.0"
+click = ">=8.1.3"
+curies = ">=0.5.3"
+pydantic = ">=1.8.2,<2.0.0"
 pyyaml = ">=5.3.1"
-typing-extensions = ">=4.4.0,<5.0.0"
+tox = ">=4.11.3,<5.0.0"
 
 [package.extras]
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 [[package]]
 name = "pydantic"
-version = "2.1.1"
-description = "Data validation using Python type hints"
+version = "1.10.14"
+description = "Data validation and settings management using python type hints"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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-typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
+dotenv = ["python-dotenv (>=0.10.4)"]
+email = ["email-validator (>=1.0.3)"]
 
 [[package]]
 name = "pyjsg"
@@ -1401,14 +1312,14 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyproject-api"
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 [package.dependencies]
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 [package.extras]
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 [[package]]
 name = "pyshex"
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 [[package]]
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+version = "8.0.0"
 description = "pytest: simple powerful testing with Python"
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 iniconfig = "*"
 packaging = "*"
-pluggy = ">=0.12,<2.0"
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 tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
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@@ -1614,14 +1536,14 @@ pyyaml = "*"
 
 [[package]]
 name = "rdflib"
-version = "6.3.2"
+version = "7.0.0"
 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,<4.0"
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 [[package]]
@@ -1982,62 +1919,71 @@ pandas = ["pandas (>=1.3.5)"]
 
 [[package]]
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 ]
 
 [package.dependencies]
 greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""}
-typing-extensions = ">=4.2.0"
+typing-extensions = ">=4.6.0"
 
 [package.extras]
-aiomysql = ["aiomysql", "greenlet (!=0.4.17)"]
-aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
+aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
+aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
+aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
 asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
 mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
@@ -2047,7 +1993,7 @@ mssql-pyodbc = ["pyodbc"]
 mypy = ["mypy (>=0.910)"]
 mysql = ["mysqlclient (>=1.4.0)"]
 mysql-connector = ["mysql-connector-python"]
-oracle = ["cx-oracle (>=7)"]
+oracle = ["cx_oracle (>=8)"]
 oracle-oracledb = ["oracledb (>=1.0.1)"]
 postgresql = ["psycopg2 (>=2.7)"]
 postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
@@ -2057,7 +2003,7 @@ postgresql-psycopg2binary = ["psycopg2-binary"]
 postgresql-psycopg2cffi = ["psycopg2cffi"]
 postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
 pymysql = ["pymysql"]
-sqlcipher = ["sqlcipher3-binary"]
+sqlcipher = ["sqlcipher3_binary"]
 
 [[package]]
 name = "tomli"
@@ -2073,42 +2019,54 @@ files = [
 
 [[package]]
 name = "tox"
-version = "4.7.0"
+version = "4.12.1"
 description = "tox is a generic virtualenv management and test command line tool"
-category = "dev"
+category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-cachetools = ">=5.3.1"
-chardet = ">=5.1"
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+chardet = ">=5.2"
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-filelock = ">=3.12.2"
-packaging = ">=23.1"
-platformdirs = ">=3.9.1"
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+platformdirs = ">=4.1"
+pluggy = ">=1.3"
+pyproject-api = ">=1.6.1"
 tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
-virtualenv = ">=20.24.1"
+virtualenv = ">=20.25"
 
 [package.extras]
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+
+[[package]]
+name = "types-python-dateutil"
+version = "2.8.19.20240106"
+description = "Typing stubs for python-dateutil"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
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 [[package]]
 name = "typing-extensions"
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-description = "Backported and Experimental Type Hints for Python 3.7+"
+version = "4.9.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
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-python-versions = ">=3.7"
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 ]
 
 [[package]]
@@ -2128,78 +2086,80 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 
 [[package]]
 name = "urllib3"
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+version = "2.2.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
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+python-versions = ">=3.8"
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-secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.24.2"
+version = "20.25.0"
 description = "Virtual Python Environment builder"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
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 filelock = ">=3.12.2,<4"
-platformdirs = ">=3.9.1,<4"
+platformdirs = ">=3.9.1,<5"
 
 [package.extras]
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 [[package]]
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+    {file = "wrapt-1.16.0-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:5f15814a33e42b04e3de432e573aa557f9f0f56458745c2074952f564c50e664"},
+    {file = "wrapt-1.16.0-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:db2e408d983b0e61e238cf579c09ef7020560441906ca990fe8412153e3b291f"},
+    {file = "wrapt-1.16.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:edfad1d29c73f9b863ebe7082ae9321374ccb10879eeabc84ba3b69f2579d537"},
+    {file = "wrapt-1.16.0-cp39-cp39-win32.whl", hash = "sha256:ed867c42c268f876097248e05b6117a65bcd1e63b779e916fe2e33cd6fd0d3c3"},
+    {file = "wrapt-1.16.0-cp39-cp39-win_amd64.whl", hash = "sha256:eb1b046be06b0fce7249f1d025cd359b4b80fc1c3e24ad9eca33e0dcdb2e4a35"},
+    {file = "wrapt-1.16.0-py3-none-any.whl", hash = "sha256:6906c4100a8fcbf2fa735f6059214bb13b97f75b1a61777fcf6432121ef12ef1"},
+    {file = "wrapt-1.16.0.tar.gz", hash = "sha256:5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d"},
 ]
 
 [[package]]
 name = "zipp"
-version = "3.16.2"
+version = "3.17.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
-    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "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 = "b86b3c3b9fbee1ec102fef19e208a60f82d2d1ad4ac2aeaa00476d915e7ff062"
+python-versions = "^3.8.1"
+content-hash = "d495894ef917c4b3752c3334fd6bdb0f2e72957549c1c8260f67cb5d70f2b1cb"
diff --git a/pyproject.toml b/pyproject.toml
index 1445a07..ddba1a0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,13 +34,13 @@ style = "pep440"
 linkml-data2owl = "linkml_owl.dumpers.owl_dumper:cli"
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = "^3.8.1"
 
 click = "*"
 funowl = ">=0.2.3"
 Jinja2 = ">=3.0.3"
-linkml = ">=1.3.0"
-linkml-runtime = ">=1.3.4"
+linkml = ">=1.7.0"
+linkml-runtime = ">=1.7.0"
 
 [tool.poetry.dev-dependencies]
 tox = ">=3.24.5"
diff --git a/tests/inputs/expected_ro.ofn b/tests/inputs/expected_ro.ofn
index 77ab071..9e0fce5 100644
--- a/tests/inputs/expected_ro.ofn
+++ b/tests/inputs/expected_ro.ofn
@@ -29,6 +29,7 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     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" )
+    AnnotationAssertion( dcterms:conformsTo BFO:0000051 rometa:ObjectProperty )
     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(
@@ -59,6 +60,7 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     ObjectPropertyRange( <http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/BFO_0000004> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002203> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002203> "develops into" )
+    AnnotationAssertion( dcterms:conformsTo RO:0002203 rometa:ObjectProperty )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/RO_0002203> )
     TransitiveObjectProperty( <http://purl.obolibrary.org/obo/RO_0002202> )
     AnnotationAssertion( IAO:0000115 RO:9999998 "Inverse of RO:0002012 occurrent part of" )
@@ -70,6 +72,7 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     ObjectPropertyRange( <http://purl.obolibrary.org/obo/RO_0002012> <http://purl.obolibrary.org/obo/BFO_0000003> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_9999998> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_9999998> "has occurrent part" )
+    AnnotationAssertion( dcterms:conformsTo RO:9999998 rometa:ObjectProperty )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0002012> <http://purl.obolibrary.org/obo/RO_9999998> )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002104> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002104> "has plasma membrane part" )
@@ -93,10 +96,12 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     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" )
+    AnnotationAssertion( dcterms:conformsTo RO:9999999 rometa:ObjectProperty )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0002447> <http://purl.obolibrary.org/obo/RO_9999999> )
     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" )
+    AnnotationAssertion( dcterms:conformsTo RO:0002481 rometa:RolifiedObjectProperty )
     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" )
@@ -112,8 +117,10 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     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" )
+    AnnotationAssertion( dcterms:conformsTo RO:0018003 rometa:ObjectProperty )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0018002> <http://purl.obolibrary.org/obo/RO_0018003> )
     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" )
+    AnnotationAssertion( dcterms:conformsTo RO:0018001 rometa:RolifiedObjectProperty )
 )
\ No newline at end of file
diff --git a/tests/inputs/monsters_and_magic.yaml b/tests/inputs/monsters_and_magic.yaml
index 5928ae5..7437636 100644
--- a/tests/inputs/monsters_and_magic.yaml
+++ b/tests/inputs/monsters_and_magic.yaml
@@ -404,7 +404,7 @@ slots:
       owl: AnnotationProperty
 
   type:
-    designates_type: true
+    #designates_type: true
     #range: Grouping
     description: >-
       The type of a thing
diff --git a/tests/output/chromo.schema.owl.ttl b/tests/output/chromo.schema.owl.ttl
index 5c17a28..2d31165 100644
--- a/tests/output/chromo.schema.owl.ttl
+++ b/tests/output/chromo.schema.owl.ttl
@@ -1,11 +1,6 @@
-@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> .
 @prefix GO: <http://purl.obolibrary.org/obo/GO_> .
-@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> .
-@prefix OIO: <http://www.geneontology.org/formats/oboInOwl#> .
-@prefix RO: <http://purl.obolibrary.org/obo/RO_> .
 @prefix biolink: <https://w3id.org/biolink/vocab/> .
 @prefix chromoschema: <https://w3id.org/biodatamodels/chromoschema/> .
-@prefix dcterms: <http://purl.org/dc/terms/> .
 @prefix edam: <http://edamontology.org/> .
 @prefix gff: <https://w3id.org/biodatamodels/gff/> .
 @prefix linkml: <https://w3id.org/linkml/> .
@@ -15,94 +10,223 @@
 @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
-<https://w3id.org/biodatamodels/chromoschema> a owl:Ontology ;
-    rdfs:label "ChromoSchema" ;
-    IAO:0000700 chromoschema:ChromosomePart,
-        chromoschema:ChromosomePartCollection,
-        chromoschema:Genome,
-        chromoschema:GenomeBuild,
-        chromoschema:OrganismTaxon ;
-    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 .
-
-linkml:topValue a owl:DatatypeProperty ;
-    rdfs:label "value" .
-
 chromoschema:ChromosomePartCollection a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "ChromosomePartCollection" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:has ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:genomes ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
             owl:allValuesFrom chromoschema:ChromosomePart ;
-            owl:onProperty dcterms:hasPart ],
+            owl:onProperty chromoschema:has ],
         [ a owl:Restriction ;
             owl:allValuesFrom chromoschema:OrganismTaxon ;
-            owl:onProperty dcterms:hasPart ],
+            owl:onProperty chromoschema:taxons ],
         [ a owl:Restriction ;
-            owl:allValuesFrom chromoschema:Genome ;
-            owl:onProperty dcterms:hasPart ],
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:name ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass linkml:String ;
-            owl:onProperty chromoschema:name ] .
-
-chromoschema:StrandType a owl:Class,
-        linkml:TypeDefinition ;
-    rdfs:label "StrandType" ;
-    rdfs:subClassOf linkml:Integer .
+            owl:allValuesFrom owl:Thing ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:taxons ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:Genome ;
+            owl:onProperty chromoschema:genomes ] ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
 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: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:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    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" .
+
+chromoschema:broad_synonyms a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "broad_synonyms" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:cell_location a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "cell_location" ;
+    rdfs:range chromoschema:LocationType ;
+    skos:definition "which organelle the chromosome is associated with. For eukaryotes this is mitochondrion or nucleus. For prokaryotes the distinction does not make sense" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    skos:note "OWL>> ObjectSomeValuesFrom" .
+
+chromoschema:children a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "children" ;
+    rdfs:range chromoschema:ChromosomePart ;
+    skos:definition "Direct parts of this chromosome. zero to many." ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
 chromoschema:chromosome_name a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "chromosome_name" ;
     rdfs:range chromoschema:ChromosomeNameType ;
-    skos:definition "E.g. chr1, chrM. Some species like C elegans may use roman numerals" .
+    skos:definition "E.g. chr1, chrM. Some species like C elegans may use roman numerals" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:common_name a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "common_name" ;
+    rdfs:range chromoschema:LabelType ;
+    skos:definition "E.g. human, mouse" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:download_url a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "download_url" ;
+    rdfs:range linkml:Uri ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:end a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "end" ;
+    rdfs:range linkml:Integer ;
+    skos:definition "Start location of the chromosomal part. Note we also include this for whole chromosomes - end will be rightmost point" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:exact_mappings a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "exact_mappings" ;
+    rdfs:range linkml:Uriorcurie ;
+    skos:definition "For a whole chromosome, this may be an assembled sequence in a database such as genbank or ensembl" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:exact_synonyms a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "exact_synonyms" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:parent a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "parent" ;
+    rdfs:range chromoschema:ChromosomePart ;
+    skos:definition "Direct chromosomal part which this is a part of. The partonomy forms a tree so this is always zero or one. Different species have different rules but typically the partonomy will be something like 1p31.1 -> 1p31 -> 1p3 -> 1p -> 1" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    skos:note "OWL>> ObjectSomeValuesFrom" .
 
 chromoschema:previous_builds a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "previous_builds" ;
     rdfs:range chromoschema:GenomeBuild ;
-    skos:definition "List of previous non-current builds" .
+    skos:definition "List of previous non-current builds" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
 chromoschema:sex_chromosome_type a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "sex_chromosome_type" ;
     rdfs:range chromoschema:SexChromosomeType ;
-    skos:definition "Only populated for sex chromosomes. Indicates the chromosome type. This is X or Y in mammals, W or Z in avians" .
+    skos:definition "Only populated for sex chromosomes. Indicates the chromosome type. This is X or Y in mammals, W or Z in avians" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
 chromoschema:somal_type a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "somal_type" ;
     rdfs:range chromoschema:AutosomeVsSexChromosome ;
-    skos:definition "indicates whether this is a sex-chromosome or not" .
+    skos:definition "indicates whether this is a sex-chromosome or not" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
-gff:strand a owl:ObjectProperty,
+chromoschema:start a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "start" ;
+    rdfs:range linkml:Integer ;
+    skos:definition "Start location of the chromosomal part. Note we also include this for whole chromosomes - start will be zero" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:strand a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "strand" ;
     rdfs:range chromoschema:StrandType ;
-    skos:exactMatch gff:strand,
-        biolink:strand .
+    skos:exactMatch biolink:strand ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
-BFO:0000050 a owl:ObjectProperty,
-        linkml:SlotDefinition .
+chromoschema:taxon a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "taxon" ;
+    rdfs:range chromoschema:TaxonIdentifier ;
+    skos:definition "The taxon to which the chromosome part belongs. Always NCBITaxon." ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    skos:note "OWL>> ObjectSomeValuesFrom" .
 
-BFO:0000051 a owl:ObjectProperty,
+chromoschema:type a owl:ObjectProperty,
         linkml:SlotDefinition ;
-    rdfs:label "children" ;
-    rdfs:range chromoschema:ChromosomePart ;
-    skos:definition "Direct parts of this chromosome. zero to many." ;
-    skos:exactMatch BFO:0000051 .
+    rdfs:label "type" ;
+    rdfs:range chromoschema:EntityType ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    skos:note "OWL>> SubClassOf" .
+
+chromoschema:BandDescriptor a owl:Class,
+        linkml:TypeDefinition ;
+    rdfs:subClassOf linkml:String .
+
+chromoschema:ChromosomeNameType a owl:Class,
+        linkml:TypeDefinition ;
+    rdfs:subClassOf linkml:String .
+
+chromoschema:Genome a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "Genome" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom owl:Thing ;
+            owl:onProperty chromoschema:build ],
+        [ a owl:Restriction ;
+            owl:minCardinality 1 ;
+            owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:build ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom owl:Thing ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom [ a rdfs:Datatype ;
+                    owl:onDatatype xsd:string ;
+                    owl:withRestrictions ( [ xsd:pattern "^\\\\w+$" ] ) ] ;
+            owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:build ],
+        [ a owl:Restriction ;
+            owl:minCardinality 1 ;
+            owl:onProperty chromoschema:name ] ;
+    skos:definition """Represents a sequenced genome, one per species.
+Each genome can be associated with one or more builds""" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:OrganismTaxon a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "OrganismTaxon" ;
+    skos:definition "Represents a species, e.g. Homo sapiens" ;
+    skos:exactMatch biolink:OrganismTaxon ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:StrandType a owl:Class,
+        linkml:TypeDefinition ;
+    rdfs:subClassOf linkml:Integer .
+
+chromoschema:TaxonIdentifier a owl:Class,
+        linkml:TypeDefinition ;
+    rdfs:subClassOf linkml:Uriorcurie .
 
 GO:0000791 a owl:Class,
         chromoschema:ChromatinType ;
@@ -152,261 +276,123 @@ GO:0098687 a owl:Class,
         chromoschema:EntityType ;
     rdfs:label "chromosome_part" .
 
-OIO:hasBroadSynonym a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "broad_synonyms" ;
-    rdfs:range linkml:String ;
-    skos:exactMatch OIO:hasBroadSynonym .
-
-OIO:hasExactSynonym a owl:ObjectProperty,
-        linkml:SlotDefinition .
-
-rdf:type a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "type" ;
-    rdfs:range chromoschema:EntityType ;
-    skos:exactMatch rdf:type .
-
-skos:exactMatch a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "exact_mappings" ;
-    rdfs:range linkml:Uriorcurie ;
-    skos:definition "For a whole chromosome, this may be an assembled sequence in a database such as genbank or ensembl" ;
-    skos:exactMatch skos:exactMatch .
-
-chromoschema:BandDescriptor a owl:Class,
-        linkml:TypeDefinition ;
-    rdfs:label "BandDescriptor" ;
-    rdfs:subClassOf linkml:String .
-
 chromoschema:ChromatinType a owl:Class,
         linkml:EnumDefinition ;
-    rdfs:label "ChromatinType" ;
     owl:unionOf ( GO:0000792 GO:0000791 ) ;
     linkml:permissible_values GO:0000791,
         GO:0000792 .
 
-chromoschema:ChromosomeNameType a owl:Class,
-        linkml:TypeDefinition ;
-    rdfs:label "ChromosomeNameType" ;
-    rdfs:subClassOf linkml:String .
-
-chromoschema:Genome a owl:Class,
-        linkml:ClassDefinition ;
-    rdfs:label "Genome" ;
-    rdfs:subClassOf [ a owl:Restriction ;
-            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:TaxonIdentifier ;
-            owl:onProperty RO:0002162 ],
-        [ a owl:Restriction ;
-            owl:onClass chromoschema:LabelType ;
-            owl:onProperty rdfs:label ;
-            owl:qualifiedCardinality 1 ] ;
-    skos:definition """Represents a sequenced genome, one per species.
-Each genome can be associated with one or more builds""" .
-
-chromoschema:OrganismTaxon a owl:Class,
+chromoschema:GenomeBuild a owl:Class,
         linkml:ClassDefinition ;
-    rdfs:label "OrganismTaxon" ;
+    rdfs:label "GenomeBuild" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:LabelType ;
-            owl:onProperty rdfs:label ],
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:id ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:LabelType ;
-            owl:onProperty OIO:hasExactSynonym ],
+            owl:minCardinality 1 ;
+            owl:onProperty chromoschema:id ],
         [ a owl:Restriction ;
-            owl:onClass linkml:String ;
-            owl:onProperty chromoschema:id ;
-            owl:qualifiedCardinality 1 ] ;
-    skos:definition "Represents a species, e.g. Homo sapiens" ;
-    skos:exactMatch biolink:OrganismTaxon .
+            owl:allValuesFrom owl:Thing ;
+            owl:onProperty chromoschema:id ] ;
+    skos:closeMatch edam:operation_0525 ;
+    skos:definition "Represents a specific build of a sequenced genome" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
-gff:end a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "end" ;
-    rdfs:range linkml:Integer ;
-    skos:definition "Start location of the chromosomal part. Note we also include this for whole chromosomes - end will be rightmost point" ;
-    skos:exactMatch gff:end .
+chromoschema:LabelType a owl:Class,
+        linkml:TypeDefinition ;
+    rdfs:subClassOf linkml:String .
 
-gff:start a owl:ObjectProperty,
+chromoschema:genomes a owl:ObjectProperty,
         linkml:SlotDefinition ;
-    rdfs:label "start" ;
-    rdfs:range linkml:Integer ;
-    skos:definition "Start location of the chromosomal part. Note we also include this for whole chromosomes - start will be zero" ;
-    skos:exactMatch gff:start .
+    rdfs:label "genomes" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
-RO:0002162 a owl:ObjectProperty,
+chromoschema:has a owl:ObjectProperty,
         linkml:SlotDefinition ;
-    rdfs:label "taxon" ;
-    rdfs:range chromoschema:TaxonIdentifier ;
-    skos:definition "The taxon to which the chromosome part belongs. Always NCBITaxon." ;
-    skos:exactMatch RO:0002162 .
+    rdfs:label "has" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
-dcterms:hasPart a owl:ObjectProperty,
-        linkml:SlotDefinition .
-
-chromoschema:LocationType a owl:Class,
-        linkml:EnumDefinition ;
-    rdfs:label "LocationType" ;
-    owl:unionOf ( GO:0005634 GO:0005739 ) ;
-    linkml:permissible_values GO:0005634,
-        GO:0005739 .
-
-chromoschema:TaxonIdentifier a owl:Class,
-        linkml:TypeDefinition ;
-    rdfs:label "TaxonIdentifier" ;
-    rdfs:subClassOf linkml:Uriorcurie .
-
-biolink:genome_build a owl:ObjectProperty,
+chromoschema:taxons a owl:ObjectProperty,
         linkml:SlotDefinition ;
-    rdfs:label "build" ;
-    rdfs:range chromoschema:GenomeBuild ;
-    skos:definition "A descriptor for the genome and build number. E.g hg38" ;
-    skos:exactMatch edam:data_2340,
-        gff:genome_build,
-        biolink:genome_build .
+    rdfs:label "taxons" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
 chromoschema:AutosomeVsSexChromosome a owl:Class,
         linkml:EnumDefinition ;
-    rdfs:label "AutosomeVsSexChromosome" ;
     owl:unionOf ( GO:0000803 GO:0030849 ) ;
     linkml:permissible_values GO:0000803,
         GO:0030849 .
 
-chromoschema:EntityType a owl:Class,
-        linkml:EnumDefinition ;
-    rdfs:label "EntityType" ;
-    owl:unionOf ( GO:0005694 GO:0098687 ) ;
-    linkml:permissible_values GO:0005694,
-        GO:0098687 .
-
-chromoschema:id a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "id" ;
-    rdfs:range linkml:String ;
-    skos:definition "A unique identifier" .
-
-rdfs:label a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "name" ;
-    rdfs:range chromoschema:LabelType ;
-    skos:definition "Unique human-readable label for the entity" ;
-    skos:exactMatch rdfs:label .
-
 chromoschema:ChromosomePart a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "ChromosomePart" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:ChromosomePart ;
-            owl:onProperty BFO:0000050 ],
-        [ 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: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:LabelType ;
-            owl:onProperty rdfs:label ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:AutosomeVsSexChromosome ;
-            owl:onProperty chromoschema:somal_type ],
+            owl:minCardinality 1 ;
+            owl:onProperty chromoschema:id ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass linkml:Integer ;
-            owl:onProperty gff:start ],
+            owl:allValuesFrom [ a rdfs:Datatype ;
+                    owl:onDatatype xsd:string ;
+                    owl:withRestrictions ( [ xsd:pattern "^CHR:\\\\S+$" ] ) ] ;
+            owl:onProperty chromoschema:id ],
         [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            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:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:BandDescriptor ;
-            owl:onProperty chromoschema:band_descriptor ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            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:EntityType ;
-            owl:onProperty rdf:type ],
-        [ a owl:Restriction ;
-            owl:onClass linkml:String ;
-            owl:onProperty chromoschema:id ;
-            owl:qualifiedCardinality 1 ] ;
-    skos:definition "A Chromosome or a part of a chromosome (includes whole chromosomes, arms, and bands)" .
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:id ] ;
+    skos:definition "A Chromosome or a part of a chromosome (includes whole chromosomes, arms, and bands)" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    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" .
 
-linkml:ClassDefinition a owl:Class .
-
-linkml:TypeDefinition a owl:Class .
+chromoschema:EntityType a owl:Class,
+        linkml:EnumDefinition ;
+    owl:unionOf ( GO:0005694 GO:0098687 ) ;
+    linkml:permissible_values GO:0005694,
+        GO:0098687 .
 
-chromoschema:GenomeBuild a owl:Class,
-        linkml:ClassDefinition ;
-    rdfs:label "GenomeBuild" ;
-    rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:LabelType ;
-            owl:onProperty rdfs:label ],
-        [ a owl:Restriction ;
-            owl:onClass linkml:String ;
-            owl:onProperty chromoschema:id ;
-            owl:qualifiedCardinality 1 ] ;
-    skos:closeMatch edam:operation_0525 ;
-    skos:definition "Represents a specific build of a sequenced genome" .
+chromoschema:LocationType a owl:Class,
+        linkml:EnumDefinition ;
+    owl:unionOf ( GO:0005634 GO:0005739 ) ;
+    linkml:permissible_values GO:0005634,
+        GO:0005739 .
 
-chromoschema:LabelType a owl:Class,
-        linkml:TypeDefinition ;
-    rdfs:label "LabelType" ;
-    rdfs:subClassOf linkml:String .
+chromoschema:build a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "build" ;
+    rdfs:range chromoschema:GenomeBuild ;
+    skos:definition "A descriptor for the genome and build number. E.g hg38" ;
+    skos:exactMatch edam:data_2340,
+        gff:genome_build ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
 chromoschema:SexChromosomeType a owl:Class,
         linkml:EnumDefinition ;
-    rdfs:label "SexChromosomeType" ;
     owl:unionOf ( GO:0000805 GO:0000806 GO:0000804 GO:0000807 ) ;
     linkml:permissible_values GO:0000804,
         GO:0000805,
         GO:0000806,
         GO:0000807 .
 
-linkml:SlotDefinition a owl:Class .
+chromoschema:name a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "name" ;
+    rdfs:range chromoschema:LabelType ;
+    skos:definition "Unique human-readable label for the entity" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:id a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "id" ;
+    rdfs:range [ a rdfs:Datatype ;
+            owl:onDatatype xsd:string ;
+            owl:withRestrictions ( [ xsd:pattern "^CHR:\\\\S+$" ] ) ] ;
+    skos:definition "A unique identifier" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    skos:note "will be of form CHR:...." .
+
+<https://w3id.org/biodatamodels/chromoschema> a owl:Ontology ;
+    rdfs:label "ChromoSchema" ;
+    skos:definition """Schema for representing Chromosomes and Chromosomal Regions.
 
+Objects created using this schema can be directly worked with in YAML/Python,
+Additionally they can be translated to OWL""" .
 
diff --git a/tests/test_examples/test_ro_metamodel.py b/tests/test_examples/test_ro_metamodel.py
index 2c8b78b..fccbd03 100644
--- a/tests/test_examples/test_ro_metamodel.py
+++ b/tests/test_examples/test_ro_metamodel.py
@@ -2,6 +2,8 @@
 import logging
 import os
 import unittest
+from typing import List
+
 from linkml.generators.pythongen import PythonGenerator
 from linkml_runtime import SchemaView
 
@@ -19,48 +21,49 @@
 EXPECTED = os.path.join(INPUT_DIR, 'expected_ro.ofn')
 
 
-class TestROMetamodel(unittest.TestCase):
-    """Relation Ontology test case."""
+def str_sorted(objs: List[object]) -> List[str]:
+    return sorted([str(o) for o in objs])
+
 
-    def test_build_relation_ontology(self):
-        """
-        Test creation of an OWL TBox
-        """
-        #logging.basicConfig(level=logging.DEBUG)
-        sv = SchemaView(SCHEMA_IN)
-        python_module = PythonGenerator(SCHEMA_IN).compile_module()
-        data = load_structured_file(DATA_IN, schemaview=sv, python_module=python_module)
-        dumper = OWLDumper()
-        dumper.schemaview = sv
-        domain_slot = sv.get_slot('domain')
-        #print(domain_slot)
-        #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}')
-        assert 'ObjectPropertyDomain' in anns
+def test_build_relation_ontology():
+    """
+    Test creation of an OWL TBox
+    """
+    #logging.basicConfig(level=logging.DEBUG)
+    sv = SchemaView(SCHEMA_IN)
+    python_module = PythonGenerator(SCHEMA_IN).compile_module()
+    data = load_structured_file(DATA_IN, schemaview=sv, python_module=python_module)
+    dumper = OWLDumper()
+    dumper.schemaview = sv
+    domain_slot = sv.get_slot('domain')
+    #print(domain_slot)
+    #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}')
+    assert 'ObjectPropertyDomain' in anns
 
-        test_slot = sv.get_slot('inverse_of')
-        #print(domain_slot)
-        #print(f'URI = {domain_slot.slot_uri}')
-        assert test_slot.slot_uri == 'owl:inverseOf'
-        anns = dumper._get_inferred_slot_annotations(test_slot, 'owl', 'TransitiveForm')
-        print(f'Anns={anns}')
-        assert 'InverseObjectProperties' in anns
-        cls = sv.get_class('TransitiveForm')
-        tmpls = dumper._get_inferred_class_annotations(cls, 'owl.template')
-        print(f'TMPLS={tmpls}')
-        assert tmpls
+    test_slot = sv.get_slot('inverse_of')
+    #print(domain_slot)
+    #print(f'URI = {domain_slot.slot_uri}')
+    assert test_slot.slot_uri == 'owl:inverseOf'
+    anns = dumper._get_inferred_slot_annotations(test_slot, 'owl', 'TransitiveForm')
+    print(f'Anns={anns}')
+    assert 'InverseObjectProperties' in anns
+    cls = sv.get_class('TransitiveForm')
+    tmpls = dumper._get_inferred_class_annotations(cls, 'owl.template')
+    print(f'TMPLS={tmpls}')
+    assert tmpls
 
-        doc = dumper.to_ontology_document(data, schema=sv.schema)
-        with open(OWL_OUT, 'w') as stream:
-            stream.write(str(doc))
-        doc_rt = to_python(str(doc))
-        axioms = doc_rt.ontology.axioms
-        logging.info(f'AXIOMS={len(axioms)}')
-        assert len(axioms) > 5
-        # compare with expected output
-        doc_expected = to_python(str(EXPECTED))
-        assert len(axioms) == len(doc_expected.ontology.axioms)
-        self.assertCountEqual(axioms, doc_expected.ontology.axioms)
+    doc = dumper.to_ontology_document(data, schema=sv.schema)
+    with open(OWL_OUT, 'w') as stream:
+        stream.write(str(doc))
+    doc_rt = to_python(str(doc))
+    axioms = doc_rt.ontology.axioms
+    logging.info(f'AXIOMS={len(axioms)}')
+    assert len(axioms) > 5
+    # compare with expected output
+    doc_expected = to_python(str(EXPECTED))
+    assert len(axioms) == len(doc_expected.ontology.axioms)
+    assert str_sorted(axioms) == str_sorted(doc_expected.ontology.axioms)
 

From a6f2a5ed5dcf8bc698bf93e096d132e99ce4bae9 Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Mon, 26 Feb 2024 16:31:30 -0800
Subject: [PATCH 2/2] bump version

---
 poetry.lock                            | 699 ++++++++++++++-----------
 pyproject.toml                         |   2 +-
 tests/output/chromo.schema.owl.ttl     | 593 ++++++++++++++-------
 tests/test_examples/test_from_dosdp.py |   2 +-
 4 files changed, 781 insertions(+), 515 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 5e5e558..c820ed3 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,5 +1,20 @@
 # This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
 
+[[package]]
+name = "annotated-types"
+version = "0.6.0"
+description = "Reusable constraint types to use with typing.Annotated"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"},
+    {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"},
+]
+
+[package.dependencies]
+typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""}
+
 [[package]]
 name = "antlr4-python3-runtime"
 version = "4.9.3"
@@ -65,34 +80,34 @@ files = [
 
 [[package]]
 name = "black"
-version = "24.1.1"
+version = "24.2.0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "black-24.1.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:2588021038bd5ada078de606f2a804cadd0a3cc6a79cb3e9bb3a8bf581325a4c"},
-    {file = "black-24.1.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:1a95915c98d6e32ca43809d46d932e2abc5f1f7d582ffbe65a5b4d1588af7445"},
-    {file = "black-24.1.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2fa6a0e965779c8f2afb286f9ef798df770ba2b6cee063c650b96adec22c056a"},
-    {file = "black-24.1.1-cp310-cp310-win_amd64.whl", hash = "sha256:5242ecd9e990aeb995b6d03dc3b2d112d4a78f2083e5a8e86d566340ae80fec4"},
-    {file = "black-24.1.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:fc1ec9aa6f4d98d022101e015261c056ddebe3da6a8ccfc2c792cbe0349d48b7"},
-    {file = "black-24.1.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:0269dfdea12442022e88043d2910429bed717b2d04523867a85dacce535916b8"},
-    {file = "black-24.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b3d64db762eae4a5ce04b6e3dd745dcca0fb9560eb931a5be97472e38652a161"},
-    {file = "black-24.1.1-cp311-cp311-win_amd64.whl", hash = "sha256:5d7b06ea8816cbd4becfe5f70accae953c53c0e53aa98730ceccb0395520ee5d"},
-    {file = "black-24.1.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:e2c8dfa14677f90d976f68e0c923947ae68fa3961d61ee30976c388adc0b02c8"},
-    {file = "black-24.1.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:a21725862d0e855ae05da1dd25e3825ed712eaaccef6b03017fe0853a01aa45e"},
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 ]
 
 [package.dependencies]
@@ -402,7 +417,7 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 name = "distlib"
 version = "0.3.8"
 description = "Distribution utilities"
-category = "main"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -441,7 +456,7 @@ test = ["pytest (>=6)"]
 name = "filelock"
 version = "3.13.1"
 description = "A platform independent file lock."
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -639,14 +654,14 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs
 
 [[package]]
 name = "importlib-resources"
-version = "6.1.1"
+version = "6.1.2"
 description = "Read resources from Python packages"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -654,7 +669,7 @@ zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
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 [[package]]
 name = "iniconfig"
@@ -851,14 +866,14 @@ referencing = ">=0.31.0"
 
 [[package]]
 name = "linkml"
-version = "1.7.2"
+version = "1.7.4"
 description = "Linked Open Data Modeling Language"
 category = "main"
 optional = false
 python-versions = ">=3.8.1,<4.0.0"
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 ]
 
 [package.dependencies]
@@ -908,14 +923,14 @@ linkml-runtime = ">=1.1.6"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.7.0"
+version = "1.7.2"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 category = "main"
 optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = ">=3.8,<4.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -1145,7 +1160,7 @@ files = [
 name = "platformdirs"
 version = "4.2.0"
 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 = ">=3.8"
 files = [
@@ -1205,79 +1220,131 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
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+version = "0.2.2"
 description = "A python library for retrieving semantic prefix maps"
 category = "main"
 optional = false
-python-versions = ">=3.8.0,<4.0.0"
+python-versions = ">=3.8,<4.0"
 files = [
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 pyyaml = ">=5.3.1"
-tox = ">=4.11.3,<5.0.0"
-
-[package.extras]
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 [[package]]
 name = "pydantic"
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-description = "Data validation and settings management using python type hints"
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+description = "Data validation using Python type hints"
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 name = "pyproject-api"
 version = "1.6.1"
 description = "API to interact with the python pyproject.toml based projects"
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "SQLAlchemy-2.0.27.tar.gz", hash = "sha256:86a6ed69a71fe6b88bf9331594fa390a2adda4a49b5c06f98e47bf0d392534f8"},
 ]
 
 [package.dependencies]
@@ -2019,14 +2086,14 @@ files = [
 
 [[package]]
 name = "tox"
-version = "4.12.1"
+version = "4.13.0"
 description = "tox is a generic virtualenv management and test command line tool"
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tox-4.12.1-py3-none-any.whl", hash = "sha256:c07ea797880a44f3c4f200ad88ad92b446b83079d4ccef89585df64cc574375c"},
-    {file = "tox-4.12.1.tar.gz", hash = "sha256:61aafbeff1bd8a5af84e54ef6e8402f53c6a6066d0782336171ddfbf5362122e"},
+    {file = "tox-4.13.0-py3-none-any.whl", hash = "sha256:1143c7e2489c68026a55d3d4ae84c02c449f073b28e62f80e3e440a3b72a4afa"},
+    {file = "tox-4.13.0.tar.gz", hash = "sha256:dd789a554c16c4b532924ba393c92fc8991323c4b3d466712bfecc8c9b9f24f7"},
 ]
 
 [package.dependencies]
@@ -2059,14 +2126,14 @@ files = [
 
 [[package]]
 name = "typing-extensions"
-version = "4.9.0"
+version = "4.10.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"},
-    {file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"},
+    {file = "typing_extensions-4.10.0-py3-none-any.whl", hash = "sha256:69b1a937c3a517342112fb4c6df7e72fc39a38e7891a5730ed4985b5214b5475"},
+    {file = "typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"},
 ]
 
 [[package]]
@@ -2086,14 +2153,14 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 
 [[package]]
 name = "urllib3"
-version = "2.2.0"
+version = "2.2.1"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "urllib3-2.2.0-py3-none-any.whl", hash = "sha256:ce3711610ddce217e6d113a2732fafad960a03fd0318c91faa79481e35c11224"},
-    {file = "urllib3-2.2.0.tar.gz", hash = "sha256:051d961ad0c62a94e50ecf1af379c3aba230c66c710493493560c0c223c49f20"},
+    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
+    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
 ]
 
 [package.extras]
@@ -2104,14 +2171,14 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.25.0"
+version = "20.25.1"
 description = "Virtual Python Environment builder"
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.25.0-py3-none-any.whl", hash = "sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3"},
-    {file = "virtualenv-20.25.0.tar.gz", hash = "sha256:bf51c0d9c7dd63ea8e44086fa1e4fb1093a31e963b86959257378aef020e1f1b"},
+    {file = "virtualenv-20.25.1-py3-none-any.whl", hash = "sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a"},
+    {file = "virtualenv-20.25.1.tar.gz", hash = "sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197"},
 ]
 
 [package.dependencies]
@@ -2280,4 +2347,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.8.1"
-content-hash = "d495894ef917c4b3752c3334fd6bdb0f2e72957549c1c8260f67cb5d70f2b1cb"
+content-hash = "07fe08e5a7b8fe24940ed67c0e4f3854c60de1de55030424f01537bd857b5dbe"
diff --git a/pyproject.toml b/pyproject.toml
index ddba1a0..bb4ceb4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ python = "^3.8.1"
 click = "*"
 funowl = ">=0.2.3"
 Jinja2 = ">=3.0.3"
-linkml = ">=1.7.0"
+linkml = ">=1.7.4"
 linkml-runtime = ">=1.7.0"
 
 [tool.poetry.dev-dependencies]
diff --git a/tests/output/chromo.schema.owl.ttl b/tests/output/chromo.schema.owl.ttl
index 2d31165..e0aa6df 100644
--- a/tests/output/chromo.schema.owl.ttl
+++ b/tests/output/chromo.schema.owl.ttl
@@ -14,20 +14,23 @@ chromoschema:ChromosomePartCollection a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "ChromosomePartCollection" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty chromoschema:has ],
+            owl:allValuesFrom chromoschema:Genome ;
+            owl:onProperty chromoschema:genomes ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty chromoschema:genomes ],
+            owl:onProperty chromoschema:taxons ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
             owl:onProperty chromoschema:name ],
         [ a owl:Restriction ;
-            owl:allValuesFrom chromoschema:ChromosomePart ;
-            owl:onProperty chromoschema:has ],
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:genomes ],
         [ a owl:Restriction ;
             owl:allValuesFrom chromoschema:OrganismTaxon ;
             owl:onProperty chromoschema:taxons ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:has ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
             owl:onProperty chromoschema:name ],
@@ -35,55 +38,8 @@ chromoschema:ChromosomePartCollection a owl:Class,
             owl:allValuesFrom owl:Thing ;
             owl:onProperty chromoschema:name ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty chromoschema:taxons ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom chromoschema:Genome ;
-            owl:onProperty chromoschema:genomes ] ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
-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:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
-    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" .
-
-chromoschema:broad_synonyms a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "broad_synonyms" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
-chromoschema:cell_location a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "cell_location" ;
-    rdfs:range chromoschema:LocationType ;
-    skos:definition "which organelle the chromosome is associated with. For eukaryotes this is mitochondrion or nucleus. For prokaryotes the distinction does not make sense" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
-    skos:note "OWL>> ObjectSomeValuesFrom" .
-
-chromoschema:children a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "children" ;
-    rdfs:range chromoschema:ChromosomePart ;
-    skos:definition "Direct parts of this chromosome. zero to many." ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
-chromoschema:chromosome_name a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "chromosome_name" ;
-    rdfs:range chromoschema:ChromosomeNameType ;
-    skos:definition "E.g. chr1, chrM. Some species like C elegans may use roman numerals" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
-chromoschema:common_name a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "common_name" ;
-    rdfs:range chromoschema:LabelType ;
-    skos:definition "E.g. human, mouse" ;
+            owl:allValuesFrom chromoschema:ChromosomePart ;
+            owl:onProperty chromoschema:has ] ;
     skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
 chromoschema:download_url a owl:ObjectProperty,
@@ -92,61 +48,6 @@ chromoschema:download_url a owl:ObjectProperty,
     rdfs:range linkml:Uri ;
     skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
-chromoschema:end a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "end" ;
-    rdfs:range linkml:Integer ;
-    skos:definition "Start location of the chromosomal part. Note we also include this for whole chromosomes - end will be rightmost point" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
-chromoschema:exact_mappings a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "exact_mappings" ;
-    rdfs:range linkml:Uriorcurie ;
-    skos:definition "For a whole chromosome, this may be an assembled sequence in a database such as genbank or ensembl" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
-chromoschema:exact_synonyms a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "exact_synonyms" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
-chromoschema:parent a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "parent" ;
-    rdfs:range chromoschema:ChromosomePart ;
-    skos:definition "Direct chromosomal part which this is a part of. The partonomy forms a tree so this is always zero or one. Different species have different rules but typically the partonomy will be something like 1p31.1 -> 1p31 -> 1p3 -> 1p -> 1" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
-    skos:note "OWL>> ObjectSomeValuesFrom" .
-
-chromoschema:previous_builds a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "previous_builds" ;
-    rdfs:range chromoschema:GenomeBuild ;
-    skos:definition "List of previous non-current builds" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
-chromoschema:sex_chromosome_type a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "sex_chromosome_type" ;
-    rdfs:range chromoschema:SexChromosomeType ;
-    skos:definition "Only populated for sex chromosomes. Indicates the chromosome type. This is X or Y in mammals, W or Z in avians" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
-chromoschema:somal_type a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "somal_type" ;
-    rdfs:range chromoschema:AutosomeVsSexChromosome ;
-    skos:definition "indicates whether this is a sex-chromosome or not" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
-chromoschema:start a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "start" ;
-    rdfs:range linkml:Integer ;
-    skos:definition "Start location of the chromosomal part. Note we also include this for whole chromosomes - start will be zero" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
 chromoschema:strand a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "strand" ;
@@ -154,61 +55,53 @@ chromoschema:strand a owl:ObjectProperty,
     skos:exactMatch biolink:strand ;
     skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
-chromoschema:taxon a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "taxon" ;
-    rdfs:range chromoschema:TaxonIdentifier ;
-    skos:definition "The taxon to which the chromosome part belongs. Always NCBITaxon." ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
-    skos:note "OWL>> ObjectSomeValuesFrom" .
-
-chromoschema:type a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "type" ;
-    rdfs:range chromoschema:EntityType ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
-    skos:note "OWL>> SubClassOf" .
-
-chromoschema:BandDescriptor a owl:Class,
-        linkml:TypeDefinition ;
-    rdfs:subClassOf linkml:String .
-
-chromoschema:ChromosomeNameType a owl:Class,
-        linkml:TypeDefinition ;
-    rdfs:subClassOf linkml:String .
-
 chromoschema:Genome a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "Genome" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty chromoschema:name ],
+            owl:allValuesFrom chromoschema:GenomeBuild ;
+            owl:onProperty chromoschema:previous_builds ],
         [ a owl:Restriction ;
-            owl:allValuesFrom owl:Thing ;
-            owl:onProperty chromoschema:build ],
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:previous_builds ],
         [ a owl:Restriction ;
-            owl:minCardinality 1 ;
+            owl:allValuesFrom [ a rdfs:Datatype ;
+                    owl:onDatatype xsd:string ;
+                    owl:withRestrictions ( [ xsd:pattern "^\\\\w+$" ] ) ] ;
             owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:taxon ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
             owl:onProperty chromoschema:build ],
         [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty chromoschema:id ],
+            owl:allValuesFrom chromoschema:GenomeBuild ;
+            owl:onProperty chromoschema:build ],
         [ a owl:Restriction ;
-            owl:allValuesFrom owl:Thing ;
+            owl:allValuesFrom chromoschema:TaxonIdentifier ;
+            owl:onProperty chromoschema:taxon ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
             owl:onProperty chromoschema:name ],
         [ a owl:Restriction ;
-            owl:allValuesFrom [ a rdfs:Datatype ;
-                    owl:onDatatype xsd:string ;
-                    owl:withRestrictions ( [ xsd:pattern "^\\\\w+$" ] ) ] ;
+            owl:minCardinality 1 ;
             owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:minCardinality 1 ;
+            owl:onProperty chromoschema:name ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
             owl:onProperty chromoschema:build ],
         [ a owl:Restriction ;
-            owl:minCardinality 1 ;
-            owl:onProperty chromoschema:name ] ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:taxon ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:LabelType ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:id ] ;
     skos:definition """Represents a sequenced genome, one per species.
 Each genome can be associated with one or more builds""" ;
     skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
@@ -216,6 +109,35 @@ Each genome can be associated with one or more builds""" ;
 chromoschema:OrganismTaxon a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "OrganismTaxon" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:allValuesFrom [ a rdfs:Datatype ;
+                    owl:onDatatype xsd:string ;
+                    owl:withRestrictions ( [ xsd:pattern "^CHR:\\\\S+$" ] ) ] ;
+            owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:LabelType ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:common_name ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:LabelType ;
+            owl:onProperty chromoschema:common_name ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:common_name ],
+        [ a owl:Restriction ;
+            owl:minCardinality 1 ;
+            owl:onProperty chromoschema:id ] ;
     skos:definition "Represents a species, e.g. Homo sapiens" ;
     skos:exactMatch biolink:OrganismTaxon ;
     skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
@@ -224,84 +146,98 @@ chromoschema:StrandType a owl:Class,
         linkml:TypeDefinition ;
     rdfs:subClassOf linkml:Integer .
 
-chromoschema:TaxonIdentifier a owl:Class,
-        linkml:TypeDefinition ;
-    rdfs:subClassOf linkml:Uriorcurie .
-
 GO:0000791 a owl:Class,
         chromoschema:ChromatinType ;
-    rdfs:label "euchromatin" .
+    rdfs:label "euchromatin" ;
+    rdfs:subClassOf chromoschema:ChromatinType .
 
 GO:0000792 a owl:Class,
         chromoschema:ChromatinType ;
-    rdfs:label "heterochromatin" .
+    rdfs:label "heterochromatin" ;
+    rdfs:subClassOf chromoschema:ChromatinType .
 
 GO:0000803 a owl:Class,
         chromoschema:AutosomeVsSexChromosome ;
-    rdfs:label "sex_chromosome" .
+    rdfs:label "sex_chromosome" ;
+    rdfs:subClassOf chromoschema:AutosomeVsSexChromosome .
 
 GO:0000804 a owl:Class,
         chromoschema:SexChromosomeType ;
-    rdfs:label "W" .
+    rdfs:label "W" ;
+    rdfs:subClassOf chromoschema:SexChromosomeType .
 
 GO:0000805 a owl:Class,
         chromoschema:SexChromosomeType ;
-    rdfs:label "X" .
+    rdfs:label "X" ;
+    rdfs:subClassOf chromoschema:SexChromosomeType .
 
 GO:0000806 a owl:Class,
         chromoschema:SexChromosomeType ;
-    rdfs:label "Y" .
+    rdfs:label "Y" ;
+    rdfs:subClassOf chromoschema:SexChromosomeType .
 
 GO:0000807 a owl:Class,
         chromoschema:SexChromosomeType ;
-    rdfs:label "Z" .
+    rdfs:label "Z" ;
+    rdfs:subClassOf chromoschema:SexChromosomeType .
 
 GO:0005634 a owl:Class,
         chromoschema:LocationType ;
-    rdfs:label "nucleus" .
+    rdfs:label "nucleus" ;
+    rdfs:subClassOf chromoschema:LocationType .
 
 GO:0005694 a owl:Class,
         chromoschema:EntityType ;
-    rdfs:label "chromosome" .
+    rdfs:label "chromosome" ;
+    rdfs:subClassOf chromoschema:EntityType .
 
 GO:0005739 a owl:Class,
         chromoschema:LocationType ;
-    rdfs:label "mitochondrion" .
+    rdfs:label "mitochondrion" ;
+    rdfs:subClassOf chromoschema:LocationType .
 
 GO:0030849 a owl:Class,
         chromoschema:AutosomeVsSexChromosome ;
-    rdfs:label "autosome" .
+    rdfs:label "autosome" ;
+    rdfs:subClassOf chromoschema:AutosomeVsSexChromosome .
 
 GO:0098687 a owl:Class,
         chromoschema:EntityType ;
-    rdfs:label "chromosome_part" .
+    rdfs:label "chromosome_part" ;
+    rdfs:subClassOf chromoschema:EntityType .
 
-chromoschema:ChromatinType a owl:Class,
-        linkml:EnumDefinition ;
-    owl:unionOf ( GO:0000792 GO:0000791 ) ;
-    linkml:permissible_values GO:0000791,
-        GO:0000792 .
-
-chromoschema:GenomeBuild a owl:Class,
-        linkml:ClassDefinition ;
-    rdfs:label "GenomeBuild" ;
-    rdfs:subClassOf [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty chromoschema:id ],
-        [ a owl:Restriction ;
-            owl:minCardinality 1 ;
-            owl:onProperty chromoschema:id ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom owl:Thing ;
-            owl:onProperty chromoschema:id ] ;
-    skos:closeMatch edam:operation_0525 ;
-    skos:definition "Represents a specific build of a sequenced genome" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+chromoschema:BandDescriptor a owl:Class,
+        linkml:TypeDefinition ;
+    rdfs:subClassOf linkml:String .
 
-chromoschema:LabelType a owl:Class,
+chromoschema:ChromosomeNameType a owl:Class,
         linkml:TypeDefinition ;
     rdfs:subClassOf linkml:String .
 
+chromoschema:broad_synonyms a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "broad_synonyms" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:children a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "children" ;
+    rdfs:range chromoschema:ChromosomePart ;
+    skos:definition "Direct parts of this chromosome. zero to many." ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:exact_mappings a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "exact_mappings" ;
+    rdfs:range linkml:Uriorcurie ;
+    skos:definition "For a whole chromosome, this may be an assembled sequence in a database such as genbank or ensembl" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:exact_synonyms a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "exact_synonyms" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
 chromoschema:genomes a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "genomes" ;
@@ -312,23 +248,130 @@ chromoschema:has a owl:ObjectProperty,
     rdfs:label "has" ;
     skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
+chromoschema:previous_builds a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "previous_builds" ;
+    rdfs:range chromoschema:GenomeBuild ;
+    skos:definition "List of previous non-current builds" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
 chromoschema:taxons a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "taxons" ;
     skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
-chromoschema:AutosomeVsSexChromosome a owl:Class,
+chromoschema:TaxonIdentifier a owl:Class,
+        linkml:TypeDefinition ;
+    rdfs:subClassOf linkml:Uriorcurie .
+
+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:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    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" .
+
+chromoschema:cell_location a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "cell_location" ;
+    rdfs:range chromoschema:LocationType ;
+    skos:definition "which organelle the chromosome is associated with. For eukaryotes this is mitochondrion or nucleus. For prokaryotes the distinction does not make sense" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    skos:note "OWL>> ObjectSomeValuesFrom" .
+
+chromoschema:chromosome_name a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "chromosome_name" ;
+    rdfs:range chromoschema:ChromosomeNameType ;
+    skos:definition "E.g. chr1, chrM. Some species like C elegans may use roman numerals" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:common_name a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "common_name" ;
+    rdfs:range chromoschema:LabelType ;
+    skos:definition "E.g. human, mouse" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:end a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "end" ;
+    rdfs:range linkml:Integer ;
+    skos:definition "Start location of the chromosomal part. Note we also include this for whole chromosomes - end will be rightmost point" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:parent a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "parent" ;
+    rdfs:range chromoschema:ChromosomePart ;
+    skos:definition "Direct chromosomal part which this is a part of. The partonomy forms a tree so this is always zero or one. Different species have different rules but typically the partonomy will be something like 1p31.1 -> 1p31 -> 1p3 -> 1p -> 1" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    skos:note "OWL>> ObjectSomeValuesFrom" .
+
+chromoschema:sex_chromosome_type a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "sex_chromosome_type" ;
+    rdfs:range chromoschema:SexChromosomeType ;
+    skos:definition "Only populated for sex chromosomes. Indicates the chromosome type. This is X or Y in mammals, W or Z in avians" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:somal_type a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "somal_type" ;
+    rdfs:range chromoschema:AutosomeVsSexChromosome ;
+    skos:definition "indicates whether this is a sex-chromosome or not" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:start a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "start" ;
+    rdfs:range linkml:Integer ;
+    skos:definition "Start location of the chromosomal part. Note we also include this for whole chromosomes - start will be zero" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:type a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "type" ;
+    rdfs:range chromoschema:EntityType ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    skos:note "OWL>> SubClassOf" .
+
+chromoschema:ChromatinType a owl:Class,
         linkml:EnumDefinition ;
-    owl:unionOf ( GO:0000803 GO:0030849 ) ;
-    linkml:permissible_values GO:0000803,
-        GO:0030849 .
+    owl:unionOf ( GO:0000792 GO:0000791 ) ;
+    linkml:permissible_values GO:0000791,
+        GO:0000792 .
 
 chromoschema:ChromosomePart a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "ChromosomePart" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:minCardinality 1 ;
-            owl:onProperty chromoschema:id ],
+            owl:allValuesFrom chromoschema:ChromosomeNameType ;
+            owl:onProperty chromoschema:chromosome_name ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:EntityType ;
+            owl:onProperty chromoschema:type ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:cell_location ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:type ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:BandDescriptor ;
+            owl:onProperty chromoschema:band_descriptor ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom linkml:Integer ;
+            owl:onProperty chromoschema:end ],
         [ a owl:Restriction ;
             owl:allValuesFrom [ a rdfs:Datatype ;
                     owl:onDatatype xsd:string ;
@@ -336,13 +379,157 @@ chromoschema:ChromosomePart a owl:Class,
             owl:onProperty chromoschema:id ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty chromoschema:id ] ;
+            owl:onProperty chromoschema:start ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:cell_location ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:SexChromosomeType ;
+            owl:onProperty chromoschema:sex_chromosome_type ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:parent ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:broad_synonyms ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:AutosomeVsSexChromosome ;
+            owl:onProperty chromoschema:somal_type ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom linkml:Integer ;
+            owl:onProperty chromoschema:start ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:taxon ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:LabelType ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:chromosome_name ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:exact_mappings ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:build ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:TaxonIdentifier ;
+            owl:onProperty chromoschema:taxon ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom owl:Thing ;
+            owl:onProperty chromoschema:broad_synonyms ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:somal_type ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:LocationType ;
+            owl:onProperty chromoschema:cell_location ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:exact_synonyms ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:end ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:sex_chromosome_type ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:parent ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:children ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:build ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:band_descriptor ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom linkml:Uriorcurie ;
+            owl:onProperty chromoschema:exact_mappings ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:type ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:start ],
+        [ a owl:Restriction ;
+            owl:minCardinality 1 ;
+            owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom owl:Thing ;
+            owl:onProperty chromoschema:exact_synonyms ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:somal_type ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:band_descriptor ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:chromosome_name ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:taxon ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:end ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:ChromosomePart ;
+            owl:onProperty chromoschema:parent ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:sex_chromosome_type ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:ChromosomePart ;
+            owl:onProperty chromoschema:children ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:GenomeBuild ;
+            owl:onProperty chromoschema:build ] ;
     skos:definition "A Chromosome or a part of a chromosome (includes whole chromosomes, arms, and bands)" ;
     skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
     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" .
 
+chromoschema:GenomeBuild a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "GenomeBuild" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:LabelType ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty chromoschema:name ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:minCardinality 1 ;
+            owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom [ a rdfs:Datatype ;
+                    owl:onDatatype xsd:string ;
+                    owl:withRestrictions ( [ xsd:pattern "^CHR:\\\\S+$" ] ) ] ;
+            owl:onProperty chromoschema:id ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty chromoschema:name ] ;
+    skos:closeMatch edam:operation_0525 ;
+    skos:definition "Represents a specific build of a sequenced genome" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
+chromoschema:AutosomeVsSexChromosome a owl:Class,
+        linkml:EnumDefinition ;
+    owl:unionOf ( GO:0000803 GO:0030849 ) ;
+    linkml:permissible_values GO:0000803,
+        GO:0030849 .
+
 chromoschema:EntityType a owl:Class,
         linkml:EnumDefinition ;
     owl:unionOf ( GO:0005694 GO:0098687 ) ;
@@ -364,6 +551,18 @@ chromoschema:build a owl:ObjectProperty,
         gff:genome_build ;
     skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
 
+chromoschema:taxon a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "taxon" ;
+    rdfs:range chromoschema:TaxonIdentifier ;
+    skos:definition "The taxon to which the chromosome part belongs. Always NCBITaxon." ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
+    skos:note "OWL>> ObjectSomeValuesFrom" .
+
+chromoschema:LabelType a owl:Class,
+        linkml:TypeDefinition ;
+    rdfs:subClassOf linkml:String .
+
 chromoschema:SexChromosomeType a owl:Class,
         linkml:EnumDefinition ;
     owl:unionOf ( GO:0000805 GO:0000806 GO:0000804 GO:0000807 ) ;
@@ -372,13 +571,6 @@ chromoschema:SexChromosomeType a owl:Class,
         GO:0000806,
         GO:0000807 .
 
-chromoschema:name a owl:ObjectProperty,
-        linkml:SlotDefinition ;
-    rdfs:label "name" ;
-    rdfs:range chromoschema:LabelType ;
-    skos:definition "Unique human-readable label for the entity" ;
-    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
-
 chromoschema:id a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "id" ;
@@ -389,6 +581,13 @@ chromoschema:id a owl:ObjectProperty,
     skos:inScheme <https://w3id.org/biodatamodels/chromoschema> ;
     skos:note "will be of form CHR:...." .
 
+chromoschema:name a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "name" ;
+    rdfs:range chromoschema:LabelType ;
+    skos:definition "Unique human-readable label for the entity" ;
+    skos:inScheme <https://w3id.org/biodatamodels/chromoschema> .
+
 <https://w3id.org/biodatamodels/chromoschema> a owl:Ontology ;
     rdfs:label "ChromoSchema" ;
     skos:definition """Schema for representing Chromosomes and Chromosomal Regions.
diff --git a/tests/test_examples/test_from_dosdp.py b/tests/test_examples/test_from_dosdp.py
index a29a4ae..e5ddfc3 100644
--- a/tests/test_examples/test_from_dosdp.py
+++ b/tests/test_examples/test_from_dosdp.py
@@ -30,7 +30,7 @@ def test_as_owl(self):
         Test creation of OWL metamodel
         """
         yd = YAMLGenerator(SCHEMA_IN)
-        schema = yd.schema
+        # schema = yd.schema
         with open(OWLSCHEMA_OUT, 'w') as stream:
             stream.write(OwlSchemaGenerator(SCHEMA_IN).serialize())