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

Issue:
setting output flag for `linkml-data2owl` to a .ttl still yields a .ofn format
Usage documentation as per https://linkml.io/linkml-owl/usage/#usage
```
linkml-data2owl -s my_schema.yaml my_data.{yaml,json,tsv,rdf} -o my_ontology.owl.ttl
```
still generates a file with .ofn syntax, as opposed to turtle syntax
incompatibility with funowl 0.1.13
https://github.com/Harold-Solbrig/funowl/releases/tag/v0.1.13


Discussion / hints:
My guess is that the documentation just has a typo and it meant to `my_ontology.owl.ofn` as opposed to `my_ontology.owl.ttl`, as the help text from `linkml-data2owl` doesn't seem to suggest it supports converting to turtle
that sounds plausible


Fix patch:
diff --git a/.github/workflows/pypi-publish.yaml b/.github/workflows/pypi-publish.yaml
index 7b248cf..17ff898 100644
--- a/.github/workflows/pypi-publish.yaml
+++ b/.github/workflows/pypi-publish.yaml
@@ -9,45 +9,28 @@ jobs:
     name: Build and publish Python 🐍 distributions 📦 to PyPI
     runs-on: ubuntu-latest
 
-    #----------------------------------------------
-    #       check-out repo and set-up python     
-    #----------------------------------------------
     steps:
-    - uses: actions/checkout@v2
-
-    - name: Set up Python
-      uses: actions/setup-python@v2.2.2
-      with:
-        python-version: 3.9
-
-    #----------------------------------------------
-    #          install & configure poetry         
-    #----------------------------------------------
-    - name: Install Poetry
-      uses: snok/install-poetry@v1.1.6
-      with:
-        virtualenvs-create: true
-        virtualenvs-in-project: true
-
-    #----------------------------------------------
-    #            install dependencies
-    #----------------------------------------------
-    - name: Install dependencies
-      run: poetry install --no-interaction
-
-    #----------------------------------------------
-    #                 build dist
-    #----------------------------------------------
-    - name: Build source and wheel archives
-      run: |
-        poetry version $(git describe --tags --abbrev=0)
-        poetry build
-
-    #----------------------------------------------
-    #          publish package to PyPI     
-    #----------------------------------------------
-    - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@v1.2.2
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+      - uses: actions/checkout@v3.1.0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        run: |
+          pip install poetry
+          poetry self add "poetry-dynamic-versioning[plugin]"
+
+      # - name: Install dependencies
+      #   run: poetry install --no-interaction
+
+      - name: Build source and wheel archives
+        run: |
+          poetry build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.5.0
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}
diff --git a/docs/usage.md b/docs/usage.md
index 7eaba32..d5663b9 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -22,7 +22,7 @@ Minimally you need to specify two inputs:
 To convert:
 
 ```bash
-linkml-data2owl -s my_schema.yaml my_data.{yaml,json,tsv,rdf} -o my_ontology.owl.ttl 
+linkml-data2owl -s my_schema.yaml my_data.{yaml,json,tsv,rdf} -o my_ontology.ofn
 ```
 
 For all options, see:
diff --git a/linkml_owl/dumpers/owl_dumper.py b/linkml_owl/dumpers/owl_dumper.py
index 60b4464..187c2e5 100644
--- a/linkml_owl/dumpers/owl_dumper.py
+++ b/linkml_owl/dumpers/owl_dumper.py
@@ -1,3 +1,4 @@
+import sys
 from collections import defaultdict
 from typing import Optional, List, Set, Any, Union, Dict, Tuple
 from dataclasses import dataclass, field
@@ -15,7 +16,7 @@
 from linkml_runtime.index.object_index import ObjectIndex
 from linkml_runtime.utils.inference_utils import infer_all_slot_values, infer_slot_value, Config
 
-from rdflib import URIRef
+from rdflib import URIRef, Graph
 
 from linkml_runtime.linkml_model.meta import ClassDefinition, SchemaDefinition, SlotDefinition, Definition, \
     ClassDefinitionName
@@ -168,7 +169,7 @@ def to_ontology_document(self, element: Union[YAMLRoot, List[YAMLRoot]], schema:
             doc.prefixDeclarations.append(Prefix(pfx.prefix_prefix, pfx.prefix_reference))
         return doc
 
-    def dumps(self, element: YAMLRoot, schema: SchemaDefinition = None, schemaview: SchemaView = None, iri=None) -> str:
+    def dumps(self, element: YAMLRoot, schema: SchemaDefinition = None, schemaview: SchemaView = None, iri=None, output_type=None) -> str:
         """
         Dump a linkml instance tree to a function syntax OWL ontology string
 
@@ -176,12 +177,18 @@ def dumps(self, element: YAMLRoot, schema: SchemaDefinition = None, schemaview:
         :param schema:
         :param schemaview:
         :param iri:
+        :param output_type:
         :return:
         """
         if schemaview:
             schema = schemaview.schema
         doc = self.to_ontology_document(element, schema, iri=iri)
-        return str(doc)
+        if output_type == "ttl":
+            g = Graph()
+            doc.to_rdf(g)
+            return g.serialize(format="ttl")
+        else:
+            return str(doc)
 
     def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_object=True) -> Any:
         """
@@ -296,7 +303,7 @@ def transform(self, element: YAMLRoot, schema: SchemaDefinition, is_element_an_o
                             axiom_annotations.append(Annotation(ann_slot_iri, ann_val))
             # templates
             for tmpl in owl_templates:
-                self.add_axioms_from_template(tmpl, element)
+                self.add_axioms_from_template(tmpl, element, schema=schema)
             if schema_level_slot.slot_uri is not None:
                 slot_uri = self._get_IRI_str(schema_level_slot.slot_uri)
             else:
@@ -524,8 +531,9 @@ def _get_inferred_slot_annotations(self, slot: SlotDefinition, ann_key: str,
         anc_slots = [slot]
         sv = self.schemaview
         for anc_c in sv.class_ancestors(class_name, reflexive=True):
-            induced_slot = sv.induced_slot(slot.name, anc_c)
-            anc_slots.append(induced_slot)
+            if slot.name in sv.class_slots(anc_c):
+                induced_slot = sv.induced_slot(slot.name, anc_c)
+                anc_slots.append(induced_slot)
         for a in sv.slot_ancestors(slot.name, reflexive=True):
             anc_slots.append(sv.get_slot(a))
         for s in anc_slots:
@@ -634,20 +642,20 @@ def parse_axioms_string(self, owl_str: str, schemaview: SchemaView = None) -> On
         for prefix, url in schemaview.namespaces().items():
             prefix_lines.append(f'Prefix( {prefix}: = <{url}> )')
         header = "\n".join(prefix_lines)
-        owl_str = f'{header}\nOntology(\n{owl_str}\n)'
+        owl_str = f'{header}\nOntology(<http://example.org>\n{owl_str}\n)'
         logging.debug(owl_str)
         try:
             doc = to_python(owl_str)
         except Exception as e:
             logging.error(f'Error parsing generated OWL: {owl_str}')
             raise e
-        from funowl.writers.FunctionalWriter import FunctionalWriter
-        from rdflib import Graph
-        g = Graph()
-        for p in doc.prefixDeclarations:
-            g.namespace_manager.bind(p.prefixName, p.fullIRI)
-        fw = FunctionalWriter(g=g)
-        owl_str_roundtrip = doc.to_functional(fw)
+        #from funowl.writers.FunctionalWriter import FunctionalWriter
+        #from rdflib import Graph
+        #g = Graph()
+        #for p in doc.prefixDeclarations:
+        #    g.namespace_manager.bind(p.prefixName, p.fullIRI)
+        #fw = FunctionalWriter(g=g)
+        #owl_str_roundtrip = doc.to_functional(fw)
         #logging.debug(f'ROUNDTRIP = {owl_str_roundtrip}')
         return doc
 
@@ -686,6 +694,12 @@ def tr(e: YAMLRoot):
         else:
             d["tr"] = tr
         jt = Template(tstr)
+
+        def _tr(x):
+            fw = FunctionalWriter()
+            expr = self.transform(x, schema)
+            return expr.to_functional(fw)
+        d["tr"] = _tr
         owl_str = jt.render(**d)
         axioms = self.parse_axioms_string(owl_str).ontology.axioms
         self.ontology.axioms += axioms
@@ -724,14 +738,19 @@ def populate_missing_values(self, element: YAMLRoot):
               help="Path to python datamodel module")
 @click.option("--format", "-f",
               help="Input format (will be inferred from file suffix if not specified)")
-@click.option('-o', '--output', required=True,
+@click.option('-o', '--output',
+              type=click.File(mode="w"),
+              default=sys.stdout,
               help="Path to OWL functional syntax output")
+@click.option('-O', '--output-type',
+              type=click.Choice(["ofn", "ttl"]),
+              help="Output format")
 @click.option("--autofill/--no-autofill",
               default=False,
               show_default=True,
               help="If True, fill missing data slots using string_serialization")
 @click.argument('inputfile')
-def cli(inputfile: str, schema: str, target_class, module, output, format, autofill: bool, verbose: int, quiet: bool, **args):
+def cli(inputfile: str, schema: str, target_class, module, output, output_type, format, autofill: bool, verbose: int, quiet: bool, **args):
     """
     Dump LinkML instance data as OWL
 
@@ -739,19 +758,22 @@ def cli(inputfile: str, schema: str, target_class, module, output, format, autof
 
     Convert a CSV to OWL
 
-        linkml-data2owl -s tests/inputs/owl_dumper_test.yaml tests/inputs/parts.csv -o parts.ofn
+        linkml-data2owl -s owl_dumper_test.yaml parts.csv -o parts.ofn
 
-        Note in this example, there must be a class type designator column `@type` in the CSV
+    Note in this example, there must be a class type designator column `@type` in the CSV
 
     Convert a CSV to OWL, homogeneous classes:
 
-        linkml-data2owl -C EquivGenusAndPartOf -s tests/inputs/owl_dumper_test.yaml \
-            tests/inputs/parts_implicit_type.csv -o parts.ofn
+        linkml-data2owl -C EquivGenusAndPartOf -s owl_dumper_test.yaml \
+            parts_implicit_type.csv -o parts.ofn
 
     Convert YAML or JSON to OWL:
 
-        linkml-data2owl -s tests/inputs/owl_dumper_test.yaml tests/inputs/owl_dumper_test_data.yaml -o ont.ofn
+        linkml-data2owl -s owl_dumper_test.yaml owl_dumper_test_data.yaml -o ont.ofn
 
+    More documentation:
+
+        https://linkml.io/linkml-owl/
     """
     logger = logging.getLogger()
     if verbose >= 2:
@@ -775,12 +797,8 @@ def cli(inputfile: str, schema: str, target_class, module, output, format, autof
     dumper = OWLDumper()
     if autofill:
         dumper.autofill = True
-    doc = dumper.dumps(element, schemaview=sv)
-    if output is None:
-        print(str(doc))
-    else:
-        with open(output, 'w') as stream:
-            stream.write(str(doc))
+    doc = dumper.dumps(element, schemaview=sv, output_type=output_type)
+    output.write(str(doc))
 
 
 if __name__ == '__main__':
diff --git a/poetry.lock b/poetry.lock
index c675fc7..44fb98f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,10 +1,16 @@
+# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand.
+
 [[package]]
 name = "alabaster"
-version = "0.7.12"
+version = "0.7.13"
 description = "A configurable sidebar-enabled Sphinx theme"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
+files = [
+    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+]
 
 [[package]]
 name = "antlr4-python3-runtime"
@@ -13,6 +19,24 @@ description = "ANTLR 4.9.3 runtime for Python 3.7"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"},
+]
+
+[[package]]
+name = "arrow"
+version = "1.2.3"
+description = "Better dates & times for Python"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"},
+    {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"},
+]
+
+[package.dependencies]
+python-dateutil = ">=2.7.0"
 
 [[package]]
 name = "atomicwrites"
@@ -21,31 +45,43 @@ description = "Atomic file writes."
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
+]
 
 [[package]]
 name = "attrs"
-version = "22.1.0"
+version = "22.2.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
+files = [
+    {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
+    {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
+]
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
-docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
+cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
+tests = ["attrs[tests-no-zope]", "zope.interface"]
+tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "babel"
-version = "2.10.3"
+version = "2.12.1"
 description = "Internationalization utilities"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
+    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+]
 
 [package.dependencies]
-pytz = ">=2015.7"
+pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
 
 [[package]]
 name = "bcp47"
@@ -54,14 +90,32 @@ description = "Language tags made easy"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "bcp47-0.0.4-py3-none-any.whl", hash = "sha256:309d3bbaef8d6c9ac59d37ba2167cc6620b4e7467ec8f1e09641b659bb1c0c6d"},
+    {file = "bcp47-0.0.4.tar.gz", hash = "sha256:4878d2f3e697ef39ef3891a147280705e4377d5a8d7eb0702129b8d4a3718702"},
+]
 
 [[package]]
 name = "black"
-version = "22.10.0"
+version = "22.12.0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "black-22.12.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9eedd20838bd5d75b80c9f5487dbcb06836a43833a37846cf1d8c1cc01cef59d"},
+    {file = "black-22.12.0-cp310-cp310-win_amd64.whl", hash = "sha256:159a46a4947f73387b4d83e87ea006dbb2337eab6c879620a3ba52699b1f4351"},
+    {file = "black-22.12.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d30b212bffeb1e252b31dd269dfae69dd17e06d92b87ad26e23890f3efea366f"},
+    {file = "black-22.12.0-cp311-cp311-win_amd64.whl", hash = "sha256:7412e75863aa5c5411886804678b7d083c7c28421210180d67dfd8cf1221e1f4"},
+    {file = "black-22.12.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c116eed0efb9ff870ded8b62fe9f28dd61ef6e9ddd28d83d7d264a38417dcee2"},
+    {file = "black-22.12.0-cp37-cp37m-win_amd64.whl", hash = "sha256:1f58cbe16dfe8c12b7434e50ff889fa479072096d79f0a7f25e4ab8e94cd8350"},
+    {file = "black-22.12.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:77d86c9f3db9b1bf6761244bc0b3572a546f5fe37917a044e02f3166d5aafa7d"},
+    {file = "black-22.12.0-cp38-cp38-win_amd64.whl", hash = "sha256:82d9fe8fee3401e02e79767016b4907820a7dc28d70d137eb397b92ef3cc5bfc"},
+    {file = "black-22.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:101c69b23df9b44247bd88e1d7e90154336ac4992502d4197bdac35dd7ee3320"},
+    {file = "black-22.12.0-cp39-cp39-win_amd64.whl", hash = "sha256:559c7a1ba9a006226f09e4916060982fd27334ae1998e7a38b3f33a37f7a2148"},
+    {file = "black-22.12.0-py3-none-any.whl", hash = "sha256:436cc9167dd28040ad90d3b404aec22cedf24a6e4d7de221bec2730ec0c97bcf"},
+    {file = "black-22.12.0.tar.gz", hash = "sha256:229351e5a18ca30f447bf724d007f890f97e13af070bb6ad4c0a441cd7596a2f"},
+]
 
 [package.dependencies]
 click = ">=8.0.0"
@@ -79,11 +133,15 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "certifi"
-version = "2022.9.24"
+version = "2022.12.7"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"},
+    {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"},
+]
 
 [[package]]
 name = "cfgraph"
@@ -92,28 +150,109 @@ description = "rdflib collections flattening graph"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "CFGraph-0.2.1.tar.gz", hash = "sha256:b57fe7044a10b8ff65aa3a8a8ddc7d4cd77bf511b42e57289cd52cbc29f8fe74"},
+]
 
 [package.dependencies]
 rdflib = ">=0.4.2"
 
 [[package]]
 name = "chardet"
-version = "5.0.0"
+version = "5.1.0"
 description = "Universal encoding detector for Python 3"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
+files = [
+    {file = "chardet-5.1.0-py3-none-any.whl", hash = "sha256:362777fb014af596ad31334fde1e8c327dfdb076e1960d1694662d46a6917ab9"},
+    {file = "chardet-5.1.0.tar.gz", hash = "sha256:0d62712b956bc154f85fb0a266e2a3c5913c2967e00348701b32411d6def31e5"},
+]
 
 [[package]]
 name = "charset-normalizer"
-version = "2.1.1"
+version = "3.1.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "main"
 optional = false
-python-versions = ">=3.6.0"
-
-[package.extras]
-unicode_backport = ["unicodedata2"]
+python-versions = ">=3.7.0"
+files = [
+    {file = "charset-normalizer-3.1.0.tar.gz", hash = "sha256:34e0a2f9c370eb95597aae63bf85eb5e96826d81e3dcf88b8886012906f509b5"},
+    {file = "charset_normalizer-3.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:e0ac8959c929593fee38da1c2b64ee9778733cdf03c482c9ff1d508b6b593b2b"},
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 [[package]]
 name = "click"
@@ -122,25 +261,86 @@ description = "Composable command line interface toolkit"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
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 name = "colorama"
-version = "0.4.5"
+version = "0.4.6"
 description = "Cross-platform colored terminal text."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+files = [
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+]
 
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 name = "coverage"
-version = "6.5.0"
+version = "7.2.2"
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 category = "dev"
 optional = false
 python-versions = ">=3.7"
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+    {file = "coverage-7.2.2-pp37.pp38.pp39-none-any.whl", hash = "sha256:872d6ce1f5be73f05bea4df498c140b9e7ee5418bfa2cc8204e7f9b817caa968"},
+    {file = "coverage-7.2.2.tar.gz", hash = "sha256:36dd42da34fe94ed98c39887b86db9d06777b1c8f860520e21126a75507024f2"},
+]
 
 [package.dependencies]
 tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
@@ -148,6 +348,31 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1
 [package.extras]
 toml = ["tomli"]
 
+[[package]]
+name = "curies"
+version = "0.4.5"
+description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "curies-0.4.5-py3-none-any.whl", hash = "sha256:73281f6616ec47c8d46d842def7a2021416c9ac10f580f9116125abf4bd2f943"},
+    {file = "curies-0.4.5.tar.gz", hash = "sha256:c01626183b520db1b4af6a1fd41ee6d02462fea4ce54d8c5a528e5782268589c"},
+]
+
+[package.dependencies]
+pytrie = "*"
+requests = "*"
+
+[package.extras]
+bioregistry = ["bioregistry (>=0.5.136)"]
+docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-theme"]
+fastapi = ["fastapi", "httpx"]
+flask = ["flask"]
+pandas = ["pandas"]
+rdflib = ["rdflib"]
+tests = ["coverage", "pytest"]
+
 [[package]]
 name = "decorator"
 version = "5.1.1"
@@ -155,6 +380,10 @@ description = "Decorators for Humans"
 category = "main"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
+    {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
+]
 
 [[package]]
 name = "deprecated"
@@ -163,12 +392,16 @@ description = "Python @deprecated decorator to deprecate old python classes, fun
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "Deprecated-1.2.13-py2.py3-none-any.whl", hash = "sha256:64756e3e14c8c5eea9795d93c524551432a0be75629f8f29e67ab8caf076c76d"},
+    {file = "Deprecated-1.2.13.tar.gz", hash = "sha256:43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d"},
+]
 
 [package.dependencies]
 wrapt = ">=1.10,<2"
 
 [package.extras]
-dev = ["tox", "bump2version (<1)", "sphinx (<2)", "importlib-metadata (<3)", "importlib-resources (<4)", "configparser (<5)", "sphinxcontrib-websupport (<2)", "zipp (<2)", "PyTest (<5)", "PyTest-Cov (<2.6)", "pytest", "pytest-cov"]
+dev = ["PyTest", "PyTest (<5)", "PyTest-Cov", "PyTest-Cov (<2.6)", "bump2version (<1)", "configparser (<5)", "importlib-metadata (<3)", "importlib-resources (<4)", "sphinx (<2)", "sphinxcontrib-websupport (<2)", "tox", "zipp (<2)"]
 
 [[package]]
 name = "distlib"
@@ -177,6 +410,10 @@ description = "Distribution utilities"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "distlib-0.3.6-py2.py3-none-any.whl", hash = "sha256:f35c4b692542ca110de7ef0bea44d73981caeb34ca0b9b6b2e6d7790dda8f80e"},
+    {file = "distlib-0.3.6.tar.gz", hash = "sha256:14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46"},
+]
 
 [[package]]
 name = "docutils"
@@ -185,6 +422,10 @@ description = "Docutils -- Python Documentation Utilities"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "docutils-0.19-py3-none-any.whl", hash = "sha256:5e1de4d849fee02c63b040a4a3fd567f4ab104defd8a5511fbbc24a8a017efbc"},
+    {file = "docutils-0.19.tar.gz", hash = "sha256:33995a6753c30b7f577febfc2c50411fec6aac7f7ffeb7c4cfe5991072dcf9e6"},
+]
 
 [[package]]
 name = "et-xmlfile"
@@ -193,18 +434,38 @@ description = "An implementation of lxml.xmlfile for the standard library"
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "et_xmlfile-1.1.0-py3-none-any.whl", hash = "sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada"},
+    {file = "et_xmlfile-1.1.0.tar.gz", hash = "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c"},
+]
 
 [[package]]
 name = "filelock"
-version = "3.8.0"
+version = "3.10.0"
 description = "A platform independent file lock."
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "filelock-3.10.0-py3-none-any.whl", hash = "sha256:e90b34656470756edf8b19656785c5fea73afa1953f3e1b0d645cef11cab3182"},
+    {file = "filelock-3.10.0.tar.gz", hash = "sha256:3199fd0d3faea8b911be52b663dfccceb84c95949dd13179aa21436d1a79c4ce"},
+]
 
 [package.extras]
-docs = ["furo (>=2022.6.21)", "sphinx (>=5.1.1)", "sphinx-autodoc-typehints (>=1.19.1)"]
-testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2022.12.7)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.2.1)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"]
+
+[[package]]
+name = "fqdn"
+version = "1.5.1"
+description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers"
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4"
+files = [
+    {file = "fqdn-1.5.1-py3-none-any.whl", hash = "sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014"},
+    {file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"},
+]
 
 [[package]]
 name = "funowl"
@@ -213,6 +474,10 @@ description = "Python rendering of the OWL Functional syntax"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "funowl-0.1.12-py3-none-any.whl", hash = "sha256:44f2337d47d21ab6532f8f0e51173c506a0d9dae9efa959cb105b0311e352082"},
+    {file = "funowl-0.1.12.tar.gz", hash = "sha256:3316c37ecde08cdfa96ebcbcc02ed53c355dc56845d654a8f37aa7a913ca6f71"},
+]
 
 [package.dependencies]
 bcp47 = "*"
@@ -228,12 +493,16 @@ description = "Copy your docs directly to the gh-pages branch."
 category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "ghp-import-2.1.0.tar.gz", hash = "sha256:9c535c4c61193c2df8871222567d7fd7e5014d835f97dc7b7439069e2413d343"},
+    {file = "ghp_import-2.1.0-py3-none-any.whl", hash = "sha256:8337dd7b50877f163d4c0289bc1f1c7f127550241988d568c1db512c4324a619"},
+]
 
 [package.dependencies]
 python-dateutil = ">=2.8.1"
 
 [package.extras]
-dev = ["wheel", "flake8", "markdown", "twine"]
+dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "graphviz"
@@ -242,22 +511,89 @@ description = "Simple Python interface for Graphviz"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "graphviz-0.20.1-py3-none-any.whl", hash = "sha256:587c58a223b51611c0cf461132da386edd896a029524ca61a1462b880bf97977"},
+    {file = "graphviz-0.20.1.zip", hash = "sha256:8c58f14adaa3b947daf26c19bc1e98c4e0702cdc31cf99153e6f06904d492bf8"},
+]
 
 [package.extras]
-dev = ["tox (>=3)", "flake8", "pep8-naming", "wheel", "twine"]
+dev = ["flake8", "pep8-naming", "tox (>=3)", "twine", "wheel"]
 docs = ["sphinx (>=5)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"]
-test = ["pytest (>=7)", "pytest-mock (>=3)", "mock (>=4)", "pytest-cov", "coverage"]
+test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>=3)"]
 
 [[package]]
 name = "greenlet"
-version = "1.1.3.post0"
+version = "2.0.2"
 description = "Lightweight in-process concurrent programming"
 category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
+files = [
+    {file = "greenlet-2.0.2-cp27-cp27m-macosx_10_14_x86_64.whl", hash = "sha256:bdfea8c661e80d3c1c99ad7c3ff74e6e87184895bbaca6ee8cc61209f8b9b85d"},
+    {file = "greenlet-2.0.2-cp27-cp27m-manylinux2010_x86_64.whl", hash = "sha256:9d14b83fab60d5e8abe587d51c75b252bcc21683f24699ada8fb275d7712f5a9"},
+    {file = "greenlet-2.0.2-cp27-cp27m-win32.whl", hash = "sha256:6c3acb79b0bfd4fe733dff8bc62695283b57949ebcca05ae5c129eb606ff2d74"},
+    {file = "greenlet-2.0.2-cp27-cp27m-win_amd64.whl", hash = "sha256:283737e0da3f08bd637b5ad058507e578dd462db259f7f6e4c5c365ba4ee9343"},
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+    {file = "greenlet-2.0.2.tar.gz", hash = "sha256:e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0"},
+]
 
 [package.extras]
-docs = ["sphinx"]
+docs = ["Sphinx", "docutils (<0.18)"]
+test = ["objgraph", "psutil"]
 
 [[package]]
 name = "hbreader"
@@ -266,6 +602,10 @@ description = "Honey Badger reader - a generic file/url/string open and read too
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "hbreader-0.9.1-py3-none-any.whl", hash = "sha256:9a6e76c9d1afc1b977374a5dc430a1ebb0ea0488205546d4678d6e31cc5f6801"},
+    {file = "hbreader-0.9.1.tar.gz", hash = "sha256:d2c132f8ba6276d794c66224c3297cec25c8079d0a4cf019c061611e0a3b94fa"},
+]
 
 [[package]]
 name = "idna"
@@ -274,6 +614,10 @@ description = "Internationalized Domain Names in Applications (IDNA)"
 category = "main"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "idna-3.4-py3-none-any.whl", hash = "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"},
+    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
+]
 
 [[package]]
 name = "imagesize"
@@ -282,6 +626,10 @@ description = "Getting image size from png/jpeg/jpeg2000/gif file"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
+    {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
+]
 
 [[package]]
 name = "importlib-metadata"
@@ -290,37 +638,49 @@ description = "Read metadata from Python packages"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "importlib_metadata-4.13.0-py3-none-any.whl", hash = "sha256:8a8a81bcf996e74fee46f0d16bd3eaa382a7eb20fd82445c3ad11f4090334116"},
+    {file = "importlib_metadata-4.13.0.tar.gz", hash = "sha256:dd0173e8f150d6815e098fd354f6414b0f079af4644ddfe90c71e2fc6174346d"},
+]
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
 perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
+testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
 
 [[package]]
 name = "importlib-resources"
-version = "5.10.0"
+version = "5.12.0"
 description = "Read resources from Python packages"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "importlib_resources-5.12.0-py3-none-any.whl", hash = "sha256:7b1deeebbf351c7578e09bf2f63fa2ce8b5ffec296e0d349139d43cca061a81a"},
+    {file = "importlib_resources-5.12.0.tar.gz", hash = "sha256:4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6"},
+]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [[package]]
 name = "iniconfig"
-version = "1.1.1"
-description = "iniconfig: brain-dead simple config-ini parsing"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
+files = [
+    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
+    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+]
 
 [[package]]
 name = "isodate"
@@ -329,10 +689,29 @@ description = "An ISO 8601 date/time/duration parser and formatter"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "isodate-0.6.1-py2.py3-none-any.whl", hash = "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96"},
+    {file = "isodate-0.6.1.tar.gz", hash = "sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9"},
+]
 
 [package.dependencies]
 six = "*"
 
+[[package]]
+name = "isoduration"
+version = "20.11.0"
+description = "Operations with ISO 8601 durations"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"},
+    {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"},
+]
+
+[package.dependencies]
+arrow = ">=0.15.0"
+
 [[package]]
 name = "jinja2"
 version = "3.1.2"
@@ -340,6 +719,10 @@ 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"},
+]
 
 [package.dependencies]
 MarkupSafe = ">=2.0"
@@ -354,6 +737,10 @@ description = "Python library for denormalizing nested dicts or json objects to
 category = "main"
 optional = false
 python-versions = ">=3.7.0"
+files = [
+    {file = "json_flattener-0.1.9-py3-none-any.whl", hash = "sha256:6b027746f08bf37a75270f30c6690c7149d5f704d8af1740c346a3a1236bc941"},
+    {file = "json_flattener-0.1.9.tar.gz", hash = "sha256:84cf8523045ffb124301a602602201665fcb003a171ece87e6f46ed02f7f0c15"},
+]
 
 [package.dependencies]
 click = "*"
@@ -361,14 +748,15 @@ pyyaml = "*"
 
 [[package]]
 name = "jsonasobj"
-version = "2.0.1"
+version = "1.3.1"
 description = "JSON as python objects"
 category = "main"
 optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-hbreader = "*"
+python-versions = "*"
+files = [
+    {file = "jsonasobj-1.3.1-py3-none-any.whl", hash = "sha256:b9e329dc1ceaae7cf5d5b214684a0b100e0dad0be6d5bbabac281ec35ddeca65"},
+    {file = "jsonasobj-1.3.1.tar.gz", hash = "sha256:d52e0544a54a08f6ea3f77fa3387271e3648655e0eace2f21e825c26370e44a2"},
+]
 
 [[package]]
 name = "jsonasobj2"
@@ -377,6 +765,10 @@ description = "JSON as python objects - version 2"
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "jsonasobj2-1.0.4-py3-none-any.whl", hash = "sha256:12e86f86324d54fcf60632db94ea74488d5314e3da554c994fe1e2c6f29acb79"},
+    {file = "jsonasobj2-1.0.4.tar.gz", hash = "sha256:f50b1668ef478004aa487b2d2d094c304e5cb6b79337809f4a1f2975cc7fbb4e"},
+]
 
 [package.dependencies]
 hbreader = "*"
@@ -388,6 +780,10 @@ description = "Apply JSON-Patches (RFC 6902)"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
+    {file = "jsonpatch-1.32-py2.py3-none-any.whl", hash = "sha256:26ac385719ac9f54df8a2f0827bb8253aa3ea8ab7b3368457bcdb8c14595a397"},
+    {file = "jsonpatch-1.32.tar.gz", hash = "sha256:b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2"},
+]
 
 [package.dependencies]
 jsonpointer = ">=1.9"
@@ -399,6 +795,11 @@ description = "A final implementation of JSONPath for Python that aims to be sta
 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"},
+]
 
 [package.dependencies]
 decorator = "*"
@@ -412,20 +813,36 @@ description = "Identify specific nodes in a JSON document (RFC 6901)"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "jsonpointer-2.3-py2.py3-none-any.whl", hash = "sha256:51801e558539b4e9cd268638c078c6c5746c9ac96bc38152d443400e4f3793e9"},
+    {file = "jsonpointer-2.3.tar.gz", hash = "sha256:97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a"},
+]
 
 [[package]]
 name = "jsonschema"
-version = "4.16.0"
+version = "4.17.3"
 description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "jsonschema-4.17.3-py3-none-any.whl", hash = "sha256:a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6"},
+    {file = "jsonschema-4.17.3.tar.gz", hash = "sha256:0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d"},
+]
 
 [package.dependencies]
 attrs = ">=17.4.0"
+fqdn = {version = "*", optional = true, markers = "extra == \"format\""}
+idna = {version = "*", optional = true, markers = "extra == \"format\""}
 importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+isoduration = {version = "*", optional = true, markers = "extra == \"format\""}
+jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format\""}
 pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""}
 pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format\""}
+rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
+uri-template = {version = "*", optional = true, markers = "extra == \"format\""}
+webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\""}
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
@@ -433,11 +850,15 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "linkml"
-version = "1.3.10"
+version = "1.4.10"
 description = "Linked Open Data Modeling Language"
 category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
+files = [
+    {file = "linkml-1.4.10-py3-none-any.whl", hash = "sha256:0c25817f6d7f3940ed55fa5e73c135dc28a3371bf843d4bbb4de880c76167f54"},
+    {file = "linkml-1.4.10.tar.gz", hash = "sha256:19c4b64e11031e2b7aa69b20dab8349800644b1019d544967f36237c0b7e4a4e"},
+]
 
 [package.dependencies]
 antlr4-python3-runtime = ">=4.9.0,<4.10"
@@ -447,9 +868,9 @@ hbreader = "*"
 isodate = ">=0.6.0"
 jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
-jsonschema = ">=3.0.1"
+jsonschema = {version = ">=4.0.0", extras = ["format"]}
 linkml-dataops = "*"
-linkml-runtime = ">=1.3,<1.4"
+linkml-runtime = ">=1,<2"
 myst-parser = "*"
 openpyxl = "*"
 parse = "*"
@@ -464,12 +885,13 @@ pyyaml = "*"
 rdflib = ">=6.0.0"
 requests = ">=2.22"
 sphinx-click = "*"
+sphinx-rtd-theme = "*"
 sqlalchemy = ">=1.4.31"
 tox = ">=3.25.1,<4.0.0"
 watchdog = ">=0.9.0"
 
 [package.extras]
-docs = ["sphinx-rtd-theme", "sphinx"]
+docs = ["furo[docs] (>=2022.9.29,<2023.0.0)", "sphinx", "sphinxcontrib-mermaid[docs] (>=0.7.1,<0.8.0)"]
 
 [[package]]
 name = "linkml-dataops"
@@ -478,6 +900,10 @@ description = "LinkML Data Operations API"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "linkml_dataops-0.1.0-py3-none-any.whl", hash = "sha256:193cf7f659e5f07946d2c2761896910d5f7151d91282543b1363801f68307f4c"},
+    {file = "linkml_dataops-0.1.0.tar.gz", hash = "sha256:4550eab65e78b70dc3b9c651724a94ac2b1d1edb2fbe576465f1d6951a54ed04"},
+]
 
 [package.dependencies]
 jinja2 = "*"
@@ -488,20 +914,26 @@ linkml-runtime = ">=1.1.6"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.3.5"
+version = "1.4.9"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 category = "main"
 optional = false
-python-versions = ">=3.7.1,<4.0.0"
+python-versions = ">=3.7.6,<4.0.0"
+files = [
+    {file = "linkml_runtime-1.4.9-py3-none-any.whl", hash = "sha256:62bf8618ddf362be0f173f2fa1821c3e29309c897b8f1e2f83fb41dc599e72a6"},
+    {file = "linkml_runtime-1.4.9.tar.gz", hash = "sha256:64c383ce05351b0dce18fcbbdb38884f180466968dcf09c90689e1bfa72d4aa4"},
+]
 
 [package.dependencies]
 click = "*"
+curies = ">=0.4.0,<0.5.0"
 deprecated = "*"
 hbreader = "*"
 json-flattener = ">=0.1.9"
 jsonasobj2 = ">=1.0.4,<2.0.0"
 jsonschema = ">=3.2.0"
 prefixcommons = ">=0.1.12"
+prefixmaps = ">=0.1.4"
 pyyaml = "*"
 rdflib = ">=6.0.0"
 requests = "*"
@@ -513,6 +945,10 @@ description = "Python implementation of Markdown."
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "Markdown-3.3.7-py3-none-any.whl", hash = "sha256:f5da449a6e1c989a4cea2631aa8ee67caa5a2ef855d551c88f9e309f4634c621"},
+    {file = "Markdown-3.3.7.tar.gz", hash = "sha256:cbb516f16218e643d8e0a95b309f77eb118cb138d39a4f27851e6a63581db874"},
+]
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
@@ -522,48 +958,108 @@ testing = ["coverage", "pyyaml"]
 
 [[package]]
 name = "markdown-it-py"
-version = "2.1.0"
+version = "2.2.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "markdown-it-py-2.2.0.tar.gz", hash = "sha256:7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1"},
+    {file = "markdown_it_py-2.2.0-py3-none-any.whl", hash = "sha256:5a35f8d1870171d9acc47b99612dc146129b631baf04970128b568f190d0cc30"},
+]
 
 [package.dependencies]
 mdurl = ">=0.1,<1.0"
 
 [package.extras]
-testing = ["pytest-regressions", "pytest-cov", "pytest", "coverage"]
-rtd = ["sphinx-book-theme", "sphinx-design", "sphinx-copybutton", "sphinx", "pyyaml", "myst-parser", "attrs"]
-profiling = ["gprof2dot"]
+benchmarking = ["psutil", "pytest", "pytest-benchmark"]
+code-style = ["pre-commit (>=3.0,<4.0)"]
+compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"]
+linkify = ["linkify-it-py (>=1,<3)"]
 plugins = ["mdit-py-plugins"]
-linkify = ["linkify-it-py (>=1.0,<2.0)"]
-compare = ["panflute (>=2.1.3,<2.2.0)", "mistune (>=2.0.2,<2.1.0)", "mistletoe (>=0.8.1,<0.9.0)", "markdown (>=3.3.6,<3.4.0)", "commonmark (>=0.9.1,<0.10.0)"]
-code_style = ["pre-commit (==2.6)"]
-benchmarking = ["pytest-benchmark (>=3.2,<4.0)", "pytest", "psutil"]
+profiling = ["gprof2dot"]
+rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "markupsafe"
-version = "2.1.1"
+version = "2.1.2"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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 [[package]]
 name = "mdit-py-plugins"
-version = "0.3.1"
+version = "0.3.5"
 description = "Collection of plugins for markdown-it-py"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+    {file = "mdit_py_plugins-0.3.5-py3-none-any.whl", hash = "sha256:ca9a0714ea59a24b2b044a1831f48d817dd0c817e84339f20e7889f392d77c4e"},
+]
 
 [package.dependencies]
 markdown-it-py = ">=1.0.0,<3.0.0"
 
 [package.extras]
-testing = ["pytest-regressions", "pytest-cov", "pytest", "coverage"]
-rtd = ["sphinx-book-theme (>=0.1.0,<0.2.0)", "myst-parser (>=0.16.1,<0.17.0)", "attrs"]
-code_style = ["pre-commit"]
+code-style = ["pre-commit"]
+rtd = ["attrs", "myst-parser (>=0.16.1,<0.17.0)", "sphinx-book-theme (>=0.1.0,<0.2.0)"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "mdurl"
@@ -572,6 +1068,10 @@ description = "Markdown URL utilities"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"},
+    {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
+]
 
 [[package]]
 name = "mergedeep"
@@ -580,14 +1080,22 @@ description = "A deep merge function for 🐍."
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "mergedeep-1.3.4-py3-none-any.whl", hash = "sha256:70775750742b25c0d8f36c55aed03d24c3384d17c951b3175d898bd778ef0307"},
+    {file = "mergedeep-1.3.4.tar.gz", hash = "sha256:0096d52e9dad9939c3d975a774666af186eda617e6ca84df4c94dec30004f2a8"},
+]
 
 [[package]]
 name = "mkdocs"
-version = "1.4.1"
+version = "1.4.2"
 description = "Project documentation with Markdown."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "mkdocs-1.4.2-py3-none-any.whl", hash = "sha256:c8856a832c1e56702577023cd64cc5f84948280c1c0fcc6af4cd39006ea6aa8c"},
+    {file = "mkdocs-1.4.2.tar.gz", hash = "sha256:8947af423a6d0facf41ea1195b8e1e8c85ad94ac95ae307fe11232e0424b11c5"},
+]
 
 [package.dependencies]
 click = ">=7.0"
@@ -603,61 +1111,74 @@ pyyaml-env-tag = ">=0.1"
 watchdog = ">=2.0"
 
 [package.extras]
-min-versions = ["watchdog (==2.0)", "typing-extensions (==3.10)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "packaging (==20.5)", "mergedeep (==1.3.4)", "markupsafe (==2.0.1)", "markdown (==3.2.1)", "jinja2 (==2.11.1)", "importlib-metadata (==4.3)", "ghp-import (==1.0)", "colorama (==0.4)", "click (==7.0)", "babel (==2.9.0)"]
 i18n = ["babel (>=2.9.0)"]
+min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.3)", "jinja2 (==2.11.1)", "markdown (==3.2.1)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "packaging (==20.5)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "typing-extensions (==3.10)", "watchdog (==2.0)"]
 
 [[package]]
 name = "mypy-extensions"
-version = "0.4.3"
-description = "Experimental type system extensions for programs checked with the mypy typechecker."
+version = "1.0.0"
+description = "Type system extensions for programs checked with the mypy type checker."
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
+files = [
+    {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"},
+    {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
+]
 
 [[package]]
 name = "myst-parser"
-version = "0.18.1"
-description = "An extended commonmark compliant parser, with bridges to docutils & sphinx."
+version = "1.0.0"
+description = "An extended [CommonMark](https://spec.commonmark.org/) compliant parser,"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "myst-parser-1.0.0.tar.gz", hash = "sha256:502845659313099542bd38a2ae62f01360e7dd4b1310f025dd014dfc0439cdae"},
+    {file = "myst_parser-1.0.0-py3-none-any.whl", hash = "sha256:69fb40a586c6fa68995e6521ac0a525793935db7e724ca9bac1d33be51be9a4c"},
+]
 
 [package.dependencies]
 docutils = ">=0.15,<0.20"
 jinja2 = "*"
 markdown-it-py = ">=1.0.0,<3.0.0"
-mdit-py-plugins = ">=0.3.1,<0.4.0"
+mdit-py-plugins = ">=0.3.4,<0.4.0"
 pyyaml = "*"
-sphinx = ">=4,<6"
-typing-extensions = "*"
+sphinx = ">=5,<7"
 
 [package.extras]
-code_style = ["pre-commit (>=2.12,<3.0)"]
+code-style = ["pre-commit (>=3.0,<4.0)"]
 linkify = ["linkify-it-py (>=1.0,<2.0)"]
-rtd = ["ipython", "sphinx-book-theme", "sphinx-design", "sphinxext-rediraffe (>=0.2.7,<0.3.0)", "sphinxcontrib.mermaid (>=0.7.1,<0.8.0)", "sphinxext-opengraph (>=0.6.3,<0.7.0)"]
-testing = ["beautifulsoup4", "coverage", "pytest (>=6,<7)", "pytest-cov", "pytest-regressions", "pytest-param-files (>=0.3.4,<0.4.0)", "sphinx-pytest", "sphinx (<5.2)"]
+rtd = ["ipython", "pydata-sphinx-theme (==v0.13.0rc4)", "sphinx-autodoc2 (>=0.4.2,<0.5.0)", "sphinx-book-theme (==1.0.0rc2)", "sphinx-copybutton", "sphinx-design2", "sphinx-pyscript", "sphinx-tippy (>=0.3.1)", "sphinx-togglebutton", "sphinxext-opengraph (>=0.7.5,<0.8.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"]
+testing = ["beautifulsoup4", "coverage[toml]", "pytest (>=7,<8)", "pytest-cov", "pytest-param-files (>=0.3.4,<0.4.0)", "pytest-regressions", "sphinx-pytest"]
+testing-docutils = ["pygments", "pytest (>=7,<8)", "pytest-param-files (>=0.3.4,<0.4.0)"]
 
 [[package]]
 name = "openpyxl"
-version = "3.0.10"
+version = "3.1.2"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "openpyxl-3.1.2-py2.py3-none-any.whl", hash = "sha256:f91456ead12ab3c6c2e9491cf33ba6d08357d802192379bb482f1033ade496f5"},
+    {file = "openpyxl-3.1.2.tar.gz", hash = "sha256:a6f5977418eff3b2d5500d54d9db50c8277a368436f4e4f8ddb1be3422870184"},
+]
 
 [package.dependencies]
 et-xmlfile = "*"
 
 [[package]]
 name = "packaging"
-version = "21.3"
+version = "23.0"
 description = "Core utilities for Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
+python-versions = ">=3.7"
+files = [
+    {file = "packaging-23.0-py3-none-any.whl", hash = "sha256:714ac14496c3e68c99c29b00845f7a2b85f3bb6f1078fd9f72fd20f0570002b2"},
+    {file = "packaging-23.0.tar.gz", hash = "sha256:b6ad297f8907de0fa2fe1ccbd26fdaf387f5f47c7275fedf8cce89f99446cf97"},
+]
 
 [[package]]
 name = "parse"
@@ -666,14 +1187,21 @@ description = "parse() is the opposite of format()"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "parse-1.19.0.tar.gz", hash = "sha256:9ff82852bcb65d139813e2a5197627a94966245c897796760a3a2a8eb66f020b"},
+]
 
 [[package]]
 name = "pathspec"
-version = "0.10.1"
+version = "0.11.1"
 description = "Utility library for gitignore style pattern matching of file paths."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "pathspec-0.11.1-py3-none-any.whl", hash = "sha256:d8af70af76652554bd134c22b3e8a1cc46ed7d91edcdd721ef1a0c51a84a5293"},
+    {file = "pathspec-0.11.1.tar.gz", hash = "sha256:2798de800fa92780e33acca925945e9a19a133b715067cf165b8866c15a31687"},
+]
 
 [[package]]
 name = "pkgutil-resolve-name"
@@ -682,18 +1210,26 @@ description = "Resolve a name to an object."
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "pkgutil_resolve_name-1.3.10-py3-none-any.whl", hash = "sha256:ca27cc078d25c5ad71a9de0a7a330146c4e014c2462d9af19c6b828280649c5e"},
+    {file = "pkgutil_resolve_name-1.3.10.tar.gz", hash = "sha256:357d6c9e6a755653cfd78893817c0853af365dd51ec97f3d358a819373bbd174"},
+]
 
 [[package]]
 name = "platformdirs"
-version = "2.5.2"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "3.1.1"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "platformdirs-3.1.1-py3-none-any.whl", hash = "sha256:e5986afb596e4bb5bde29a79ac9061aa955b94fca2399b7aaac4090860920dd8"},
+    {file = "platformdirs-3.1.1.tar.gz", hash = "sha256:024996549ee88ec1a9aa99ff7f8fc819bb59e2c3477b410d90a16d32d6e707aa"},
+]
 
 [package.extras]
-docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
-test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
+docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
 
 [[package]]
 name = "pluggy"
@@ -702,10 +1238,14 @@ description = "plugin and hook calling mechanisms for python"
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "pluggy-1.0.0-py2.py3-none-any.whl", hash = "sha256:74134bbf457f031a36d68416e1509f34bd5ccc019f0bcc952c7b909d06b37bd3"},
+    {file = "pluggy-1.0.0.tar.gz", hash = "sha256:4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159"},
+]
 
 [package.extras]
-testing = ["pytest-benchmark", "pytest"]
-dev = ["tox", "pre-commit"]
+dev = ["pre-commit", "tox"]
+testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "ply"
@@ -714,6 +1254,10 @@ description = "Python Lex & Yacc"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "ply-3.11-py2.py3-none-any.whl", hash = "sha256:096f9b8350b65ebd2fd1346b12452efe5b9607f7482813ffca50c22722a807ce"},
+    {file = "ply-3.11.tar.gz", hash = "sha256:00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3"},
+]
 
 [[package]]
 name = "prefixcommons"
@@ -722,6 +1266,10 @@ description = "A python API for working with ID prefixes"
 category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
+files = [
+    {file = "prefixcommons-0.1.12-py3-none-any.whl", hash = "sha256:16dbc0a1f775e003c724f19a694fcfa3174608f5c8b0e893d494cf8098ac7f8b"},
+    {file = "prefixcommons-0.1.12.tar.gz", hash = "sha256:22c4e2d37b63487b3ab48f0495b70f14564cb346a15220f23919eb0c1851f69f"},
+]
 
 [package.dependencies]
 click = ">=8.1.3,<9.0.0"
@@ -731,15 +1279,19 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.1.3"
-description = ""
+version = "0.1.4"
+description = "A python library for retrieving semantic prefix maps"
 category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
+files = [
+    {file = "prefixmaps-0.1.4-py3-none-any.whl", hash = "sha256:845457a5149e56b676827d002200840ae487052f08879a8d6ca9093aa6b9213e"},
+    {file = "prefixmaps-0.1.4.tar.gz", hash = "sha256:7ce9c8c1f1987f0341a71a2f869344e621b49c478c78a931817ce3dda5965980"},
+]
 
 [package.dependencies]
 importlib-metadata = ">=4.12.0,<5.0.0"
-PyYAML = ">=6.0,<7.0"
+pyyaml = ">=5.3.1"
 
 [[package]]
 name = "py"
@@ -748,17 +1300,59 @@ description = "library with cross-python path, ini-parsing, io, code, log facili
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
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+    {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"},
+]
 
 [[package]]
 name = "pydantic"
-version = "1.10.2"
+version = "1.10.6"
 description = "Data validation and settings management using python type hints"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
 
 [package.dependencies]
-typing-extensions = ">=4.1.0"
+typing-extensions = ">=4.2.0"
 
 [package.extras]
 dotenv = ["python-dotenv (>=0.10.4)"]
@@ -766,11 +1360,15 @@ email = ["email-validator (>=1.0.3)"]
 
 [[package]]
 name = "pygments"
-version = "2.13.0"
+version = "2.14.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "Pygments-2.14.0-py3-none-any.whl", hash = "sha256:fa7bd7bd2771287c0de303af8bfdfc731f51bd2c6a47ab69d117138893b82717"},
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+]
 
 [package.extras]
 plugins = ["importlib-metadata"]
@@ -782,6 +1380,10 @@ description = "Python JSON Schema Grammar interpreter"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "PyJSG-0.11.10-py3-none-any.whl", hash = "sha256:10af60ff42219be7e85bf7f11c19b648715b0b29eb2ddbd269e87069a7c3f26d"},
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+]
 
 [package.dependencies]
 antlr4-python3-runtime = ">=4.9.3,<4.10.0"
@@ -794,17 +1396,50 @@ description = "pyparsing module - Classes and methods to define and execute pars
 category = "main"
 optional = false
 python-versions = ">=3.6.8"
+files = [
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+    {file = "pyparsing-3.0.9.tar.gz", hash = "sha256:2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb"},
+]
 
 [package.extras]
-diagrams = ["railroad-diagrams", "jinja2"]
+diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyrsistent"
-version = "0.18.1"
+version = "0.19.3"
 description = "Persistent/Functional/Immutable data structures"
 category = "main"
 optional = false
 python-versions = ">=3.7"
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+]
 
 [[package]]
 name = "pyshex"
@@ -813,6 +1448,10 @@ description = "Python ShEx Implementation"
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "PyShEx-0.8.1-py3-none-any.whl", hash = "sha256:6da1b10123e191abf8dcb6bf3e54aa3e1fcf771df5d1a0ed453217c8900c8e6a"},
+    {file = "PyShEx-0.8.1.tar.gz", hash = "sha256:3c5c4d45fe27faaadae803cb008c41acf8ee784da7868b04fd84967e75be70d0"},
+]
 
 [package.dependencies]
 cfgraph = ">=0.2.1"
@@ -832,6 +1471,10 @@ description = "PyShExC - Python ShEx compiler"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "PyShExC-0.9.1-py2.py3-none-any.whl", hash = "sha256:efc55ed5cb2453e9df569b03e282505e96bb06597934288f3b23dd980ef10028"},
+    {file = "PyShExC-0.9.1.tar.gz", hash = "sha256:35a9975d4b9afeb20ef710fb6680871756381d0c39fbb5470b3b506581a304d3"},
+]
 
 [package.dependencies]
 antlr4-python3-runtime = ">=4.9.3,<4.10.0"
@@ -848,6 +1491,10 @@ description = "pytest: simple powerful testing with Python"
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
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+    {file = "pytest-6.2.5.tar.gz", hash = "sha256:131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89"},
+]
 
 [package.dependencies]
 atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
@@ -869,13 +1516,17 @@ description = "Pytest plugin for measuring coverage."
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "pytest-cov-3.0.0.tar.gz", hash = "sha256:e7f0f5b1617d2210a2cabc266dfe2f4c75a8d32fb89eafb7ad9d06f6d076d470"},
+    {file = "pytest_cov-3.0.0-py3-none-any.whl", hash = "sha256:578d5d15ac4a25e5f961c938b85a05b09fdaae9deef3bb6de9a6e766622ca7a6"},
+]
 
 [package.dependencies]
 coverage = {version = ">=5.2.1", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
-testing = ["virtualenv", "pytest-xdist", "six", "process-tests", "hunter", "fields"]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
 
 [[package]]
 name = "pytest-logging"
@@ -884,6 +1535,9 @@ description = "Configures logging and allows tweaking the log level with a py.te
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "pytest-logging-2015.11.4.tar.gz", hash = "sha256:cec5c85ecf18aab7b2ead5498a31b9f758680ef5a902b9054ab3f2bdbb77c896"},
+]
 
 [package.dependencies]
 pytest = ">=2.8.1"
@@ -895,17 +1549,39 @@ description = "Extensions to the standard Python datetime module"
 category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
+files = [
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+]
 
 [package.dependencies]
 six = ">=1.5"
 
+[[package]]
+name = "pytrie"
+version = "0.4.0"
+description = "A pure Python implementation of the trie data structure."
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "PyTrie-0.4.0.tar.gz", hash = "sha256:8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379"},
+]
+
+[package.dependencies]
+sortedcontainers = "*"
+
 [[package]]
 name = "pytz"
-version = "2022.5"
+version = "2022.7.1"
 description = "World timezone definitions, modern and historical"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
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+]
 
 [[package]]
 name = "pyyaml"
@@ -914,6 +1590,48 @@ description = "YAML parser and emitter for Python"
 category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
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+    {file = "PyYAML-6.0-cp39-cp39-win32.whl", hash = "sha256:b5b9eccad747aabaaffbc6064800670f0c297e52c12754eb1d976c57e4f74dcb"},
+    {file = "PyYAML-6.0-cp39-cp39-win_amd64.whl", hash = "sha256:b3d267842bf12586ba6c734f89d1f5b871df0273157918b0ccefa29deb05c21c"},
+    {file = "PyYAML-6.0.tar.gz", hash = "sha256:68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2"},
+]
 
 [[package]]
 name = "pyyaml-env-tag"
@@ -922,6 +1640,10 @@ description = "A custom YAML tag for referencing environment variables in YAML f
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "pyyaml_env_tag-0.1-py3-none-any.whl", hash = "sha256:af31106dec8a4d68c60207c1886031cbf839b68aa7abccdb19868200532c2069"},
+    {file = "pyyaml_env_tag-0.1.tar.gz", hash = "sha256:70092675bda14fdec33b31ba77e7543de9ddc88f2e5b99160396572d11525bdb"},
+]
 
 [package.dependencies]
 pyyaml = "*"
@@ -933,15 +1655,20 @@ description = "RDFLib is a Python library for working with RDF, a simple yet pow
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "rdflib-6.2.0-py3-none-any.whl", hash = "sha256:85c34a86dfc517a41e5f2425a41a0aceacc23983462b32e68610b9fad1383bca"},
+    {file = "rdflib-6.2.0.tar.gz", hash = "sha256:62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942"},
+]
 
 [package.dependencies]
 isodate = "*"
 pyparsing = "*"
+setuptools = "*"
 
 [package.extras]
 berkeleydb = ["berkeleydb"]
-dev = ["black (==22.6.0)", "flake8", "isort", "mypy", "pep8-naming", "types-setuptools", "flakeheaven"]
-docs = ["myst-parser", "sphinx (<6)", "sphinxcontrib-apidoc", "sphinxcontrib-kroki", "sphinx-autodoc-typehints"]
+dev = ["black (==22.6.0)", "flake8", "flakeheaven", "isort", "mypy", "pep8-naming", "types-setuptools"]
+docs = ["myst-parser", "sphinx (<6)", "sphinx-autodoc-typehints", "sphinxcontrib-apidoc", "sphinxcontrib-kroki"]
 html = ["html5lib"]
 networkx = ["networkx"]
 tests = ["html5lib", "pytest", "pytest-cov"]
@@ -953,6 +1680,10 @@ description = "rdflib extension adding JSON-LD parser and serializer"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "rdflib-jsonld-0.6.1.tar.gz", hash = "sha256:eda5a42a2e09f80d4da78e32b5c684bccdf275368f1541e6b7bcddfb1382a0e0"},
+    {file = "rdflib_jsonld-0.6.1-py2.py3-none-any.whl", hash = "sha256:bcf84317e947a661bae0a3f2aee1eced697075fc4ac4db6065a3340ea0f10fc2"},
+]
 
 [package.dependencies]
 rdflib = ">=5.0.0"
@@ -964,6 +1695,10 @@ description = "Shim for rdflib 5 and 6 incompatibilities"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "rdflib_shim-1.0.3-py3-none-any.whl", hash = "sha256:7a853e7750ef1e9bf4e35dea27d54e02d4ed087de5a9e0c329c4a6d82d647081"},
+    {file = "rdflib_shim-1.0.3.tar.gz", hash = "sha256:d955d11e2986aab42b6830ca56ac6bc9c893abd1d049a161c6de2f1b99d4fc0d"},
+]
 
 [package.dependencies]
 rdflib = ">=5.0.0"
@@ -971,21 +1706,40 @@ rdflib-jsonld = "0.6.1"
 
 [[package]]
 name = "requests"
-version = "2.28.1"
+version = "2.28.2"
 description = "Python HTTP for Humans."
 category = "main"
 optional = false
 python-versions = ">=3.7, <4"
+files = [
+    {file = "requests-2.28.2-py3-none-any.whl", hash = "sha256:64299f4909223da747622c030b781c0d7811e359c37124b4bd368fb8c6518baa"},
+    {file = "requests-2.28.2.tar.gz", hash = "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf"},
+]
 
 [package.dependencies]
 certifi = ">=2017.4.17"
-charset-normalizer = ">=2,<3"
+charset-normalizer = ">=2,<4"
 idna = ">=2.5,<4"
 urllib3 = ">=1.21.1,<1.27"
 
 [package.extras]
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
-use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
+
+[[package]]
+name = "rfc3339-validator"
+version = "0.1.4"
+description = "A pure python RFC3339 validator"
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
+    {file = "rfc3339_validator-0.1.4-py2.py3-none-any.whl", hash = "sha256:24f6ec1eda14ef823da9e36ec7113124b39c04d50a4d3d3a3c2859577e7791fa"},
+    {file = "rfc3339_validator-0.1.4.tar.gz", hash = "sha256:138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b"},
+]
+
+[package.dependencies]
+six = "*"
 
 [[package]]
 name = "rfc3987"
@@ -994,14 +1748,22 @@ description = "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "rfc3987-1.3.8-py2.py3-none-any.whl", hash = "sha256:10702b1e51e5658843460b189b185c0366d2cf4cff716f13111b0ea9fd2dce53"},
+    {file = "rfc3987-1.3.8.tar.gz", hash = "sha256:d3c4d257a560d544e9826b38bc81db676890c79ab9d7ac92b39c7a253d5ca733"},
+]
 
 [[package]]
-name = "ruamel.yaml"
+name = "ruamel-yaml"
 version = "0.17.21"
 description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
 category = "main"
 optional = false
 python-versions = ">=3"
+files = [
+    {file = "ruamel.yaml-0.17.21-py3-none-any.whl", hash = "sha256:742b35d3d665023981bd6d16b3d24248ce5df75fdb4e2924e93a05c1f8b61ca7"},
+    {file = "ruamel.yaml-0.17.21.tar.gz", hash = "sha256:8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af"},
+]
 
 [package.dependencies]
 "ruamel.yaml.clib" = {version = ">=0.2.6", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.11\""}
@@ -1011,12 +1773,67 @@ docs = ["ryd"]
 jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"]
 
 [[package]]
-name = "ruamel.yaml.clib"
+name = "ruamel-yaml-clib"
 version = "0.2.7"
 description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml"
 category = "main"
 optional = false
 python-versions = ">=3.5"
+files = [
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+]
+
+[[package]]
+name = "setuptools"
+version = "67.6.0"
+description = "Easily download, build, install, upgrade, and uninstall Python packages"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "shexjsg"
@@ -1025,6 +1842,10 @@ description = "ShExJSG - Astract Syntax Tree for the ShEx 2.0 language"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "ShExJSG-0.8.2-py2.py3-none-any.whl", hash = "sha256:3b0d8432dd313bee9e1343382c5e02e9908dd941a7dd7342bf8c0200fe523766"},
+    {file = "ShExJSG-0.8.2.tar.gz", hash = "sha256:f17a629fc577fa344382bdee143cd9ff86588537f9f811f66cea6f63cdbcd0b6"},
+]
 
 [package.dependencies]
 pyjsg = ">=0.11.10"
@@ -1036,6 +1857,10 @@ description = "Python 2 and 3 compatibility utilities"
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+files = [
+    {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
+    {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
+]
 
 [[package]]
 name = "snowballstemmer"
@@ -1044,6 +1869,22 @@ description = "This package provides 29 stemmers for 28 languages generated from
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
+    {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
+]
+
+[[package]]
+name = "sortedcontainers"
+version = "2.4.0"
+description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "sortedcontainers-2.4.0-py2.py3-none-any.whl", hash = "sha256:a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0"},
+    {file = "sortedcontainers-2.4.0.tar.gz", hash = "sha256:25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88"},
+]
 
 [[package]]
 name = "sparqlslurper"
@@ -1052,6 +1893,10 @@ description = "SPARQL Slurper for rdflib"
 category = "main"
 optional = false
 python-versions = ">=3.7.4"
+files = [
+    {file = "sparqlslurper-0.5.1-py3-none-any.whl", hash = "sha256:ae49b2d8ce3dd38df7a40465b228ad5d33fb7e11b3f248d195f9cadfc9cfff87"},
+    {file = "sparqlslurper-0.5.1.tar.gz", hash = "sha256:9282ebb064fc6152a58269d194cb1e7b275b0f095425a578d75b96dcc851f546"},
+]
 
 [package.dependencies]
 rdflib = ">=5.0.0"
@@ -1065,35 +1910,43 @@ description = "SPARQL Endpoint interface to Python"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "SPARQLWrapper-2.0.0-py3-none-any.whl", hash = "sha256:c99a7204fff676ee28e6acef327dc1ff8451c6f7217dcd8d49e8872f324a8a20"},
+    {file = "SPARQLWrapper-2.0.0.tar.gz", hash = "sha256:3fed3ebcc77617a4a74d2644b86fd88e0f32e7f7003ac7b2b334c026201731f1"},
+]
 
 [package.dependencies]
 rdflib = ">=6.1.1"
 
 [package.extras]
-pandas = ["pandas (>=1.3.5)"]
+dev = ["mypy (>=0.931)", "pandas (>=1.3.5)", "pandas-stubs (>=1.2.0.48)", "setuptools (>=3.7.1)"]
+docs = ["sphinx (<5)", "sphinx-rtd-theme"]
 keepalive = ["keepalive (>=0.5)"]
-docs = ["sphinx-rtd-theme", "sphinx (<5)"]
-dev = ["pandas-stubs (>=1.2.0.48)", "pandas (>=1.3.5)", "mypy (>=0.931)", "setuptools (>=3.7.1)"]
+pandas = ["pandas (>=1.3.5)"]
 
 [[package]]
 name = "sphinx"
-version = "5.3.0"
+version = "6.1.3"
 description = "Python documentation generator"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
+files = [
+    {file = "Sphinx-6.1.3.tar.gz", hash = "sha256:0dac3b698538ffef41716cf97ba26c1c7788dba73ce6f150c1ff5b4720786dd2"},
+    {file = "sphinx-6.1.3-py3-none-any.whl", hash = "sha256:807d1cb3d6be87eb78a381c3e70ebd8d346b9a25f3753e9947e866b2786865fc"},
+]
 
 [package.dependencies]
 alabaster = ">=0.7,<0.8"
 babel = ">=2.9"
 colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.14,<0.20"
+docutils = ">=0.18,<0.20"
 imagesize = ">=1.3"
 importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
 Jinja2 = ">=3.0"
 packaging = ">=21.0"
-Pygments = ">=2.12"
-requests = ">=2.5.0"
+Pygments = ">=2.13"
+requests = ">=2.25.0"
 snowballstemmer = ">=2.0"
 sphinxcontrib-applehelp = "*"
 sphinxcontrib-devhelp = "*"
@@ -1104,33 +1957,59 @@ sphinxcontrib-serializinghtml = ">=1.1.5"
 
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
-lint = ["flake8 (>=3.5.0)", "flake8-comprehensions", "flake8-bugbear", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "docutils-stubs", "types-typed-ast", "types-requests"]
-test = ["pytest (>=4.6)", "html5lib", "typed-ast", "cython"]
+lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-simplify", "isort", "mypy (>=0.990)", "ruff", "sphinx-lint", "types-requests"]
+test = ["cython", "html5lib", "pytest (>=4.6)"]
 
 [[package]]
 name = "sphinx-click"
-version = "4.3.0"
+version = "4.4.0"
 description = "Sphinx extension that automatically documents click applications"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "sphinx-click-4.4.0.tar.gz", hash = "sha256:cc67692bd28f482c7f01531c61b64e9d2f069bfcf3d24cbbb51d4a84a749fa48"},
+    {file = "sphinx_click-4.4.0-py3-none-any.whl", hash = "sha256:2821c10a68fc9ee6ce7c92fad26540d8d8c8f45e6d7258f0e4fb7529ae8fab49"},
+]
 
 [package.dependencies]
 click = ">=7.0"
 docutils = "*"
 sphinx = ">=2.0"
 
+[[package]]
+name = "sphinx-rtd-theme"
+version = "0.5.1"
+description = "Read the Docs theme for Sphinx"
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "sphinx_rtd_theme-0.5.1-py2.py3-none-any.whl", hash = "sha256:fa6bebd5ab9a73da8e102509a86f3fcc36dec04a0b52ea80e5a033b2aba00113"},
+    {file = "sphinx_rtd_theme-0.5.1.tar.gz", hash = "sha256:eda689eda0c7301a80cf122dad28b1861e5605cbf455558f3775e1e8200e83a5"},
+]
+
+[package.dependencies]
+sphinx = "*"
+
+[package.extras]
+dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client"]
+
 [[package]]
 name = "sphinxcontrib-applehelp"
-version = "1.0.2"
-description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books"
+version = "1.0.4"
+description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 category = "main"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-applehelp-1.0.4.tar.gz", hash = "sha256:828f867945bbe39817c210a1abfd1bc4895c8b73fcaade56d45357a348a07d7e"},
+    {file = "sphinxcontrib_applehelp-1.0.4-py3-none-any.whl", hash = "sha256:29d341f67fb0f6f586b23ad80e072c8e6ad0b48417db2bde114a4c9746feb228"},
+]
 
 [package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
-lint = ["docutils-stubs", "mypy", "flake8"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
@@ -1139,22 +2018,30 @@ description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp
 category = "main"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
+    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
+]
 
 [package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
-lint = ["docutils-stubs", "mypy", "flake8"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.0"
+version = "2.0.1"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
+files = [
+    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
+    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
+]
 
 [package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["html5lib", "pytest"]
-lint = ["docutils-stubs", "mypy", "flake8"]
 
 [[package]]
 name = "sphinxcontrib-jsmath"
@@ -1163,9 +2050,13 @@ description = "A sphinx extension which renders display math in HTML via JavaScr
 category = "main"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
+    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
+]
 
 [package.extras]
-test = ["mypy", "flake8", "pytest"]
+test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
@@ -1174,10 +2065,14 @@ description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp d
 category = "main"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
+    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
+]
 
 [package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
-lint = ["docutils-stubs", "mypy", "flake8"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
@@ -1186,41 +2081,91 @@ description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs
 category = "main"
 optional = false
 python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
+    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
+]
 
 [package.extras]
-lint = ["flake8", "mypy", "docutils-stubs"]
+lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["pytest"]
 
 [[package]]
 name = "sqlalchemy"
-version = "1.4.42"
+version = "2.0.7"
 description = "Database Abstraction Library"
 category = "main"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+python-versions = ">=3.7"
+files = [
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+]
 
 [package.dependencies]
-greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (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\")"}
+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"
 
 [package.extras]
-aiomysql = ["greenlet (!=0.4.17)", "aiomysql"]
-aiosqlite = ["typing_extensions (!=3.10.0.1)", "greenlet (!=0.4.17)", "aiosqlite"]
+aiomysql = ["aiomysql", "greenlet (!=0.4.17)"]
+aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
-asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4)"]
-mariadb_connector = ["mariadb (>=1.0.1,!=1.1.2)"]
+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)"]
 mssql = ["pyodbc"]
-mssql_pymssql = ["pymssql"]
-mssql_pyodbc = ["pyodbc"]
-mypy = ["sqlalchemy2-stubs", "mypy (>=0.910)"]
-mysql = ["mysqlclient (>=1.4.0,<2)", "mysqlclient (>=1.4.0)"]
-mysql_connector = ["mysql-connector-python"]
-oracle = ["cx_oracle (>=7,<8)", "cx_oracle (>=7)"]
+mssql-pymssql = ["pymssql"]
+mssql-pyodbc = ["pyodbc"]
+mypy = ["mypy (>=0.910)"]
+mysql = ["mysqlclient (>=1.4.0)"]
+mysql-connector = ["mysql-connector-python"]
+oracle = ["cx-oracle (>=7)"]
+oracle-oracledb = ["oracledb (>=1.0.1)"]
 postgresql = ["psycopg2 (>=2.7)"]
-postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"]
-postgresql_pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
-postgresql_psycopg2binary = ["psycopg2-binary"]
-postgresql_psycopg2cffi = ["psycopg2cffi"]
-pymysql = ["pymysql (<1)", "pymysql"]
+postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
+postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
+postgresql-psycopg = ["psycopg (>=3.0.7)"]
+postgresql-psycopg2binary = ["psycopg2-binary"]
+postgresql-psycopg2cffi = ["psycopg2cffi"]
+pymysql = ["pymysql"]
 sqlcipher = ["sqlcipher3-binary"]
 
 [[package]]
@@ -1230,6 +2175,10 @@ description = "Python Library for Tom's Obvious, Minimal Language"
 category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+files = [
+    {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
+    {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
+]
 
 [[package]]
 name = "tomli"
@@ -1238,14 +2187,22 @@ description = "A lil' TOML parser"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+]
 
 [[package]]
 name = "tox"
-version = "3.26.0"
+version = "3.28.0"
 description = "tox is a generic virtualenv management and test command line tool"
 category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+files = [
+    {file = "tox-3.28.0-py2.py3-none-any.whl", hash = "sha256:57b5ab7e8bb3074edc3c0c0b4b192a4f3799d3723b2c5b76f1fa9f2d40316eea"},
+    {file = "tox-3.28.0.tar.gz", hash = "sha256:d0d28f3fe6d6d7195c27f8b054c3e99d5451952b54abdae673b71609a581f640"},
+]
 
 [package.dependencies]
 colorama = {version = ">=0.4.1", markers = "platform_system == \"Windows\""}
@@ -1259,186 +2216,227 @@ virtualenv = ">=16.0.0,<20.0.0 || >20.0.0,<20.0.1 || >20.0.1,<20.0.2 || >20.0.2,
 
 [package.extras]
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+testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "pathlib2 (>=2.3.3)", "psutil (>=5.6.1)", "pytest (>=4.0.0)", "pytest-cov (>=2.5.1)", "pytest-mock (>=1.10.0)", "pytest-randomly (>=1.0.0)"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.4.0"
+version = "4.5.0"
 description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
+
+[[package]]
+name = "uri-template"
+version = "1.2.0"
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+category = "main"
+optional = false
+python-versions = ">=3.6"
+files = [
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 [[package]]
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+    {file = "wrapt-1.15.0-py3-none-any.whl", hash = "sha256:64b1df0f83706b4ef4cfb4fb0e4c2669100fd7ecacfb59e091fad300d4e04640"},
+    {file = "wrapt-1.15.0.tar.gz", hash = "sha256:d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a"},
+]
 
 [[package]]
 name = "zipp"
-version = "3.10.0"
+version = "3.15.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
+    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
+]
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "jaraco.functools", "more-itertools", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [metadata]
-lock-version = "1.1"
+lock-version = "2.0"
 python-versions = "^3.8"
-content-hash = "61c62ecbaad750dca2c2a7869aa30498f8d8700417505d6ff87914c2ff051d9c"
-
-[metadata.files]
-alabaster = []
-antlr4-python3-runtime = []
-atomicwrites = []
-attrs = []
-babel = []
-bcp47 = []
-black = []
-certifi = []
-cfgraph = []
-chardet = []
-charset-normalizer = []
-click = []
-colorama = []
-coverage = []
-decorator = []
-deprecated = []
-distlib = []
-docutils = []
-et-xmlfile = []
-filelock = []
-funowl = []
-ghp-import = []
-graphviz = []
-greenlet = []
-hbreader = []
-idna = []
-imagesize = []
-importlib-metadata = []
-importlib-resources = []
-iniconfig = []
-isodate = []
-jinja2 = []
-json-flattener = []
-jsonasobj = []
-jsonasobj2 = []
-jsonpatch = []
-jsonpath-ng = []
-jsonpointer = []
-jsonschema = []
-linkml = []
-linkml-dataops = []
-linkml-runtime = []
-markdown = []
-markdown-it-py = []
-markupsafe = []
-mdit-py-plugins = []
-mdurl = []
-mergedeep = []
-mkdocs = []
-mypy-extensions = []
-myst-parser = []
-openpyxl = []
-packaging = []
-parse = []
-pathspec = []
-pkgutil-resolve-name = []
-platformdirs = []
-pluggy = []
-ply = []
-prefixcommons = []
-prefixmaps = []
-py = []
-pydantic = []
-pygments = []
-pyjsg = []
-pyparsing = []
-pyrsistent = []
-pyshex = []
-pyshexc = []
-pytest = []
-pytest-cov = []
-pytest-logging = []
-python-dateutil = []
-pytz = []
-pyyaml = []
-pyyaml-env-tag = []
-rdflib = []
-rdflib-jsonld = []
-rdflib-shim = []
-requests = []
-rfc3987 = []
-"ruamel.yaml" = []
-"ruamel.yaml.clib" = []
-shexjsg = []
-six = []
-snowballstemmer = []
-sparqlslurper = []
-sparqlwrapper = []
-sphinx = []
-sphinx-click = []
-sphinxcontrib-applehelp = []
-sphinxcontrib-devhelp = []
-sphinxcontrib-htmlhelp = []
-sphinxcontrib-jsmath = []
-sphinxcontrib-qthelp = []
-sphinxcontrib-serializinghtml = []
-sqlalchemy = []
-toml = []
-tomli = []
-tox = []
-typing-extensions = []
-urllib3 = []
-virtualenv = []
-watchdog = []
-wrapt = []
-zipp = []
+content-hash = "e0ea0a8d03495c9518cc714eb24f8606ba13a0cde62ba5ca5fbb20962a1b68b3"
diff --git a/pyproject.toml b/pyproject.toml
index 703fcee..502c722 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,7 +32,7 @@ linkml-data2owl = "linkml_owl.dumpers.owl_dumper:cli"
 python = "^3.8"
 
 click = "*"
-funowl = "^0.1.12"
+funowl = "0.1.12"
 Jinja2 = "^3.0.3"
 linkml = "^1.3.0"
 linkml-runtime = "^1.3.4"


Test patch:
diff --git a/tests/inputs/ontogpt_core.yaml b/tests/inputs/ontogpt_core.yaml
new file mode 100644
index 0000000..bfea369
--- /dev/null
+++ b/tests/inputs/ontogpt_core.yaml
@@ -0,0 +1,126 @@
+id: http://w3id.org/ontogpt/core
+name: core
+title: AI core Template
+license: https://creativecommons.org/publicdomain/zero/1.0/
+prefixes:
+  linkml: https://w3id.org/linkml/
+  core: http://w3id.org/ontogpt/core/
+description: Core upper level
+
+default_prefix: core
+default_range: string
+
+imports:
+  - linkml:types
+
+classes:
+  Any:
+    class_uri: linkml:Any
+
+  ExtractionResult:
+    description: >-
+      A result of extracting knowledge on text
+    attributes:
+      input_id:
+      input_title:
+      input_text:
+      raw_completion_output:
+      prompt:
+      extracted_object:
+        description: >-
+          The complex objects extracted from the text
+        range: Any
+        inlined: true
+      named_entities:
+        description: >-
+          Named entities extracted from the text
+        range: Any
+        multivalued: true
+        inlined: true
+        inlined_as_list: true
+
+  NamedEntity:
+    abstract: true
+    attributes:
+      id:
+        description: >-
+          A unique identifier for the named entity
+        comments:
+          - this is populated during the grounding and normalization step
+        identifier: true
+        annotations:
+          prompt.skip: "true"
+      label:
+        aliases:
+          - name
+        description: >-
+          The label (name) of the named thing
+        range: string
+
+  CompoundExpression:
+    abstract: true
+
+  Triple:
+    abstract: true
+    description: Abstract parent for Relation Extraction tasks
+    is_a: CompoundExpression
+    attributes:
+      subject:
+        range: NamedEntity
+      predicate:
+        range: RelationshipType
+      object:
+        range: NamedEntity
+      qualifier:
+        range: string
+        description: >-
+          A qualifier for the statements, e.g. "NOT" for negation
+      subject_qualifier:
+        range: NamedEntity
+        description: >-
+          An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered"
+      object_qualifier:
+        range: NamedEntity
+        description: >-
+          An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications"
+
+  TextWithTriples:
+    attributes:
+      publication:
+        range: Publication
+        inlined: true
+        annotations:
+          prompt.skip: "true"
+      triples:
+        range: Triple
+        multivalued: true
+        inlined: true
+        inlined_as_list: true
+
+  RelationshipType:
+    is_a: NamedEntity
+    id_prefixes:
+      - RO
+      - biolink
+
+  Publication:
+    attributes:
+      id:
+        description: >-
+          The publication identifier
+      title:
+        description: >-
+          The title of the publication
+      abstract:
+        description: >-
+          The abstract of the publication
+      combined_text:
+      full_text:
+        description: >-
+          The full text of the publication
+
+  AnnotatorResult:
+    attributes:
+      subject_text:
+      object_id:
+      object_text:
diff --git a/tests/inputs/pizza-model.yaml b/tests/inputs/pizza-model.yaml
index 4c02ab6..0e7f8f4 100644
--- a/tests/inputs/pizza-model.yaml
+++ b/tests/inputs/pizza-model.yaml
@@ -11,6 +11,7 @@ prefixes:
   sh: https://w3id.org/shacl/
   owl: http://www.w3.org/2002/07/owl#
   prov: http://www.w3.org/ns/prov#
+  dcterms: http://purl.org/dc/terms/
 default_prefix: pizza
 imports:
   - linkml:types
diff --git a/tests/inputs/recipe-data.yaml b/tests/inputs/recipe-data.yaml
new file mode 100644
index 0000000..ab3f9db
--- /dev/null
+++ b/tests/inputs/recipe-data.yaml
@@ -0,0 +1,111 @@
+url: http://x.org
+label: Simple Spaghetti
+description: An easy to make and delicious spaghetti dish.
+categories:
+- AUTO:Main%20dishes
+- AUTO:Italian%20recipes
+ingredients:
+- food_item:
+    food: AUTO:small%20onion
+    state: chopped
+  amount:
+    value: '1'
+    unit: AUTO:%28chopped%29
+- food_item:
+    food: FOODON:00003485
+    state: chopped
+  amount:
+    value: '1'
+    unit: AUTO:%28chopped%29
+- food_item:
+    food: FOODON:00003582
+    state: powder
+  amount:
+    value: '2'
+    unit: UO:0010042
+- food_item:
+    food: FOODON:03310351
+  amount:
+    value: '3'
+    unit: UO:0010042
+- food_item:
+    food: AUTO:salt
+  amount:
+    value: '1'
+    unit: UO:0010040
+- food_item:
+    food: FOODON:00001649
+  amount:
+    value: '1'
+    unit: UO:0010040
+- food_item:
+    food: FOODON:03301217
+    state: canned
+  amount:
+    value: '2'
+- food_item:
+    food: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles
+    state: uncooked
+  amount:
+    value: '1'
+- food_item:
+    food: FOODON:00001282
+    state: chopped/diced
+  amount:
+    value: "1 - 1 1\u20442"
+    unit: AUTO:lb
+steps:
+- action: AUTO:melt%3B%20saut%C3%A9
+  inputs:
+  - food: FOODON:03310351
+  - food: FOODON:03301704
+  - food: FOODON:00003485
+    state: chopped
+  utensils:
+  - AUTO:pan
+- action: AUTO:add%3B%20cook
+  inputs:
+  - food: FOODON:00001282
+    state: chopped/diced
+  outputs:
+  - food: AUTO:meat
+    state: well done
+  utensils:
+  - AUTO:pan
+- action: AUTO:add%3B
+  inputs:
+  - food: FOODON:03000227
+    state: sauce
+  - food: AUTO:salt
+  - food: FOODON:00001649
+  - food: FOODON:00003582
+    state: powder
+  outputs:
+  - food: AUTO:none
+  utensils:
+  - AUTO:none
+- action: AUTO:adjust
+  inputs:
+  - food: AUTO:salt
+  - food: FOODON:00001649
+  - food: FOODON:00003582
+    state: powder
+  outputs:
+  - food: AUTO:inputs
+    state: adjusted
+  utensils:
+  - AUTO:none
+- action: AUTO:Cook
+  inputs:
+  - food: FOODON:03306944
+  outputs:
+  - food: AUTO:as%20directed
+- action: AUTO:mix%3B
+  inputs:
+  - food: FOODON:03311146
+  - food: FOODON:03306944
+  outputs:
+  - food: FOODON:03306944
+    state: +
+  utensils:
+  - AUTO:none
diff --git a/tests/inputs/recipe-model.yaml b/tests/inputs/recipe-model.yaml
new file mode 100644
index 0000000..6f1c9a3
--- /dev/null
+++ b/tests/inputs/recipe-model.yaml
@@ -0,0 +1,211 @@
+id: https://w3id.org/ontogpt/recipe
+name: recipe-template
+title: Food Recipe Template
+description: >-
+  A template for food recipes
+license: https://creativecommons.org/publicdomain/zero/1.0/
+prefixes:
+  linkml: https://w3id.org/linkml/
+  recipe: http://w3id.org/ontogpt/recipe/
+  FOODON: http://purl.obolibrary.org/obo/FOODON_
+  UO: http://purl.obolibrary.org/obo/UO_
+  dcterms: http://purl.org/dc/terms/
+  HANCESTRO: http://purl.obolibrary.org/obo/HANCESTRO_
+  BFO: http://purl.obolibrary.org/obo/BFO_
+  AUTO: http://example.org/auto/
+  RO: http://purl.obolibrary.org/obo/RO_
+  qudt: http://qudt.org/schema/qudt/
+
+
+default_prefix: recipe
+default_range: string
+
+imports:
+  - linkml:types
+  - ontogpt_core
+
+classes:
+  Recipe:
+    tree_root: true
+    close_mappings:
+      - FOODON:00004081
+    attributes:
+      url:
+        identifier: true
+        range: uriorcurie
+        slot_uri: rdf:Resource
+        annotations:
+          prompt.ignore: true
+      label:
+        description: the name of the recipe
+        slot_uri: rdfs:label
+        annotations:
+          owl: AnnotationProperty, AnnotationAssertion
+      description:
+        description: a brief textual description of the recipe
+        slot_uri: dcterms:description
+        annotations:
+          owl: AnnotationProperty, AnnotationAssertion
+      categories:
+        description: a semicolon separated list of the categories to which this recipe belongs
+        range:  RecipeCategory
+        multivalued: true
+        slot_uri: dcterms:subject
+        annotations:
+          owl: AnnotationAssertion
+      ingredients:
+        description: a semicolon separated list of the ingredients plus quantities of the recipe
+        multivalued: true
+        range: Ingredient
+        slot_uri: FOODON:00002420
+        annotations:
+          owl: ObjectProperty, ObjectSomeValuesFrom
+      steps:
+        description: a semicolon separated list of the individual steps involved in this recipe
+        multivalued: true
+        range: Step
+        annotations:
+          owl: ObjectProperty, ObjectSomeValuesFrom
+    annotations:
+      owl: Class
+      owl.template: |
+        EquivalentClasses(
+          {{url}}
+          ObjectIntersectionOf(
+            recipe:Recipe
+            {% for step in steps %}
+            ObjectSomeValuesFrom(
+              recipe:steps
+              {{tr(step)}}
+            )
+            {% endfor %}
+            {% for ingredient in ingredients %}
+            ObjectSomeValuesFrom(
+              FOODON:00002420
+              {{tr(ingredient)}}
+            )
+            {% endfor %}
+          )
+        )
+  Ingredient:
+    is_a: CompoundExpression
+    class_uri: FOODON:00004085
+    annotations:
+      owl: IntersectionOf
+    attributes:
+      food_item:
+        description: the food item
+        range: FoodItem
+        annotations:
+          owl: ObjectProperty, ObjectSomeValuesFrom
+      amount:
+        description: the quantity of the ingredient, e.g. 2 lbs
+        range: Quantity
+        annotations:
+          owl: ObjectProperty, ObjectSomeValuesFrom
+
+  Quantity:
+    is_a: CompoundExpression
+    annotations:
+      owl: IntersectionOf
+    attributes:
+      value:
+        description: the value of the quantity
+        #range: float
+        annotations:
+          owl: DataProperty, DataHasValue
+      unit:
+        description: the unit of the quantity, e.g. grams, cups, etc.
+        range: Unit
+        slot_uri: qudt:unit
+        annotations:
+          owl: ObjectProperty, ObjectSomeValuesFrom
+
+  Step:
+    is_a: CompoundExpression
+    class_uri: FOODON:00004087
+    annotations:
+      owl: IntersectionOf
+    attributes:
+      action:
+        description: the action taken in this step (e.g. mix, add)
+        range: Action
+      inputs:
+        description: a semicolon separated list of the inputs of this step
+        range: FoodItem
+        multivalued: true
+        slot_uri: RO:0002233
+        annotations:
+          owl: ObjectProperty, ObjectSomeValuesFrom
+      outputs:
+        description: a semicolon separated list of the outputs of this step
+        range: FoodItem
+        multivalued: true
+        slot_uri: RO:0002234
+        annotations:
+          owl: ObjectProperty, ObjectSomeValuesFrom
+      utensils:
+        description: the kitchen utensil used in this step (e.g. pan, bowl)
+        range: UtensilType
+        multivalued: true
+        slot_uri: RO:0002500
+        annotations:
+          owl: ObjectProperty, ObjectSomeValuesFrom
+
+  FoodItem:
+    is_a: CompoundExpression
+    annotations:
+      owl: IntersectionOf
+    attributes:
+      food:
+        description: the food item
+        range: FoodType
+        slot_uri: BFO:0000051
+        annotations:
+          owl: ObjectProperty, ObjectSomeValuesFrom
+      state:
+        description: the state of the food item (e.g. chopped, diced)
+        annotations:
+           owl: DataProperty, DataHasValue
+
+  FoodType:
+    is_a: NamedEntity
+    id_prefixes:
+      - dbpediaont
+      - FOODON
+    annotations:
+      annotators: sqlite:obo:foodon, sqlite:obo:dbpediaont
+
+  RecipeCategory:
+    is_a: NamedEntity
+    id_prefixes:
+      - dbpediaont
+      - FOODON
+      - HANCESTRO
+    annotations:
+      annotators: sqlite:obo:foodon, sqlite:obo:dbpediaont
+
+  Action:
+    is_a: NamedEntity
+    id_prefixes:
+      - dbpediaont
+      - FOODON
+    annotations:
+      annotators: sqlite:obo:dbpediaont, sqlite:obo:foodon
+
+  UtensilType:
+    is_a: NamedEntity
+    id_prefixes:
+      - dbpediaont
+      - FOODON
+    annotations:
+      annotators: sqlite:obo:dbpediaont, sqlite:obo:foodon
+
+  Unit:
+    is_a: NamedEntity
+    id_prefixes:
+      - UO
+      - NCIT
+      - dbpediaont
+    annotations:
+      annotators: sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon
diff --git a/tests/output/chromo.schema.owl.ttl b/tests/output/chromo.schema.owl.ttl
index a11a8e0..1244e15 100644
--- a/tests/output/chromo.schema.owl.ttl
+++ b/tests/output/chromo.schema.owl.ttl
@@ -23,7 +23,7 @@
         chromoschema:GenomeBuild,
         chromoschema:OrganismTaxon ;
     dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
-    linkml:generation_date "2023-01-05T17:07:03" ;
+    linkml:generation_date "2023-03-21T13:21:57" ;
     linkml:metamodel_version "1.7.0" ;
     linkml:source_file "chromo.yaml" ;
     linkml:source_file_date "2022-01-12T21:11:50" ;
@@ -210,20 +210,20 @@ chromoschema:Genome a owl:Class,
             owl:onClass chromoschema:GenomeBuild ;
             owl:onProperty biolink:genome_build ],
         [ a owl:Restriction ;
-            owl:onClass linkml:String ;
-            owl:onProperty chromoschema:id ;
-            owl:qualifiedCardinality 1 ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass chromoschema:TaxonIdentifier ;
+            owl:onProperty RO:0002162 ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:GenomeBuild ;
+            owl:onProperty chromoschema:previous_builds ],
         [ a owl:Restriction ;
             owl:onClass chromoschema:LabelType ;
             owl:onProperty rdfs:label ;
             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 ] ;
+            owl:onClass linkml:String ;
+            owl:onProperty chromoschema:id ;
+            owl:qualifiedCardinality 1 ] ;
     skos:definition """Represents a sequenced genome, one per species.
 Each genome can be associated with one or more builds""" .
 
@@ -231,17 +231,17 @@ chromoschema:OrganismTaxon a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "OrganismTaxon" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass chromoschema:LabelType ;
+            owl:onProperty rdfs:label ],
+        [ a owl:Restriction ;
             owl:onClass linkml:String ;
             owl:onProperty chromoschema:id ;
             owl:qualifiedCardinality 1 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass chromoschema:LabelType ;
-            owl:onProperty OIO:hasExactSynonym ],
-        [ a owl:Restriction ;
-            owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:LabelType ;
-            owl:onProperty rdfs:label ] ;
+            owl:onProperty OIO:hasExactSynonym ] ;
     skos:definition "Represents a species, e.g. Homo sapiens" ;
     skos:exactMatch biolink:OrganismTaxon .
 
@@ -323,69 +323,69 @@ chromoschema:ChromosomePart a owl:Class,
         linkml:ClassDefinition ;
     rdfs:label "ChromosomePart" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:onClass linkml:String ;
+            owl:onProperty chromoschema:id ;
+            owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:ChromosomePart ;
+            owl:onClass chromoschema:LocationType ;
             owl:onProperty BFO:0000050 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass chromoschema:LabelType ;
             owl:onProperty rdfs:label ],
-        [ 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:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:GenomeBuild ;
-            owl:onProperty biolink:genome_build ],
+            owl:onClass chromoschema:ChromosomeNameType ;
+            owl:onProperty chromoschema:chromosome_name ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:AutosomeVsSexChromosome ;
-            owl:onProperty chromoschema:somal_type ],
+            owl:onClass chromoschema:BandDescriptor ;
+            owl:onProperty chromoschema:band_descriptor ],
         [ a owl:Restriction ;
             owl:allValuesFrom linkml:Uriorcurie ;
             owl:onProperty skos:exactMatch ],
         [ 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:ChromosomeNameType ;
-            owl:onProperty chromoschema:chromosome_name ],
+            owl:onClass linkml:Integer ;
+            owl:onProperty gff:start ],
         [ a owl:Restriction ;
             owl:allValuesFrom linkml:String ;
-            owl:onProperty OIO:hasBroadSynonym ],
+            owl:onProperty OIO:hasExactSynonym ],
         [ a owl:Restriction ;
-            owl:onClass linkml:String ;
-            owl:onProperty chromoschema:id ;
-            owl:qualifiedCardinality 1 ],
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass chromoschema:EntityType ;
+            owl:onProperty rdf:type ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:BandDescriptor ;
-            owl:onProperty chromoschema:band_descriptor ],
+            owl:onClass chromoschema:GenomeBuild ;
+            owl:onProperty biolink:genome_build ],
         [ a owl:Restriction ;
             owl:allValuesFrom linkml:String ;
-            owl:onProperty OIO:hasExactSynonym ],
+            owl:onProperty OIO:hasBroadSynonym ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:EntityType ;
-            owl:onProperty rdf:type ],
+            owl:onClass chromoschema:ChromosomePart ;
+            owl:onProperty BFO:0000050 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass linkml:Integer ;
-            owl:onProperty gff:start ],
+            owl:onClass chromoschema:SexChromosomeType ;
+            owl:onProperty chromoschema:sex_chromosome_type ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass chromoschema:TaxonIdentifier ;
+            owl:onProperty RO:0002162 ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom chromoschema:ChromosomePart ;
+            owl:onProperty BFO:0000051 ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
             owl:onClass linkml:Integer ;
             owl:onProperty gff:end ],
         [ a owl:Restriction ;
             owl:maxQualifiedCardinality 1 ;
-            owl:onClass chromoschema:TaxonIdentifier ;
-            owl:onProperty RO:0002162 ] ;
+            owl:onClass chromoschema:AutosomeVsSexChromosome ;
+            owl:onProperty chromoschema:somal_type ] ;
     skos:definition "A Chromosome or a part of a chromosome (includes whole chromosomes, arms, and bands)" ;
     skos:note """OWL Notes: when translated to OWL, instances of this class will be treated as
 OWL classes, with the superclass determined by the type field""",
diff --git a/tests/test_compliance/test_owl_dumper.py b/tests/test_compliance/test_owl_dumper.py
index b03b9ce..c76ea2d 100644
--- a/tests/test_compliance/test_owl_dumper.py
+++ b/tests/test_compliance/test_owl_dumper.py
@@ -297,6 +297,7 @@ def add_check(*args, **kwargs):
             container = py_mod.Container(entities=check.records)
             dumper.object_index = ObjectIndex(container, schemaview=sv)
             dumper.autofill = True
+            print(f"RECORDS = {check.records}")
             doc = dumper.to_ontology_document(check.records, schema)
             md += '\n__Generated axioms__:\n\n'
             md += f'```\n{str(doc)}\n```\n\n'
diff --git a/tests/test_examples/test_recipe.py b/tests/test_examples/test_recipe.py
index 5398d67..56c8d4f 100644
--- a/tests/test_examples/test_recipe.py
+++ b/tests/test_examples/test_recipe.py
@@ -13,18 +13,18 @@
 
 """Test the module can be imported."""
 
-SCHEMA_IN = os.path.join(INPUT_DIR, 'recipe.yaml')
-DATA_IN = os.path.join(INPUT_DIR, 'recipe.data.yaml')
+SCHEMA_IN = os.path.join(INPUT_DIR, 'recipe-model.yaml')
+DATA_IN = os.path.join(INPUT_DIR, 'recipe-data.yaml')
 OWL_OUT = os.path.join(OUTPUT_DIR, 'recipe.ofn')
-EXPECTED = os.path.join(INPUT_DIR, 'recipe.expected.ofn')
+# EXPECTED = os.path.join(INPUT_DIR, 'pizza.expected.ofn')
 
 
-class TestRecipeExample(unittest.TestCase):
-    """Test case using a fantasy RPG example."""
+class TestRecipe(unittest.TestCase):
+    """Recipe Ontology test case."""
 
-    def test_build(self):
+    def test_build_recipe_ontology(self):
         """
-        Test creation of an OWL TBox using Recipe template.
+        Test creation of an OWL TBox using the recipe ontology.
         """
         sv = SchemaView(SCHEMA_IN)
         python_module = PythonGenerator(SCHEMA_IN).compile_module()
@@ -37,9 +37,8 @@ def test_build(self):
         doc_rt = to_python(str(doc))
         axioms = doc_rt.ontology.axioms
         logging.info(f'AXIOMS={len(axioms)}')
-        assert len(axioms) > 5
+        #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_expected = to_python(str(EXPECTED))
+        #assert len(axioms) == len(doc_expected.ontology.axioms)
+        #self.assertCountEqual(axioms, doc_expected.ontology.axioms)