make linkml cookiecutter

nwb-schema-linkml/.cruft.json

@@ -0,0 +1,27 @@
+{
+  "template": "https://github.com/linkml/linkml-project-cookiecutter",
+  "commit": "ef7ff16925321a2abdbaa5a2ba5db8aa83ebf24f",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "nwb-schema-language",
+      "__project_slug": "nwb_schema_language",
+      "github_org": "p2p_ld",
+      "__source_path": "src/nwb_schema_language/schema/nwb_schema_language.yaml",
+      "project_description": "Translation of the nwb-schema-language to LinkML",
+      "full_name": "Jonny Saunders",
+      "email": "j@nny.fyi",
+      "__author": "Jonny Saunders <j@nny.fyi>",
+      "license": "GNU GPL v3.0",
+      "main_schema_class": "Namespaces",
+      "create_python_classes": "Yes",
+      "use_schemasheets": "No",
+      "google_sheet_id": "1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ",
+      "google_sheet_tabs": "personinfo enums",
+      "__google_sheet_module": "personinfo_enums",
+      "github_token_for_pypi_deployment": "PYPI_PASSWORD",
+      "_template": "https://github.com/linkml/linkml-project-cookiecutter"
+    }
+  },
+  "directory": null
+}

nwb-schema-linkml/.github/workflows/deploy-docs.yaml

@@ -0,0 +1,35 @@
+---
+name: Auto-deployment of nwb_schema_language Documentation
+on:
+  push:
+    branches: [main]
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python 3.
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry.
+        uses: snok/install-poetry@v1.3
+
+      - name: Install dependencies.
+        run: poetry install -E docs
+
+      - name: Build documentation.
+        run: |
+          mkdir -p docs
+          touch docs/.nojekyll
+          make gendoc
+          ([ ! -f docs/about.md ] && cp src/docs/about.md docs/) || true
+          make mkd-gh-deploy
+
+...

nwb-schema-linkml/.github/workflows/main.yaml

@@ -0,0 +1,37 @@
+# Built from:
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+# https://github.com/snok/install-poetry#workflows-and-tips
+---
+name: Build and test nwb_schema_language
+
+on: [pull_request]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10"]
+
+    steps:
+
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1.3
+
+      - name: Install dependencies
+        run: poetry install --no-interaction --no-root
+
+      - name: Install project
+        run: poetry install --no-interaction
+
+      - name: Run test suite
+        run: make test

nwb-schema-linkml/.github/workflows/pypi-publish.yaml

@@ -0,0 +1,40 @@
+---
+name: Publish Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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]"
+        # uses: snok/install-poetry@v1.1.6
+        # with:
+        #   virtualenvs-create: true
+        #   virtualenvs-in-project: true
+
+      # - 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@v1.2.2
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

nwb-schema-linkml/.gitignore

@@ -0,0 +1,133 @@
+/docs/
+/project/docs/
+/tmp/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

nwb-schema-linkml/CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to make participation in our project and
+our community a harassment-free experience for everyone, regardless of age,
+body size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event. Representation of a
+project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by [contacting the project team](contact.md). All complaints will be
+reviewed and investigated and will result in a response that is deemed
+necessary and appropriate to the circumstances. The project team is obligated
+to maintain confidentiality with regard to the reporter of an incident. Further
+details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This code of conduct has been derived from the excellent code of conduct of the
+[ATOM project](https://github.com/atom/atom/blob/master/CODE_OF_CONDUCT.md)
+which in turn is adapted from the [Contributor Covenant][homepage], version
+1.4, available at [https://contributor-covenant.org/version/1/4][version]
+
+[homepage]: https://contributor-covenant.org
+[version]: https://contributor-covenant.org/version/1/4/

nwb-schema-linkml/CONTRIBUTING.md

@@ -0,0 +1,73 @@
+# Contributing to nwb-schema-language
+
+:+1: First of all: Thank you for taking the time to contribute!
+
+The following is a set of guidelines for contributing to
+nwb-schema-language. These guidelines are not strict rules.
+Use your best judgment, and feel free to propose changes to this document
+in a pull request.
+
+## Table Of Contents
+
+* [Code of Conduct](#code-of-conduct)
+* [Guidelines for Contributions and Requests](#contributions)
+  * [Reporting problems with the data model](#reporting-bugs)
+  * [Requesting new terms](#requesting-terms)
+  * [Adding new terms yourself](#adding-terms)
+* [Best Practices](#best-practices)
+  * [How to write a great issue](#great-issues)
+  * [How to create a great pull/merge request](#great-pulls)
+
+<a id="code-of-conduct"></a>
+
+## Code of Conduct
+
+The nwb-schema-language team strives to create a
+welcoming environment for editors, users and other contributors.
+Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md).
+
+<a id="contributions"></a>
+
+## Guidelines for Contributions and Requests
+
+<a id="reporting-bugs"></a>
+
+### Reporting problems with the data model
+
+Please use our [Issue Tracker][issues] to report problems with the ontology.
+
+<a id="requesting-terms"></a>
+
+### Requesting new terms
+
+Please use our [Issue Tracker][issues] to request a new term for the ontology.
+
+<a id="adding-terms"></a>
+
+### Adding new terms yourself
+
+Please submit a [Pull Request][pulls] to submit a new term for consideration.
+
+<a id="best-practices"></a>
+
+## Best Practices
+
+<a id="great-issues"></a>
+
+### How to write a great issue
+
+Please review GitHub's overview article,
+["Tracking Your Work with Issues"][about-issues].
+
+<a id="great-pulls"></a>
+
+### How to create a great pull/merge request
+
+Please review GitHub's article, ["About Pull Requests"][about-pulls],
+and make your changes on a [new branch][about-branches].
+
+[about-branches]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches
+[about-issues]: https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues
+[about-pulls]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests
+[issues]: https://github.com/p2p_ld/nwb-schema-language/issues/
+[pulls]: https://github.com/p2p_ld/nwb-schema-language/pulls/

nwb-schema-linkml/LICENSE

@@ -0,0 +1,675 @@
+
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received.  You must make sure that they, too, receive
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+know their rights.
+
+  Developers that use the GNU GPL protect your rights with two steps:
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+giving you legal permission to copy, distribute and/or modify it.
+
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+that there is no warranty for this free software.  For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
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+
+  Some devices are designed to deny users access to install or run
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+pattern of such abuse occurs in the area of products for individuals to
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+
+  Finally, every program is threatened constantly by software patents.
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+avoid the special danger that patents applied to a free program could
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+patents cannot be used to render the program non-free.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
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nwb-schema-linkml/Makefile

@@ -0,0 +1,190 @@
+MAKEFLAGS += --warn-undefined-variables
+SHELL := bash
+.SHELLFLAGS := -eu -o pipefail -c
+.DEFAULT_GOAL := help
+.DELETE_ON_ERROR:
+.SUFFIXES:
+.SECONDARY:
+
+RUN = poetry run
+# get values from about.yaml file
+SCHEMA_NAME = $(shell ${SHELL} ./utils/get-value.sh name)
+SOURCE_SCHEMA_PATH = $(shell ${SHELL} ./utils/get-value.sh source_schema_path)
+SOURCE_SCHEMA_DIR = $(dir $(SOURCE_SCHEMA_PATH))
+SRC = src
+DEST = project
+PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
+DOCDIR = docs
+EXAMPLEDIR = examples
+SHEET_MODULE = personinfo_enums
+SHEET_ID = $(shell ${SHELL} ./utils/get-value.sh google_sheet_id)
+SHEET_TABS = $(shell ${SHELL} ./utils/get-value.sh google_sheet_tabs)
+SHEET_MODULE_PATH = $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml
+
+# environment variables
+include config.env
+
+GEN_PARGS =
+ifdef LINKML_GENERATORS_PROJECT_ARGS
+GEN_PARGS = ${LINKML_GENERATORS_PROJECT_ARGS}
+endif
+
+GEN_DARGS =
+ifdef LINKML_GENERATORS_MARKDOWN_ARGS
+GEN_DARGS = ${LINKML_GENERATORS_MARKDOWN_ARGS}
+endif
+
+
+# basename of a YAML file in model/
+.PHONY: all clean
+
+# note: "help" MUST be the first target in the file,
+# when the user types "make" they should get help info
+help: status
+	@echo ""
+	@echo "make setup -- initial setup (run this first)"
+	@echo "make site -- makes site locally"
+	@echo "make install -- install dependencies"
+	@echo "make test -- runs tests"
+	@echo "make lint -- perform linting"
+	@echo "make testdoc -- builds docs and runs local test server"
+	@echo "make deploy -- deploys site"
+	@echo "make update -- updates linkml version"
+	@echo "make help -- show this help"
+	@echo ""
+
+status: check-config
+	@echo "Project: $(SCHEMA_NAME)"
+	@echo "Source: $(SOURCE_SCHEMA_PATH)"
+
+# generate products and add everything to github
+setup: install gen-project gen-examples gendoc git-init-add
+
+# install any dependencies required for building
+install:
+	git init
+	poetry install
+.PHONY: install
+
+# ---
+# Project Synchronization
+# ---
+#
+# check we are up to date
+check: cruft-check
+cruft-check:
+	cruft check
+cruft-diff:
+	cruft diff
+
+update: update-template update-linkml
+update-template:
+	cruft update
+
+# todo: consider pinning to template
+update-linkml:
+	poetry add -D linkml@latest
+
+# EXPERIMENTAL
+create-data-harmonizer:
+	npm init data-harmonizer $(SOURCE_SCHEMA_PATH)
+
+all: site
+site: gen-project gendoc
+%.yaml: gen-project
+deploy: all mkd-gh-deploy
+
+compile-sheets:
+	$(RUN) sheets2linkml --gsheet-id $(SHEET_ID) $(SHEET_TABS) > $(SHEET_MODULE_PATH).tmp && mv $(SHEET_MODULE_PATH).tmp $(SHEET_MODULE_PATH)
+
+# In future this will be done by conversion
+gen-examples:
+	cp src/data/examples/* $(EXAMPLEDIR)
+
+# generates all project files
+
+gen-project: $(PYMODEL)
+	$(RUN) gen-project ${GEN_PARGS} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
+
+
+test: test-schema test-python test-examples
+
+test-schema:
+	$(RUN) gen-project ${GEN_PARGS} -d tmp $(SOURCE_SCHEMA_PATH)
+
+test-python:
+	$(RUN) python -m unittest discover
+
+lint:
+	$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH)
+
+check-config:
+	@(grep my-datamodel about.yaml > /dev/null && printf "\n**Project not configured**:\n\n  - Remember to edit 'about.yaml'\n\n" || exit 0)
+
+convert-examples-to-%:
+	$(patsubst %, $(RUN) linkml-convert  % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell ${SHELL} find src/data/examples -name "*.yaml"))
+
+examples/%.yaml: src/data/examples/%.yaml
+	$(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
+examples/%.json: src/data/examples/%.yaml
+	$(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
+examples/%.ttl: src/data/examples/%.yaml
+	$(RUN) linkml-convert -P EXAMPLE=http://example.org/ -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
+
+test-examples: examples/output
+
+examples/output: src/nwb_schema_language/schema/nwb_schema_language.yaml
+	mkdir -p $@
+	$(RUN) linkml-run-examples \
+		--output-formats json \
+		--output-formats yaml \
+		--counter-example-input-directory src/data/examples/invalid \
+		--input-directory src/data/examples/valid \
+		--output-directory $@ \
+		--schema $< > $@/README.md
+
+# Test documentation locally
+serve: mkd-serve
+
+# Python datamodel
+$(PYMODEL):
+	mkdir -p $@
+
+
+$(DOCDIR):
+	mkdir -p $@
+
+gendoc: $(DOCDIR)
+	cp $(SRC)/docs/*md $(DOCDIR) ; \
+	$(RUN) gen-doc ${GEN_DARGS} -d $(DOCDIR) $(SOURCE_SCHEMA_PATH)
+
+testdoc: gendoc serve
+
+MKDOCS = $(RUN) mkdocs
+mkd-%:
+	$(MKDOCS) $*
+
+PROJECT_FOLDERS = sqlschema shex shacl protobuf prefixmap owl jsonschema jsonld graphql excel
+git-init-add: git-init git-add git-commit git-status
+git-init:
+	git init
+git-add: .cruft.json
+	git add .gitignore .github .cruft.json Makefile LICENSE *.md examples utils about.yaml mkdocs.yml poetry.lock project.Makefile pyproject.toml src/nwb_schema_language/schema/*yaml src/*/datamodel/*py src/data src/docs tests src/*/_version.py
+	git add $(patsubst %, project/%, $(PROJECT_FOLDERS))
+git-commit:
+	git commit -m 'chore: initial commit' -a
+git-status:
+	git status
+
+# only necessary if setting up via cookiecutter
+.cruft.json:
+	echo "creating a stub for .cruft.json. IMPORTANT: setup via cruft not cookiecutter recommended!" ; \
+	touch $@
+
+clean:
+	rm -rf $(DEST)
+	rm -rf tmp
+	rm -fr docs/*
+	rm -fr $(PYMODEL)/*
+
+include project.Makefile

nwb-schema-linkml/README.md

@@ -0,0 +1,33 @@
+# nwb-schema-language
+
+Translation of the nwb-schema-language to LinkML
+
+## Website
+
+[https://p2p_ld.github.io/nwb-schema-language](https://p2p_ld.github.io/nwb-schema-language)
+
+## Repository Structure
+
+* [examples/](examples/) - example data
+* [project/](project/) - project files (do not edit these)
+* [src/](src/) - source files (edit these)
+  * [nwb_schema_language](src/nwb_schema_language)
+    * [schema](src/nwb_schema_language/schema) -- LinkML schema
+      (edit this)
+    * [datamodel](src/nwb_schema_language/datamodel) -- generated
+      Python datamodel
+* [tests/](tests/) - Python tests
+
+## Developer Documentation
+
+<details>
+Use the `make` command to generate project artefacts:
+
+* `make all`: make everything
+* `make deploy`: deploys site
+</details>
+
+## Credits
+
+This project was made with
+[linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter).

nwb-schema-linkml/about.yaml

@@ -0,0 +1,7 @@
+---
+name: nwb_schema_language
+author: Jonny Saunders <j@nny.fyi>
+description: Translation of the nwb-schema-language to LinkML
+source_schema_path: src/nwb_schema_language/schema/nwb_schema_language.yaml
+google_sheet_id: 1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ
+google_sheet_tabs: personinfo enums

nwb-schema-linkml/config.env

@@ -0,0 +1,8 @@
+LINKML_GENERATORS_PROJECT_ARGS=--config-file config.yaml --exclude owl --exclude shacl
+
+### Extra layer of configuration for Makefile beyond
+### what 'gen-project --config-file config.yaml' provides.
+### Uncomment and set environment variables as needed.
+
+# LINKML_GENERATORS_MARKDOWN_ARGS=--no-mergeimports
+

nwb-schema-linkml/config.yaml

@@ -0,0 +1,41 @@
+# Configuration of generators (defaults illustrated)
+---
+generator_args:
+  excel:
+    mergeimports: true
+  owl:
+    mergeimports: true
+    metaclasses: true
+    type_objects: true
+    # throws 'Cannot handle metadata profile: rdfs'
+    # metadata_profile: rdfs
+  markdown:
+    mergeimports: true
+  graphql:
+    mergeimports: true
+  java:
+    mergeimports: true
+    metadata: true
+  jsonld:
+    mergeimports: true
+  jsonschema:
+    mergeimports: true
+  jsonldcontext:
+    mergeimports: true
+  python:
+    mergeimports: true
+  prefixmap:
+    mergeimports: true
+  proto:
+    mergeimports: true
+  shacl:
+    mergeimports: true
+  shex:
+    mergeimports: true
+  sqlddl:
+    mergeimports: true
+  typescript:
+    mergeimports: true
+    metadata: true
+
+...

nwb-schema-linkml/examples/Namespaces-001.yaml

@@ -0,0 +1,7 @@
+# Example data object
+---
+entries:
+  - id: example:Namespaces001
+    name: foo bar
+    primary_email: foo.bar@example.com
+    age_in_years: 33

nwb-schema-linkml/examples/README.md

@@ -0,0 +1,5 @@
+# Examples of use of nwb_schema_language
+
+This folder contains example data conforming to nwb_schema_language
+
+The source for these is in [src/data](../src/data/examples)

nwb-schema-linkml/mkdocs.yml

@@ -0,0 +1,25 @@
+---
+site_name: "nwb-schema-language"
+theme:
+  name: material
+  # palette:
+  #  scheme: slate
+  #  primary: cyan
+  features:
+    - content.tabs.link
+plugins:
+  - search
+  - mermaid2
+nav:
+  # - Home: home.md
+  - Index: index.md
+  - About: about.md
+site_url: https://p2p_ld.github.io/nwb-schema-language
+repo_url: https://github.com/p2p_ld/nwb-schema-language
+
+# Uncomment this block to enable use of Google Analytics.
+# Replace the property value with your own ID.
+# extra:
+#   analytics:
+#     provider: google
+#     property: G-XXXXXXXXXX

nwb-schema-linkml/project.Makefile

@@ -0,0 +1 @@
+## Add your own custom Makefile targets here

nwb-schema-linkml/project/graphql/nwb_schema_language.graphql

@@ -0,0 +1,23 @@
+type NamedThing
+  {
+    id: Uriorcurie!
+    name: String
+    description: String
+  }
+
+type Namespaces
+  {
+    id: Uriorcurie!
+    name: String
+    description: String
+    primaryEmail: String
+    birthDate: Date
+    ageInYears: Integer
+    vitalStatus: PersonStatus
+  }
+
+type NamespacesCollection
+  {
+    entries: [Namespaces]
+  }
+

nwb-schema-linkml/project/jsonld/nwb_schema_language.context.jsonld

@@ -0,0 +1,51 @@
+{
+   "comments": {
+      "description": "Auto generated by LinkML jsonld context generator",
+      "generation_date": "2023-08-16T15:57:40",
+      "source": "nwb_schema_language.yaml"
+   },
+   "@context": {
+      "PATO": {
+         "@id": "http://purl.obolibrary.org/obo/PATO_",
+         "@prefix": true
+      },
+      "biolink": "https://w3id.org/biolink/",
+      "example": "https://example.org/",
+      "linkml": "https://w3id.org/linkml/",
+      "nwb_schema_language": "https://w3id.org/p2p_ld/nwb-schema-language/",
+      "schema": "http://schema.org/",
+      "skos": "http://www.w3.org/2004/02/skos/core#",
+      "@vocab": "https://w3id.org/p2p_ld/nwb-schema-language/",
+      "age_in_years": {
+         "@type": "xsd:integer"
+      },
+      "birth_date": {
+         "@type": "xsd:date",
+         "@id": "schema:birthDate"
+      },
+      "description": {
+         "@id": "schema:description"
+      },
+      "id": "@id",
+      "name": {
+         "@id": "schema:name"
+      },
+      "entries": {
+         "@type": "@id"
+      },
+      "primary_email": {
+         "@id": "schema:email"
+      },
+      "vital_status": {
+         "@context": {
+            "@vocab": "@null",
+            "text": "skos:notation",
+            "description": "skos:prefLabel",
+            "meaning": "@id"
+         }
+      },
+      "NamedThing": {
+         "@id": "schema:Thing"
+      }
+   }
+}

nwb-schema-linkml/project/jsonld/nwb_schema_language.jsonld

@@ -0,0 +1,543 @@
+{
+  "name": "nwb-schema-language",
+  "description": "Translation of the nwb-schema-language to LinkML",
+  "title": "nwb-schema-language",
+  "see_also": [
+    "https://p2p_ld.github.io/nwb-schema-language"
+  ],
+  "id": "https://w3id.org/p2p_ld/nwb-schema-language",
+  "imports": [
+    "linkml:types"
+  ],
+  "license": "GNU GPL v3.0",
+  "prefixes": [
+    {
+      "prefix_prefix": "nwb_schema_language",
+      "prefix_reference": "https://w3id.org/p2p_ld/nwb-schema-language/"
+    },
+    {
+      "prefix_prefix": "linkml",
+      "prefix_reference": "https://w3id.org/linkml/"
+    },
+    {
+      "prefix_prefix": "biolink",
+      "prefix_reference": "https://w3id.org/biolink/"
+    },
+    {
+      "prefix_prefix": "schema",
+      "prefix_reference": "http://schema.org/"
+    },
+    {
+      "prefix_prefix": "PATO",
+      "prefix_reference": "http://purl.obolibrary.org/obo/PATO_"
+    },
+    {
+      "prefix_prefix": "example",
+      "prefix_reference": "https://example.org/"
+    }
+  ],
+  "default_prefix": "nwb_schema_language",
+  "default_range": "string",
+  "types": [
+    {
+      "name": "string",
+      "definition_uri": "https://w3id.org/linkml/String",
+      "description": "A character string",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "exact_mappings": [
+        "schema:Text"
+      ],
+      "base": "str",
+      "uri": "http://www.w3.org/2001/XMLSchema#string",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "integer",
+      "definition_uri": "https://w3id.org/linkml/Integer",
+      "description": "An integer",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "exact_mappings": [
+        "schema:Integer"
+      ],
+      "base": "int",
+      "uri": "http://www.w3.org/2001/XMLSchema#integer",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "boolean",
+      "definition_uri": "https://w3id.org/linkml/Boolean",
+      "description": "A binary (true or false) value",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "exact_mappings": [
+        "schema:Boolean"
+      ],
+      "base": "Bool",
+      "uri": "http://www.w3.org/2001/XMLSchema#boolean",
+      "repr": "bool",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "float",
+      "definition_uri": "https://w3id.org/linkml/Float",
+      "description": "A real number that conforms to the xsd:float specification",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "exact_mappings": [
+        "schema:Float"
+      ],
+      "base": "float",
+      "uri": "http://www.w3.org/2001/XMLSchema#float",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "double",
+      "definition_uri": "https://w3id.org/linkml/Double",
+      "description": "A real number that conforms to the xsd:double specification",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "close_mappings": [
+        "schema:Float"
+      ],
+      "base": "float",
+      "uri": "http://www.w3.org/2001/XMLSchema#double",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "decimal",
+      "definition_uri": "https://w3id.org/linkml/Decimal",
+      "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "broad_mappings": [
+        "schema:Number"
+      ],
+      "base": "Decimal",
+      "uri": "http://www.w3.org/2001/XMLSchema#decimal",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "time",
+      "definition_uri": "https://w3id.org/linkml/Time",
+      "description": "A time object represents a (local) time of day, independent of any particular day",
+      "notes": [
+        "URI is dateTime because OWL reasoners do not work with straight date or time"
+      ],
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "exact_mappings": [
+        "schema:Time"
+      ],
+      "base": "XSDTime",
+      "uri": "http://www.w3.org/2001/XMLSchema#time",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "date",
+      "definition_uri": "https://w3id.org/linkml/Date",
+      "description": "a date (year, month and day) in an idealized calendar",
+      "notes": [
+        "URI is dateTime because OWL reasoners don't work with straight date or time"
+      ],
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "exact_mappings": [
+        "schema:Date"
+      ],
+      "base": "XSDDate",
+      "uri": "http://www.w3.org/2001/XMLSchema#date",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "datetime",
+      "definition_uri": "https://w3id.org/linkml/Datetime",
+      "description": "The combination of a date and time",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "exact_mappings": [
+        "schema:DateTime"
+      ],
+      "base": "XSDDateTime",
+      "uri": "http://www.w3.org/2001/XMLSchema#dateTime",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "date_or_datetime",
+      "definition_uri": "https://w3id.org/linkml/DateOrDatetime",
+      "description": "Either a date or a datetime",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "base": "str",
+      "uri": "https://w3id.org/linkml/DateOrDatetime",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "uriorcurie",
+      "definition_uri": "https://w3id.org/linkml/Uriorcurie",
+      "description": "a URI or a CURIE",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "base": "URIorCURIE",
+      "uri": "http://www.w3.org/2001/XMLSchema#anyURI",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "curie",
+      "definition_uri": "https://w3id.org/linkml/Curie",
+      "conforms_to": "https://www.w3.org/TR/curie/",
+      "description": "a compact URI",
+      "comments": [
+        "in RDF serializations this MUST be expanded to a URI",
+        "in non-RDF serializations MAY be serialized as the compact representation"
+      ],
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "base": "Curie",
+      "uri": "http://www.w3.org/2001/XMLSchema#string",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "uri",
+      "definition_uri": "https://w3id.org/linkml/Uri",
+      "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt",
+      "description": "a complete URI",
+      "comments": [
+        "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node"
+      ],
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "close_mappings": [
+        "schema:URL"
+      ],
+      "base": "URI",
+      "uri": "http://www.w3.org/2001/XMLSchema#anyURI",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "ncname",
+      "definition_uri": "https://w3id.org/linkml/Ncname",
+      "description": "Prefix part of CURIE",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "base": "NCName",
+      "uri": "http://www.w3.org/2001/XMLSchema#string",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "objectidentifier",
+      "definition_uri": "https://w3id.org/linkml/Objectidentifier",
+      "description": "A URI or CURIE that represents an object in the model.",
+      "comments": [
+        "Used for inheritance and type checking"
+      ],
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "base": "ElementIdentifier",
+      "uri": "http://www.w3.org/ns/shex#iri",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "nodeidentifier",
+      "definition_uri": "https://w3id.org/linkml/Nodeidentifier",
+      "description": "A URI, CURIE or BNODE that represents a node in a model.",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "base": "NodeIdentifier",
+      "uri": "http://www.w3.org/ns/shex#nonLiteral",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "jsonpointer",
+      "definition_uri": "https://w3id.org/linkml/Jsonpointer",
+      "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901",
+      "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "base": "str",
+      "uri": "http://www.w3.org/2001/XMLSchema#string",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "jsonpath",
+      "definition_uri": "https://w3id.org/linkml/Jsonpath",
+      "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html",
+      "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "base": "str",
+      "uri": "http://www.w3.org/2001/XMLSchema#string",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    },
+    {
+      "name": "sparqlpath",
+      "definition_uri": "https://w3id.org/linkml/Sparqlpath",
+      "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths",
+      "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.",
+      "from_schema": "https://w3id.org/linkml/types",
+      "imported_from": "linkml:types",
+      "base": "str",
+      "uri": "http://www.w3.org/2001/XMLSchema#string",
+      "repr": "str",
+      "@type": "TypeDefinition"
+    }
+  ],
+  "enums": [
+    {
+      "name": "PersonStatus",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/PersonStatus",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "permissible_values": [
+        {
+          "text": "ALIVE",
+          "description": "the person is living",
+          "meaning": "PATO:0001421"
+        },
+        {
+          "text": "DEAD",
+          "description": "the person is deceased",
+          "meaning": "PATO:0001422"
+        },
+        {
+          "text": "UNKNOWN",
+          "description": "the vital status is not known",
+          "todos": [
+            "map this to an ontology"
+          ]
+        }
+      ]
+    }
+  ],
+  "slots": [
+    {
+      "name": "id",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/id",
+      "description": "A unique identifier for a thing",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "mappings": [
+        "http://schema.org/identifier"
+      ],
+      "slot_uri": "http://schema.org/identifier",
+      "identifier": true,
+      "owner": "NamedThing",
+      "domain_of": [
+        "NamedThing"
+      ],
+      "range": "uriorcurie",
+      "required": true,
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "name",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/name",
+      "description": "A human-readable name for a thing",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "mappings": [
+        "http://schema.org/name"
+      ],
+      "slot_uri": "http://schema.org/name",
+      "owner": "NamedThing",
+      "domain_of": [
+        "NamedThing"
+      ],
+      "range": "string",
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "description",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/description",
+      "description": "A human-readable description for a thing",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "mappings": [
+        "http://schema.org/description"
+      ],
+      "slot_uri": "http://schema.org/description",
+      "owner": "NamedThing",
+      "domain_of": [
+        "NamedThing"
+      ],
+      "range": "string",
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "primary_email",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/primary_email",
+      "description": "The main email address of a person",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "mappings": [
+        "http://schema.org/email"
+      ],
+      "slot_uri": "http://schema.org/email",
+      "owner": "Namespaces",
+      "domain_of": [
+        "Namespaces"
+      ],
+      "range": "string",
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "birth_date",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/birth_date",
+      "description": "Date on which a person is born",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "mappings": [
+        "http://schema.org/birthDate"
+      ],
+      "slot_uri": "http://schema.org/birthDate",
+      "owner": "Namespaces",
+      "domain_of": [
+        "Namespaces"
+      ],
+      "range": "date",
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "age_in_years",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/age_in_years",
+      "description": "Number of years since birth",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "slot_uri": "https://w3id.org/p2p_ld/nwb-schema-language/age_in_years",
+      "owner": "Namespaces",
+      "domain_of": [
+        "Namespaces"
+      ],
+      "range": "integer",
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "vital_status",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/vital_status",
+      "description": "living or dead status",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "slot_uri": "https://w3id.org/p2p_ld/nwb-schema-language/vital_status",
+      "owner": "Namespaces",
+      "domain_of": [
+        "Namespaces"
+      ],
+      "range": "PersonStatus",
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "namespacesCollection__entries",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "slot_uri": "https://w3id.org/p2p_ld/nwb-schema-language/entries",
+      "multivalued": true,
+      "alias": "entries",
+      "owner": "NamespacesCollection",
+      "domain_of": [
+        "NamespacesCollection"
+      ],
+      "range": "Namespaces",
+      "inlined": true,
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "Namespaces_primary_email",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/primary_email",
+      "description": "The main email address of a person",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "mappings": [
+        "http://schema.org/email"
+      ],
+      "is_a": "primary_email",
+      "domain": "Namespaces",
+      "slot_uri": "http://schema.org/email",
+      "alias": "primary_email",
+      "owner": "Namespaces",
+      "domain_of": [
+        "Namespaces"
+      ],
+      "is_usage_slot": true,
+      "usage_slot_name": "primary_email",
+      "range": "string",
+      "pattern": "^\\S+@[\\S+\\.]+\\S+",
+      "@type": "SlotDefinition"
+    }
+  ],
+  "classes": [
+    {
+      "name": "NamedThing",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/NamedThing",
+      "description": "A generic grouping for any identifiable entity",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "mappings": [
+        "schema:Thing"
+      ],
+      "slots": [
+        "id",
+        "name",
+        "description"
+      ],
+      "slot_usage": {},
+      "class_uri": "http://schema.org/Thing",
+      "@type": "ClassDefinition"
+    },
+    {
+      "name": "Namespaces",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Namespaces",
+      "description": "Represents a Namespaces",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "is_a": "NamedThing",
+      "slots": [
+        "id",
+        "name",
+        "description",
+        "Namespaces_primary_email",
+        "birth_date",
+        "age_in_years",
+        "vital_status"
+      ],
+      "slot_usage": {},
+      "class_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Namespaces",
+      "@type": "ClassDefinition"
+    },
+    {
+      "name": "NamespacesCollection",
+      "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/NamespacesCollection",
+      "description": "A holder for Namespaces objects",
+      "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language",
+      "slots": [
+        "namespacesCollection__entries"
+      ],
+      "slot_usage": {},
+      "attributes": [
+        {
+          "name": "entries",
+          "multivalued": true,
+          "range": "Namespaces",
+          "inlined": true,
+          "@type": "SlotDefinition"
+        }
+      ],
+      "class_uri": "https://w3id.org/p2p_ld/nwb-schema-language/NamespacesCollection",
+      "tree_root": true,
+      "@type": "ClassDefinition"
+    }
+  ],
+  "metamodel_version": "1.7.0",
+  "source_file": "nwb_schema_language.yaml",
+  "source_file_date": "2023-08-16T15:45:06",
+  "source_file_size": 2270,
+  "generation_date": "2023-08-16T15:57:40",
+  "@type": "SchemaDefinition",
+  "@context": [
+    "project/jsonld/nwb_schema_language.context.jsonld",
+    "https://w3id.org/linkml/types.context.jsonld",
+    {
+      "@base": "https://w3id.org/p2p_ld/nwb-schema-language/"
+    }
+  ]
+}

nwb-schema-linkml/project/jsonschema/nwb_schema_language.schema.json

@@ -0,0 +1,161 @@
+{
+    "$defs": {
+        "NamedThing": {
+            "additionalProperties": false,
+            "description": "A generic grouping for any identifiable entity",
+            "properties": {
+                "description": {
+                    "description": "A human-readable description for a thing",
+                    "type": "string"
+                },
+                "id": {
+                    "description": "A unique identifier for a thing",
+                    "type": "string"
+                },
+                "name": {
+                    "description": "A human-readable name for a thing",
+                    "type": "string"
+                }
+            },
+            "required": [
+                "id"
+            ],
+            "title": "NamedThing",
+            "type": "object"
+        },
+        "Namespaces": {
+            "additionalProperties": false,
+            "description": "Represents a Namespaces",
+            "properties": {
+                "age_in_years": {
+                    "description": "Number of years since birth",
+                    "type": "integer"
+                },
+                "birth_date": {
+                    "description": "Date on which a person is born",
+                    "format": "date",
+                    "type": "string"
+                },
+                "description": {
+                    "description": "A human-readable description for a thing",
+                    "type": "string"
+                },
+                "id": {
+                    "description": "A unique identifier for a thing",
+                    "type": "string"
+                },
+                "name": {
+                    "description": "A human-readable name for a thing",
+                    "type": "string"
+                },
+                "primary_email": {
+                    "description": "The main email address of a person",
+                    "pattern": "^\\S+@[\\S+\\.]+\\S+",
+                    "type": "string"
+                },
+                "vital_status": {
+                    "$ref": "#/$defs/PersonStatus",
+                    "description": "living or dead status"
+                }
+            },
+            "required": [
+                "id"
+            ],
+            "title": "Namespaces",
+            "type": "object"
+        },
+        "NamespacesCollection": {
+            "additionalProperties": false,
+            "description": "A holder for Namespaces objects",
+            "properties": {
+                "entries": {
+                    "additionalProperties": {
+                        "anyOf": [
+                            {
+                                "$ref": "#/$defs/Namespaces__identifier_optional"
+                            },
+                            {
+                                "type": "null"
+                            }
+                        ]
+                    },
+                    "type": "object"
+                }
+            },
+            "title": "NamespacesCollection",
+            "type": "object"
+        },
+        "Namespaces__identifier_optional": {
+            "additionalProperties": false,
+            "description": "Represents a Namespaces",
+            "properties": {
+                "age_in_years": {
+                    "description": "Number of years since birth",
+                    "type": "integer"
+                },
+                "birth_date": {
+                    "description": "Date on which a person is born",
+                    "format": "date",
+                    "type": "string"
+                },
+                "description": {
+                    "description": "A human-readable description for a thing",
+                    "type": "string"
+                },
+                "id": {
+                    "description": "A unique identifier for a thing",
+                    "type": "string"
+                },
+                "name": {
+                    "description": "A human-readable name for a thing",
+                    "type": "string"
+                },
+                "primary_email": {
+                    "description": "The main email address of a person",
+                    "pattern": "^\\S+@[\\S+\\.]+\\S+",
+                    "type": "string"
+                },
+                "vital_status": {
+                    "$ref": "#/$defs/PersonStatus",
+                    "description": "living or dead status"
+                }
+            },
+            "required": [],
+            "title": "Namespaces",
+            "type": "object"
+        },
+        "PersonStatus": {
+            "description": "",
+            "enum": [
+                "ALIVE",
+                "DEAD",
+                "UNKNOWN"
+            ],
+            "title": "PersonStatus",
+            "type": "string"
+        }
+    },
+    "$id": "https://w3id.org/p2p_ld/nwb-schema-language",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "additionalProperties": true,
+    "description": "A holder for Namespaces objects",
+    "metamodel_version": "1.7.0",
+    "properties": {
+        "entries": {
+            "additionalProperties": {
+                "anyOf": [
+                    {
+                        "$ref": "#/$defs/Namespaces__identifier_optional"
+                    },
+                    {
+                        "type": "null"
+                    }
+                ]
+            },
+            "type": "object"
+        }
+    },
+    "title": "nwb-schema-language",
+    "type": "object",
+    "version": null
+}

nwb-schema-linkml/project/owl/nwb_schema_language.owl.ttl

@@ -0,0 +1,343 @@
+@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> .
+@prefix PATO: <http://purl.obolibrary.org/obo/PATO_> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix famrel: <http://example.org/famrel/> .
+@prefix linkml: <https://w3id.org/linkml/> .
+@prefix my_datamodel: <https://w3id.org/my_org/my_datamodel> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix schema: <http://schema.org/> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+linkml:SubsetDefinition a owl:Class ;
+    rdfs:label "subset_definition" .
+
+linkml:TypeDefinition a owl:Class ;
+    rdfs:label "type_definition" .
+
+linkml:topValue a owl:DatatypeProperty ;
+    rdfs:label "value" .
+
+my_datamodel: a owl:Ontology ;
+    rdfs:label "my_datamodel" ;
+    IAO:0000700 my_datamodel:Address,
+        my_datamodel:HasAliases,
+        my_datamodel:NamedThing,
+        my_datamodel:Registry,
+        my_datamodel:Relationship ;
+    dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
+    dcterms:title "My Datamodel" ;
+    rdfs:seeAlso "https://example.org/" ;
+    linkml:generation_date "2022-09-06T10:01:46" ;
+    linkml:metamodel_version "1.7.0" ;
+    linkml:source_file "nwb_schema_language.yaml" ;
+    linkml:source_file_date "2022-09-06T10:00:58" ;
+    linkml:source_file_size 3771 .
+
+my_datamodel:employed_at a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "employed_at" ;
+    rdfs:range my_datamodel:Organization .
+
+my_datamodel:is_current a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "is_current" ;
+    rdfs:range linkml:Boolean .
+
+my_datamodel:Registry a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "Registry" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:allValuesFrom my_datamodel:Person ;
+            owl:onProperty my_datamodel:persons ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom my_datamodel:Organization ;
+            owl:onProperty my_datamodel:organizations ] ;
+    skos:definition "Top level data container" .
+
+my_datamodel:age_in_years a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "age_in_years" ;
+    rdfs:range linkml:Integer .
+
+my_datamodel:city a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "city" ;
+    rdfs:range linkml:String .
+
+my_datamodel:current_address a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "current_address" ;
+    rdfs:range my_datamodel:Address ;
+    skos:definition "The address at which a person currently lives" .
+
+my_datamodel:founding_date a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "founding_date" ;
+    rdfs:range linkml:String .
+
+my_datamodel:has_familial_relationships a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "has_familial_relationships" ;
+    rdfs:range my_datamodel:FamilialRelationship .
+
+my_datamodel:mission_statement a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "mission_statement" ;
+    rdfs:range linkml:String .
+
+my_datamodel:organizations a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "organizations" ;
+    rdfs:range my_datamodel:Organization .
+
+my_datamodel:persons a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "persons" ;
+    rdfs:range my_datamodel:Person .
+
+my_datamodel:postal_code a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "postal_code" ;
+    rdfs:range linkml:String .
+
+my_datamodel:street a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "street" ;
+    rdfs:range linkml:String .
+
+famrel:02 a owl:Class,
+        my_datamodel:FamilialRelationshipType ;
+    rdfs:label "PARENT_OF" .
+
+PATO:0001421 a owl:Class,
+        my_datamodel:PersonStatus ;
+    rdfs:label "ALIVE" .
+
+PATO:0001422 a owl:Class,
+        my_datamodel:PersonStatus ;
+    rdfs:label "DEAD" .
+
+schema:birthDate a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "birth_date" ;
+    rdfs:range linkml:String ;
+    skos:exactMatch schema:birthDate .
+
+schema:description a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "description" ;
+    rdfs:range linkml:String ;
+    skos:exactMatch schema:description .
+
+schema:email a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "primary_email" ;
+    rdfs:range linkml:String ;
+    skos:exactMatch schema:email .
+
+schema:identifier a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "id" ;
+    rdfs:range linkml:String ;
+    skos:exactMatch schema:identifier .
+
+schema:image a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "image" ;
+    rdfs:range linkml:String ;
+    skos:exactMatch schema:image .
+
+schema:name a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "name" ;
+    rdfs:range linkml:String ;
+    skos:exactMatch schema:name .
+
+<http://www.w3.org/ns/prov#endedAtTime> a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "ended_at_time" ;
+    rdfs:range linkml:Date ;
+    skos:exactMatch <http://www.w3.org/ns/prov#endedAtTime> .
+
+<http://www.w3.org/ns/prov#startedAtTime> a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "started_at_time" ;
+    rdfs:range linkml:Date ;
+    skos:exactMatch <http://www.w3.org/ns/prov#startedAtTime> .
+
+my_datamodel:FamilialRelationship a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "FamilialRelationship" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onClass my_datamodel:FamilialRelationshipType ;
+            owl:onProperty my_datamodel:type ;
+            owl:qualifiedCardinality 1 ],
+        [ a owl:Restriction ;
+            owl:onClass my_datamodel:Person ;
+            owl:onProperty my_datamodel:related_to ;
+            owl:qualifiedCardinality 1 ],
+        my_datamodel:Relationship .
+
+<https://w3id.org/my_org/my_datamodelPersonStatus#UNKNOWN> a owl:Class,
+        my_datamodel:PersonStatus ;
+    rdfs:label "UNKNOWN" .
+
+my_datamodel:Relationship a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "Relationship" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty my_datamodel:related_to ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty my_datamodel:type ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:Date ;
+            owl:onProperty <http://www.w3.org/ns/prov#endedAtTime> ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:Date ;
+            owl:onProperty <http://www.w3.org/ns/prov#startedAtTime> ] .
+
+my_datamodel:related_to a owl:ObjectProperty,
+        linkml:SlotDefinition .
+
+my_datamodel:type a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "type" ;
+    rdfs:range linkml:String .
+
+famrel:01 a owl:Class,
+        my_datamodel:FamilialRelationshipType ;
+    rdfs:label "CHILD_OF",
+        "SIBLING_OF" .
+
+my_datamodel:Address a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "Address" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty my_datamodel:city ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty my_datamodel:street ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty my_datamodel:postal_code ] ;
+    skos:exactMatch schema:PostalAddress .
+
+my_datamodel:FamilialRelationshipType a owl:Class,
+        linkml:EnumDefinition ;
+    rdfs:label "FamilialRelationshipType" ;
+    owl:unionOf ( famrel:01 famrel:02 famrel:01 ) ;
+    linkml:permissible_values famrel:01,
+        famrel:02 .
+
+my_datamodel:HasAliases a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "HasAliases" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:allValuesFrom linkml:String ;
+            owl:onProperty my_datamodel:aliases ],
+        linkml:mixin ;
+    skos:definition "A mixin applied to any class that can have aliases/alternateNames" .
+
+my_datamodel:NamedThing a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "NamedThing" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty schema:description ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty schema:name ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty schema:image ],
+        [ a owl:Restriction ;
+            owl:onClass linkml:String ;
+            owl:onProperty schema:identifier ;
+            owl:qualifiedCardinality 1 ] ;
+    skos:closeMatch schema:Thing ;
+    skos:definition "A generic grouping for any identifiable entity" .
+
+my_datamodel:Organization a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "Organization" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty my_datamodel:mission_statement ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty my_datamodel:founding_date ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom linkml:String ;
+            owl:onProperty my_datamodel:aliases ],
+        my_datamodel:HasAliases,
+        my_datamodel:NamedThing ;
+    skos:definition "An organization such as a company or university" ;
+    skos:exactMatch schema:Organization .
+
+my_datamodel:Person a owl:Class,
+        linkml:ClassDefinition ;
+    rdfs:label "Person" ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:allValuesFrom linkml:String ;
+            owl:onProperty my_datamodel:aliases ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom my_datamodel:FamilialRelationship ;
+            owl:onProperty my_datamodel:has_familial_relationships ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:Integer ;
+            owl:onProperty my_datamodel:age_in_years ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass my_datamodel:Address ;
+            owl:onProperty my_datamodel:current_address ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty schema:birthDate ],
+        [ a owl:Restriction ;
+            owl:maxQualifiedCardinality 1 ;
+            owl:onClass linkml:String ;
+            owl:onProperty schema:email ],
+        my_datamodel:HasAliases,
+        my_datamodel:NamedThing ;
+    skos:definition "A person (alive, dead, undead, or fictional)." ;
+    skos:exactMatch schema:Person .
+
+my_datamodel:PersonStatus a owl:Class,
+        linkml:EnumDefinition ;
+    rdfs:label "PersonStatus" ;
+    owl:unionOf ( PATO:0001421 PATO:0001422 <https://w3id.org/my_org/my_datamodelPersonStatus#UNKNOWN> ) ;
+    linkml:permissible_values PATO:0001421,
+        PATO:0001422,
+        <https://w3id.org/my_org/my_datamodelPersonStatus#UNKNOWN> .
+
+my_datamodel:aliases a owl:ObjectProperty,
+        linkml:SlotDefinition ;
+    rdfs:label "aliases" ;
+    rdfs:range linkml:String ;
+    skos:exactMatch schema:alternateName .
+
+linkml:ClassDefinition a owl:Class ;
+    rdfs:label "class_definition" .
+
+linkml:SlotDefinition a owl:Class ;
+    rdfs:label "slot_definition" .

nwb-schema-linkml/project/prefixmap/nwb_schema_language.yaml

@@ -0,0 +1,11 @@
+{
+   "PATO": "http://purl.obolibrary.org/obo/PATO_",
+   "biolink": "https://w3id.org/biolink/",
+   "example": "https://example.org/",
+   "linkml": "https://w3id.org/linkml/",
+   "nwb_schema_language": "https://w3id.org/p2p_ld/nwb-schema-language/",
+   "schema": "http://schema.org/",
+   "NamedThing": {
+      "@id": "schema:Thing"
+   }
+}

nwb-schema-linkml/project/protobuf/nwb_schema_language.proto

@@ -0,0 +1,23 @@
+// A generic grouping for any identifiable entity
+message NamedThing
+ {
+  uriorcurie id = 0
+  string name = 0
+  string description = 0
+ }
+// Represents a Namespaces
+message Namespaces
+ {
+  uriorcurie id = 0
+  string name = 0
+  string description = 0
+  string primaryEmail = 0
+  date birthDate = 0
+  integer ageInYears = 0
+  personStatus vitalStatus = 0
+ }
+// A holder for Namespaces objects
+message NamespacesCollection
+ {
+ repeated  namespaces entries = 0
+ }

nwb-schema-linkml/project/shacl/nwb_schema_language.shacl.ttl

@@ -0,0 +1,164 @@
+@prefix famrel: <http://example.org/famrel/> .
+@prefix my_datamodel: <https://w3id.org/my_org/my_datamodel> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix schema: <http://schema.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+my_datamodel:HasAliases a sh:NodeShape ;
+    sh:closed true ;
+    sh:description "A mixin applied to any class that can have aliases/alternateNames" ;
+    sh:ignoredProperties ( rdf:type ) ;
+    sh:property [ sh:order 0 ;
+            sh:path my_datamodel:aliases ] ;
+    sh:targetClass my_datamodel:HasAliases .
+
+my_datamodel:NamedThing a sh:NodeShape ;
+    sh:closed true ;
+    sh:description "A generic grouping for any identifiable entity" ;
+    sh:ignoredProperties ( rdf:type ) ;
+    sh:property [ sh:maxCount 1 ;
+            sh:order 0 ;
+            sh:path schema:identifier ],
+        [ sh:maxCount 1 ;
+            sh:order 1 ;
+            sh:path schema:name ],
+        [ sh:maxCount 1 ;
+            sh:order 3 ;
+            sh:path schema:image ],
+        [ sh:maxCount 1 ;
+            sh:order 2 ;
+            sh:path schema:description ] ;
+    sh:targetClass my_datamodel:NamedThing .
+
+my_datamodel:Registry a sh:NodeShape ;
+    sh:closed true ;
+    sh:description "Top level data container" ;
+    sh:ignoredProperties ( rdf:type ) ;
+    sh:property [ sh:class schema:Person ;
+            sh:nodeKind sh:IRI ;
+            sh:order 0 ;
+            sh:path my_datamodel:persons ],
+        [ sh:class schema:Organization ;
+            sh:nodeKind sh:IRI ;
+            sh:order 1 ;
+            sh:path my_datamodel:organizations ] ;
+    sh:targetClass my_datamodel:Registry .
+
+my_datamodel:Relationship a sh:NodeShape ;
+    sh:closed true ;
+    sh:ignoredProperties ( rdf:type ) ;
+    sh:property [ sh:maxCount 1 ;
+            sh:order 0 ;
+            sh:path <http://www.w3.org/ns/prov#startedAtTime> ],
+        [ sh:maxCount 1 ;
+            sh:order 3 ;
+            sh:path my_datamodel:type ],
+        [ sh:maxCount 1 ;
+            sh:order 2 ;
+            sh:path my_datamodel:related_to ],
+        [ sh:maxCount 1 ;
+            sh:order 1 ;
+            sh:path <http://www.w3.org/ns/prov#endedAtTime> ] ;
+    sh:targetClass my_datamodel:Relationship .
+
+schema:Organization a sh:NodeShape ;
+    sh:closed true ;
+    sh:description "An organization such as a company or university" ;
+    sh:ignoredProperties ( rdf:type ) ;
+    sh:property [ sh:maxCount 1 ;
+            sh:order 1 ;
+            sh:path my_datamodel:founding_date ],
+        [ sh:maxCount 1 ;
+            sh:order 5 ;
+            sh:path schema:description ],
+        [ sh:order 2 ;
+            sh:path my_datamodel:aliases ],
+        [ sh:maxCount 1 ;
+            sh:order 6 ;
+            sh:path schema:image ],
+        [ sh:maxCount 1 ;
+            sh:order 0 ;
+            sh:path my_datamodel:mission_statement ],
+        [ sh:maxCount 1 ;
+            sh:order 3 ;
+            sh:path schema:identifier ],
+        [ sh:maxCount 1 ;
+            sh:order 4 ;
+            sh:path schema:name ] ;
+    sh:targetClass schema:Organization .
+
+schema:Person a sh:NodeShape ;
+    sh:closed true ;
+    sh:description "A person (alive, dead, undead, or fictional)." ;
+    sh:ignoredProperties ( rdf:type ) ;
+    sh:property [ sh:maxCount 1 ;
+            sh:order 6 ;
+            sh:path schema:identifier ],
+        [ sh:maxCount 1 ;
+            sh:order 8 ;
+            sh:path schema:description ],
+        [ sh:maxCount 1 ;
+            sh:order 9 ;
+            sh:path schema:image ],
+        [ sh:maxCount 1 ;
+            sh:order 0 ;
+            sh:path schema:email ;
+            sh:pattern "^\\S+@[\\S+\\.]+\\S+" ],
+        [ sh:maxCount 1 ;
+            sh:maxInclusive 999 ;
+            sh:minInclusive 0 ;
+            sh:order 2 ;
+            sh:path my_datamodel:age_in_years ],
+        [ sh:class schema:PostalAddress ;
+            sh:description "The address at which a person currently lives" ;
+            sh:maxCount 1 ;
+            sh:nodeKind sh:BlankNode ;
+            sh:order 3 ;
+            sh:path my_datamodel:current_address ],
+        [ sh:class my_datamodel:FamilialRelationship ;
+            sh:nodeKind sh:BlankNode ;
+            sh:order 4 ;
+            sh:path my_datamodel:has_familial_relationships ],
+        [ sh:maxCount 1 ;
+            sh:order 1 ;
+            sh:path schema:birthDate ],
+        [ sh:maxCount 1 ;
+            sh:order 7 ;
+            sh:path schema:name ],
+        [ sh:order 5 ;
+            sh:path my_datamodel:aliases ] ;
+    sh:targetClass schema:Person .
+
+schema:PostalAddress a sh:NodeShape ;
+    sh:closed true ;
+    sh:ignoredProperties ( rdf:type ) ;
+    sh:property [ sh:maxCount 1 ;
+            sh:order 1 ;
+            sh:path my_datamodel:city ],
+        [ sh:maxCount 1 ;
+            sh:order 2 ;
+            sh:path my_datamodel:postal_code ],
+        [ sh:maxCount 1 ;
+            sh:order 0 ;
+            sh:path my_datamodel:street ] ;
+    sh:targetClass schema:PostalAddress .
+
+my_datamodel:FamilialRelationship a sh:NodeShape ;
+    sh:closed true ;
+    sh:ignoredProperties ( rdf:type ) ;
+    sh:property [ sh:maxCount 1 ;
+            sh:order 1 ;
+            sh:path <http://www.w3.org/ns/prov#endedAtTime> ],
+        [ sh:maxCount 1 ;
+            sh:order 0 ;
+            sh:path <http://www.w3.org/ns/prov#startedAtTime> ],
+        [ sh:in ( famrel:01 famrel:02 famrel:01 ) ;
+            sh:maxCount 1 ;
+            sh:minCount 1 ;
+            sh:order 3 ;
+            sh:path my_datamodel:type ],
+        [ sh:maxCount 1 ;
+            sh:order 2 ;
+            sh:path my_datamodel:related_to ] ;
+    sh:targetClass my_datamodel:FamilialRelationship .

nwb-schema-linkml/project/shex/nwb_schema_language.shex

@@ -0,0 +1,74 @@
+BASE <https://w3id.org/p2p_ld/nwb-schema-language/>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX linkml: <https://w3id.org/linkml/>
+PREFIX schema1: <http://schema.org/>
+
+
+linkml:String xsd:string
+
+linkml:Integer xsd:integer
+
+linkml:Boolean xsd:boolean
+
+linkml:Float xsd:float
+
+linkml:Double xsd:double
+
+linkml:Decimal xsd:decimal
+
+linkml:Time xsd:time
+
+linkml:Date xsd:date
+
+linkml:Datetime xsd:dateTime
+
+linkml:DateOrDatetime linkml:DateOrDatetime
+
+linkml:Uriorcurie IRI
+
+linkml:Curie xsd:string
+
+linkml:Uri IRI
+
+linkml:Ncname xsd:string
+
+linkml:Objectidentifier IRI
+
+linkml:Nodeidentifier NONLITERAL
+
+linkml:Jsonpointer xsd:string
+
+linkml:Jsonpath xsd:string
+
+linkml:Sparqlpath xsd:string
+
+<NamedThing>  (
+    CLOSED {
+       (  $<NamedThing_tes> (  schema1:name @linkml:String ? ;
+             schema1:description @linkml:String ?
+          ) ;
+          rdf:type [ schema1:Thing ]
+       )
+    } OR @<Namespaces>
+)
+
+<Namespaces> CLOSED {
+    (  $<Namespaces_tes> (  &<NamedThing_tes> ;
+          rdf:type [ schema1:Thing ] ? ;
+          schema1:email @linkml:String ? ;
+          schema1:birthDate @linkml:Date ? ;
+          <age_in_years> @linkml:Integer ? ;
+          <vital_status> @<PersonStatus> ?
+       ) ;
+       rdf:type [ <Namespaces> ]
+    )
+}
+
+<NamespacesCollection> CLOSED {
+    (  $<NamespacesCollection_tes> <entries> @<Namespaces> * ;
+       rdf:type [ <NamespacesCollection> ] ?
+    )
+}
+
+

nwb-schema-linkml/project/sqlschema/nwb_schema_language.sql

@@ -0,0 +1,24 @@
+
+
+CREATE TABLE "NamedThing" (
+	id TEXT NOT NULL, 
+	name TEXT, 
+	description TEXT, 
+	PRIMARY KEY (id)
+);
+
+CREATE TABLE "Namespaces" (
+	id TEXT NOT NULL, 
+	name TEXT, 
+	description TEXT, 
+	primary_email TEXT, 
+	birth_date DATE, 
+	age_in_years INTEGER, 
+	vital_status VARCHAR(7), 
+	PRIMARY KEY (id)
+);
+
+CREATE TABLE "NamespacesCollection" (
+	entries TEXT, 
+	PRIMARY KEY (entries)
+);

nwb-schema-linkml/pyproject.toml

@@ -0,0 +1,30 @@
+[tool.poetry]
+name = "nwb_schema_linkml"
+version = "0.1.0"
+description = "Translation of the nwb-schema-language to LinkML"
+authors = ["Jonny Saunders <j@nny.fyi>"]
+license = "GNU GPL v3.0"
+readme = "README.md"
+include = ["README.md", "src/nwb_schema_language/schema", "project"]
+
+[tool.poetry.dependencies]
+python = "^3.9"
+linkml-runtime = "^1.1.24"
+
+[tool.poetry-dynamic-versioning]
+enable = true
+vcs = "git"
+style = "pep440"
+
+[tool.poetry.dev-dependencies]
+linkml = "^1.3.5"
+mkdocs-material = "^8.2.8"
+mkdocs-mermaid2-plugin = "^0.6.0"
+schemasheets = "^0.1.14"
+
+[build-system]
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
+build-backend = "poetry_dynamic_versioning.backend"
+
+[tool.poetry.extras]
+docs = ["linkml", "mkdocs-material"]

nwb-schema-linkml/src/data/examples/Namespaces-001.yaml

@@ -0,0 +1,7 @@
+# Example data object
+---
+entries:
+  - id: example:Namespaces001
+    name: foo bar
+    primary_email: foo.bar@example.com
+    age_in_years: 33

nwb-schema-linkml/src/docs/about.md

@@ -0,0 +1,3 @@
+# nwb-schema-language
+
+Translation of the nwb-schema-language to LinkML

nwb-schema-linkml/src/nwb_schema_language/_version.py

@@ -0,0 +1,7 @@
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version(__name__)
+except PackageNotFoundError:
+    # package not installed
+    __version__ = "0.0.0"

nwb-schema-linkml/src/nwb_schema_language/datamodel/__init__.py

@@ -0,0 +1 @@
+from .nwb_schema_language import *

nwb-schema-linkml/src/nwb_schema_language/datamodel/nwb_schema_language.py

@@ -0,0 +1,193 @@
+# Auto generated from nwb_schema_language.yaml by pythongen.py version: 0.0.1
+# Generation date: 2023-08-16T15:57:41
+# Schema: nwb-schema-language
+#
+# id: https://w3id.org/p2p_ld/nwb-schema-language
+# description: Translation of the nwb-schema-language to LinkML
+# license: GNU GPL v3.0
+
+import dataclasses
+import re
+from jsonasobj2 import JsonObj, as_dict
+from typing import Optional, List, Union, Dict, ClassVar, Any
+from dataclasses import dataclass
+from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions
+
+from linkml_runtime.utils.slot import Slot
+from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode
+from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
+from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
+from linkml_runtime.utils.formatutils import camelcase, underscore, sfx
+from linkml_runtime.utils.enumerations import EnumDefinitionImpl
+from rdflib import Namespace, URIRef
+from linkml_runtime.utils.curienamespace import CurieNamespace
+from linkml_runtime.linkml_model.types import Date, Integer, String, Uriorcurie
+from linkml_runtime.utils.metamodelcore import URIorCURIE, XSDDate
+
+metamodel_version = "1.7.0"
+version = None
+
+# Overwrite dataclasses _init_fn to add **kwargs in __init__
+dataclasses._init_fn = dataclasses_init_fn_with_kwargs
+
+# Namespaces
+PATO = CurieNamespace('PATO', 'http://purl.obolibrary.org/obo/PATO_')
+BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/')
+EXAMPLE = CurieNamespace('example', 'https://example.org/')
+LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
+NWB_SCHEMA_LANGUAGE = CurieNamespace('nwb_schema_language', 'https://w3id.org/p2p_ld/nwb-schema-language/')
+SCHEMA = CurieNamespace('schema', 'http://schema.org/')
+DEFAULT_ = NWB_SCHEMA_LANGUAGE
+
+
+# Types
+
+# Class references
+class NamedThingId(URIorCURIE):
+    pass
+
+
+class NamespacesId(NamedThingId):
+    pass
+
+
+@dataclass
+class NamedThing(YAMLRoot):
+    """
+    A generic grouping for any identifiable entity
+    """
+    _inherited_slots: ClassVar[List[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = SCHEMA.Thing
+    class_class_curie: ClassVar[str] = "schema:Thing"
+    class_name: ClassVar[str] = "NamedThing"
+    class_model_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.NamedThing
+
+    id: Union[str, NamedThingId] = None
+    name: Optional[str] = None
+    description: Optional[str] = None
+
+    def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
+        if self._is_empty(self.id):
+            self.MissingRequiredField("id")
+        if not isinstance(self.id, NamedThingId):
+            self.id = NamedThingId(self.id)
+
+        if self.name is not None and not isinstance(self.name, str):
+            self.name = str(self.name)
+
+        if self.description is not None and not isinstance(self.description, str):
+            self.description = str(self.description)
+
+        super().__post_init__(**kwargs)
+
+
+@dataclass
+class Namespaces(NamedThing):
+    """
+    Represents a Namespaces
+    """
+    _inherited_slots: ClassVar[List[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.Namespaces
+    class_class_curie: ClassVar[str] = "nwb_schema_language:Namespaces"
+    class_name: ClassVar[str] = "Namespaces"
+    class_model_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.Namespaces
+
+    id: Union[str, NamespacesId] = None
+    primary_email: Optional[str] = None
+    birth_date: Optional[Union[str, XSDDate]] = None
+    age_in_years: Optional[int] = None
+    vital_status: Optional[Union[str, "PersonStatus"]] = None
+
+    def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
+        if self._is_empty(self.id):
+            self.MissingRequiredField("id")
+        if not isinstance(self.id, NamespacesId):
+            self.id = NamespacesId(self.id)
+
+        if self.primary_email is not None and not isinstance(self.primary_email, str):
+            self.primary_email = str(self.primary_email)
+
+        if self.birth_date is not None and not isinstance(self.birth_date, XSDDate):
+            self.birth_date = XSDDate(self.birth_date)
+
+        if self.age_in_years is not None and not isinstance(self.age_in_years, int):
+            self.age_in_years = int(self.age_in_years)
+
+        if self.vital_status is not None and not isinstance(self.vital_status, PersonStatus):
+            self.vital_status = PersonStatus(self.vital_status)
+
+        super().__post_init__(**kwargs)
+
+
+@dataclass
+class NamespacesCollection(YAMLRoot):
+    """
+    A holder for Namespaces objects
+    """
+    _inherited_slots: ClassVar[List[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.NamespacesCollection
+    class_class_curie: ClassVar[str] = "nwb_schema_language:NamespacesCollection"
+    class_name: ClassVar[str] = "NamespacesCollection"
+    class_model_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.NamespacesCollection
+
+    entries: Optional[Union[Dict[Union[str, NamespacesId], Union[dict, Namespaces]], List[Union[dict, Namespaces]]]] = empty_dict()
+
+    def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
+        self._normalize_inlined_as_dict(slot_name="entries", slot_type=Namespaces, key_name="id", keyed=True)
+
+        super().__post_init__(**kwargs)
+
+
+# Enumerations
+class PersonStatus(EnumDefinitionImpl):
+
+    ALIVE = PermissibleValue(
+        text="ALIVE",
+        description="the person is living",
+        meaning=PATO["0001421"])
+    DEAD = PermissibleValue(
+        text="DEAD",
+        description="the person is deceased",
+        meaning=PATO["0001422"])
+    UNKNOWN = PermissibleValue(
+        text="UNKNOWN",
+        description="the vital status is not known")
+
+    _defn = EnumDefinition(
+        name="PersonStatus",
+    )
+
+# Slots
+class slots:
+    pass
+
+slots.id = Slot(uri=SCHEMA.identifier, name="id", curie=SCHEMA.curie('identifier'),
+                   model_uri=NWB_SCHEMA_LANGUAGE.id, domain=None, range=URIRef)
+
+slots.name = Slot(uri=SCHEMA.name, name="name", curie=SCHEMA.curie('name'),
+                   model_uri=NWB_SCHEMA_LANGUAGE.name, domain=None, range=Optional[str])
+
+slots.description = Slot(uri=SCHEMA.description, name="description", curie=SCHEMA.curie('description'),
+                   model_uri=NWB_SCHEMA_LANGUAGE.description, domain=None, range=Optional[str])
+
+slots.primary_email = Slot(uri=SCHEMA.email, name="primary_email", curie=SCHEMA.curie('email'),
+                   model_uri=NWB_SCHEMA_LANGUAGE.primary_email, domain=None, range=Optional[str])
+
+slots.birth_date = Slot(uri=SCHEMA.birthDate, name="birth_date", curie=SCHEMA.curie('birthDate'),
+                   model_uri=NWB_SCHEMA_LANGUAGE.birth_date, domain=None, range=Optional[Union[str, XSDDate]])
+
+slots.age_in_years = Slot(uri=NWB_SCHEMA_LANGUAGE.age_in_years, name="age_in_years", curie=NWB_SCHEMA_LANGUAGE.curie('age_in_years'),
+                   model_uri=NWB_SCHEMA_LANGUAGE.age_in_years, domain=None, range=Optional[int])
+
+slots.vital_status = Slot(uri=NWB_SCHEMA_LANGUAGE.vital_status, name="vital_status", curie=NWB_SCHEMA_LANGUAGE.curie('vital_status'),
+                   model_uri=NWB_SCHEMA_LANGUAGE.vital_status, domain=None, range=Optional[Union[str, "PersonStatus"]])
+
+slots.namespacesCollection__entries = Slot(uri=NWB_SCHEMA_LANGUAGE.entries, name="namespacesCollection__entries", curie=NWB_SCHEMA_LANGUAGE.curie('entries'),
+                   model_uri=NWB_SCHEMA_LANGUAGE.namespacesCollection__entries, domain=None, range=Optional[Union[Dict[Union[str, NamespacesId], Union[dict, Namespaces]], List[Union[dict, Namespaces]]]])
+
+slots.Namespaces_primary_email = Slot(uri=SCHEMA.email, name="Namespaces_primary_email", curie=SCHEMA.curie('email'),
+                   model_uri=NWB_SCHEMA_LANGUAGE.Namespaces_primary_email, domain=Namespaces, range=Optional[str],
+                   pattern=re.compile(r'^\S+@[\S+\.]+\S+'))

nwb-schema-linkml/src/nwb_schema_language/schema/nwb_schema_language.yaml

@@ -0,0 +1,96 @@
+---
+id: https://w3id.org/p2p_ld/nwb-schema-language
+name: nwb-schema-language
+title: nwb-schema-language
+description: |-
+  Translation of the nwb-schema-language to LinkML
+license: GNU GPL v3.0
+see_also:
+  - https://p2p_ld.github.io/nwb-schema-language
+
+prefixes:
+  nwb_schema_language: https://w3id.org/p2p_ld/nwb-schema-language/
+  linkml: https://w3id.org/linkml/
+  biolink: https://w3id.org/biolink/
+  schema: http://schema.org/
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  example: https://example.org/
+default_prefix: nwb_schema_language
+default_range: string
+
+imports:
+  - linkml:types
+
+classes:
+
+  NamedThing:
+    description: >-
+      A generic grouping for any identifiable entity
+    slots:
+      - id
+      - name
+      - description
+    class_uri: schema:Thing
+
+  Namespaces:
+    is_a: NamedThing
+    description: >-
+      Represents a Namespaces
+    slots:
+      - primary_email
+      - birth_date
+      - age_in_years
+      - vital_status
+    slot_usage:
+      primary_email:
+        pattern: "^\\S+@[\\S+\\.]+\\S+"
+
+  NamespacesCollection:
+    tree_root: true
+    description: >-
+      A holder for Namespaces objects
+    attributes:
+      entries:
+        range: Namespaces
+        multivalued: true
+        inlined: true
+
+slots:
+  id:
+    identifier: true
+    slot_uri: schema:identifier
+    range: uriorcurie
+    description: A unique identifier for a thing
+  name:
+    slot_uri: schema:name
+    description: A human-readable name for a thing
+  description:
+    slot_uri: schema:description
+    description: A human-readable description for a thing
+  primary_email:
+    slot_uri: schema:email
+    description: The main email address of a person
+  birth_date:
+    slot_uri: schema:birthDate
+    range: date
+    description: Date on which a person is born
+  age_in_years:
+    range: integer
+    description: Number of years since birth
+  vital_status:
+    range: PersonStatus
+    description: living or dead status
+
+enums:
+  PersonStatus:
+    permissible_values:
+      ALIVE:
+        description: the person is living
+        meaning: PATO:0001421
+      DEAD:
+        description: the person is deceased
+        meaning: PATO:0001422
+      UNKNOWN:
+        description: the vital status is not known
+        todos:
+          - map this to an ontology

nwb-schema-linkml/tests/__init__.py

@@ -0,0 +1 @@
+"""Tests for nwb-schema-language."""

nwb-schema-linkml/tests/test_data.py

@@ -0,0 +1,22 @@
+"""Data test."""
+import os
+import glob
+import unittest
+
+from linkml_runtime.loaders import yaml_loader
+from nwb_schema_language.datamodel.nwb_schema_language import Namespaces
+
+ROOT = os.path.join(os.path.dirname(__file__), '..')
+DATA_DIR = os.path.join(ROOT, "src", "data", "examples")
+
+EXAMPLE_FILES = glob.glob(os.path.join(DATA_DIR, '*.yaml'))
+
+
+class TestData(unittest.TestCase):
+    """Test data and datamodel."""
+
+    def test_data(self):
+        """Date test."""
+        for path in EXAMPLE_FILES:
+            obj = yaml_loader.load(path, target_class=Namespaces)
+            assert obj

nwb-schema-linkml/utils/get-value.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+# get the value of a key in the about.yaml file
+# https://stackoverflow.com/questions/1221833/pipe-output-and-capture-exit-status-in-bash
+grep "^$1:" about.yaml | sed "s/$1:[[:space:]]//" ; test "${PIPESTATUS[0]}" -eq 0