diff --git a/.copier-answers.yml b/.copier-answers.yml
new file mode 100644
index 00000000..917de112
--- /dev/null
+++ b/.copier-answers.yml
@@ -0,0 +1,15 @@
+# Changes here will be overwritten by Copier
+_commit: v0.4.1
+_src_path: https://github.com/linkml/linkml-project-copier
+add_example: false
+copyright_year: '2025'
+email: eric.s.torstenson@vumc.org
+full_name: Eric S Torstenson
+gh_action_docs_preview: false
+gh_action_pypi: false
+github_org: include-dcc
+license: MIT
+project_description: TBD
+project_name: INCLUDE LinkML Data Model
+project_slug: include_linkml_data_model
+
diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 00000000..bee5e782
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,18 @@
+# Check http://editorconfig.org for more information
+# This is the main config file for this project:
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true
+
+[*.py]
+indent_style = space
+indent_size = 4
+
+[*.md]
+trim_trailing_whitespace = false
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..da995f76
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,9 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/dependabot-options-reference
+
+version: 2
+updates:
+ - package-ecosystem: github-actions
+ directory: "/"
+ schedule:
+ interval: monthly
diff --git a/.github/workflows/deploy-docs.yaml b/.github/workflows/deploy-docs.yaml
index dea0416b..ddf02305 100644
--- a/.github/workflows/deploy-docs.yaml
+++ b/.github/workflows/deploy-docs.yaml
@@ -1,33 +1,58 @@
-name: Auto-deployment of Documentation
-on:
+---
+name: Deploy docs
+on: # yamllint disable-line rule:truthy
push:
- branches: [ main ]
+ branches: [main]
+ workflow_dispatch:
+
+permissions: {}
jobs:
build-docs:
runs-on: ubuntu-latest
+
+ # Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment
+ permissions:
+ contents: write # to let mkdocs write the new docs
+ pages: write # to deploy to Pages
+ id-token: write # allow to generate an OpenID Connect (OIDC) token
+
steps:
- - name: Checkout
- uses: actions/checkout@main
- with:
- fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
-
- - name: Set up Python 3.
- uses: actions/setup-python@v3
- 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
- cp src/docs/*md docs
- poetry run gen-erdiagram src/linkml/include_schema.yaml > docs/erdiagram.md
- poetry run gen-doc -d docs --template-directory src/doc_templates src/linkml/include_schema.yaml
- poetry run mkdocs gh-deploy
\ No newline at end of file
+ # https://github.com/actions/checkout
+ - name: Checkout
+ uses: actions/checkout@v4.2.2
+ with:
+ fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
+
+ - name: Configure git for the bot
+ # Gives the bot that commits to gh-pages a name & email address
+ # so that the commits have an author in the commit log.
+ run: |
+ git config user.name github-actions[bot]
+ git config user.email github-actions[bot]@users.noreply.github.com
+
+ # https://github.com/astral-sh/setup-uv
+ - name: Install uv
+ uses: astral-sh/setup-uv@v6.4.3
+ with:
+ python-version: 3.13
+ enable-cache: true
+ cache-dependency-glob: "uv.lock"
+
+ # https://github.com/actions/setup-python
+ - name: Set up Python
+ uses: actions/setup-python@v5.6.0
+ with:
+ python-version: 3.13
+
+ - name: Install just
+ run: |
+ uv tool install rust-just
+
+ - name: Install dependencies
+ run: uv sync --dev --no-progress
+
+ - name: Generate schema documentation
+ run: |
+ just gen-doc
+ uv run mkdocs gh-deploy
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index 95d0085a..87333d2b 100644
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -1,10 +1,17 @@
# 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
-name: Build and test linkml-runtime
+on: # yamllint disable-line rule:truthy
+ push:
+ branches: [main]
+ pull_request:
-on: [pull_request]
+env:
+ FORCE_COLOR: "1" # Make tools pretty.
+
+permissions: {}
jobs:
test:
@@ -12,42 +19,37 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
- python-version: ["3.9", "3.10"]
+ python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+ fail-fast: false
steps:
- #----------------------------------------------
- # check-out repo and set-up python
- #----------------------------------------------
+ # https://github.com/actions/checkout
- name: Check out repository
- uses: actions/checkout@v2
+ uses: actions/checkout@v4.2.2
+ with:
+ persist-credentials: false
+
+ # https://github.com/astral-sh/setup-uv
+ - name: Install uv
+ uses: astral-sh/setup-uv@v6.4.3
+ with:
+ python-version: ${{ matrix.python-version }}
+ enable-cache: true
+ cache-dependency-glob: "uv.lock"
+ # https://github.com/actions/setup-python
- name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v2
+ uses: actions/setup-python@v5.6.0
with:
python-version: ${{ matrix.python-version }}
- #----------------------------------------------
- # install & configure poetry
- #----------------------------------------------
- - name: Install Poetry
- uses: snok/install-poetry@v1.3
-
- #----------------------------------------------
- # install dependencies if cache does not exist
- #----------------------------------------------
- - name: Install dependencies
- run: poetry install --no-interaction --no-root
-
- #----------------------------------------------
- # install your root project, if required
- #----------------------------------------------
- - name: Install library
- run: poetry install --no-interaction
-
- #----------------------------------------------
- # run test suite
- #----------------------------------------------
- - name: Run tests
- run: make test
+ - name: Install just
+ run: |
+ uv tool install rust-just
+
+ - name: Install project
+ run: uv sync --dev
+ - name: Run test suite
+ run: just test
diff --git a/.gitignore b/.gitignore
index 7f601c2e..421e9a90 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,10 +1,21 @@
+# generated part of documentation
+/docs/elements/*.md
+# linkml-run-examples output (not useful to have in git in its current form)
+/examples/output/
+
+# Derived schemas, generated from the schema.yaml
+tmp/
+project/
+!project/README.md
+
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
+
# C extensions
*.so
-poetry.lock
+
# Distribution / packaging
.Python
build/
@@ -69,23 +80,16 @@ instance/
# Sphinx documentation
docs/_build/
-site/
-docs/*md
-docs/types/
-project/
+
# PyBuilder
target/
# Jupyter Notebook
.ipynb_checkpoints
-# Pycharm
-.idea
-
# IPython
profile_default/
ipython_config.py
-*.ipynb
# pyenv
.python-version
@@ -134,13 +138,7 @@ dmypy.json
# Pyre type checker
.pyre/
-#local dev environment
-/local_data
-.DS_Store
-#cogs
-.cogs/
-
-config.yml
-great_expectations/
-harmonized_data/
-schematic_service_account_creds.json
\ No newline at end of file
+# pycharm
+.idea
+# Local vscode editor config
+.vscode
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..3641b7a6
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,45 @@
+---
+# https://pre-commit.com/
+repos:
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v5.0.0
+ hooks:
+ - id: check-toml
+ - id: check-yaml
+ - id: end-of-file-fixer
+ - id: trailing-whitespace
+ args: [--markdown-linebreak-ext=md]
+
+ - repo: https://github.com/adrienverge/yamllint.git
+ rev: v1.37.0
+ hooks:
+ - id: yamllint
+ args: [-c=.yamllint.yaml]
+
+ - repo: https://github.com/codespell-project/codespell
+ rev: v2.4.1
+ hooks:
+ - id: codespell
+ additional_dependencies:
+ - tomli
+
+ - repo: https://github.com/crate-ci/typos
+ rev: v1.31.1
+ hooks:
+ - id: typos
+
+ - repo: https://github.com/astral-sh/ruff-pre-commit
+ # Ruff version.
+ rev: v0.11.3
+ hooks:
+ # Run the linter.
+ - id: ruff
+ args: [--fix, --exit-non-zero-on-fix]
+ # Run the formatter.
+ - id: ruff-format
+
+ - repo: https://github.com/astral-sh/uv-pre-commit
+ # uv version.
+ rev: 0.6.12
+ hooks:
+ - id: uv-lock
diff --git a/.yamllint.yaml b/.yamllint.yaml
new file mode 100644
index 00000000..f44a825d
--- /dev/null
+++ b/.yamllint.yaml
@@ -0,0 +1,12 @@
+# Configuration for https://github.com/adrienverge/yamllint
+
+extends: default
+
+rules:
+ document-start: disable # Don't check if document has a start marker (---).
+ line-length:
+ max: 80
+ level: warning
+ allow-non-breakable-words: true
+ allow-non-breakable-inline-mappings: true
+ new-lines: disable # Don't check for type of new line characters.
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
new file mode 100644
index 00000000..2b301c64
--- /dev/null
+++ b/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/
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index fee62815..d47f4c81 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,7 +1,121 @@
-# Contributing
+# Contributing to INCLUDE LinkML Data Model
-## Create an issue in the GitHub repository
+:+1: First of all: Thank you for taking the time to contribute!
-## Create a Pull Request (PR)
+The following is a set of guidelines for contributing to
+INCLUDE LinkML Data Model. These guidelines are not strict rules.
+Use your best judgment, and feel free to propose changes to this document
+in a pull request.
-Thank you for contributing to include-linkml
\ No newline at end of file
+## Table Of Contents
+
+* [Code of Conduct](#code-of-conduct)
+* [Guidelines for Contributions and Requests](#contributions)
+ * [Reporting issues and making requests](#reporting-issues)
+ * [Questions and Discussion](#questions-and-discussion)
+ * [Adding new elements yourself](#adding-elements)
+* [Best Practices](#best-practices)
+ * [How to write a great issue](#great-issues)
+ * [How to create a great pull/merge request](#great-pulls)
+
+
+
+## Code of Conduct
+
+The INCLUDE LinkML Data Model team strives to create a
+welcoming environment for editors, users and other contributors.
+Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md).
+
+
+
+## Guidelines for Contributions and Requests
+
+
+
+### Reporting problems and suggesting changes to with the data model
+
+Please use our [Issue Tracker][issues] for any of the following:
+
+- Reporting problems
+- Requesting new schema elements
+
+
+
+### Questions and Discussions
+
+Please use our [Discussions forum][discussions] to ask general questions or contribute to discussions.
+
+
+
+### Adding new elements yourself
+
+Please submit a [Pull Request][pulls] to submit a new term for consideration.
+
+
+
+## Best Practices
+
+
+
+### GitHub Best Practice
+
+- Creating and curating issues
+ - Read ["About Issues"][[about-issues]]
+ - Issues should be focused and actionable
+ - Complex issues should be broken down into simpler issues where possible
+- Pull Requests
+ - Read ["About Pull Requests"][about-pulls]
+ - Read [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/)
+ - Pull Requests (PRs) should be atomic and aim to close a single issue
+ - Long running PRs should be avoided where possible
+ - PRs should reference issues following standard conventions (e.g. “fixes #123”)
+ - Schema developers should always be working on a single issue at any one time
+ - Never work on the main branch, always work on an issue/feature branch
+ - Core developers can work on branches off origin rather than forks
+ - Always create a PR on a branch to maximize transparency of what you are doing
+ - PRs should be reviewed and merged in a timely fashion by the INCLUDE LinkML Data Model technical leads
+ - PRs that do not pass GitHub actions should never be merged
+ - In the case of git conflicts, the contributor should try and resolve the conflict
+ - If a PR fails a GitHub action check, the contributor should try and resolve the issue in a timely fashion
+
+### Understanding LinkML
+
+Core developers should read the material on the [LinkML site](https://linkml.io/linkml), in particular:
+
+- [Overview](https://linkml.io/linkml/intro/overview.html)
+- [Tutorial](https://linkml.io/linkml/intro/tutorial.html)
+- [Schemas](https://linkml.io/linkml/schemas/index.html)
+- [FAQ](https://linkml.io/linkml/faq/index.html)
+
+### Modeling Best Practice
+
+- Follow Naming conventions
+ - Standard LinkML naming conventions should be followed (UpperCamelCase for classes and enums, snake_case for slots)
+ - Know how to use the LinkML linter to check style and conventions
+ - The names for classes should be nouns or noun-phrases: Person, GenomeAnnotation, Address, Sample
+ - Spell out abbreviations and short forms, except where this goes against convention (e.g. do not spell out DNA)
+ - Elements that are imported from outside (e.g. schema.org) need not follow the same naming conventions
+ - Multivalued slots should be named as plurals
+- Document model elements
+ - All model elements should have documentation (descriptions) and other textual annotations (e.g. comments, notes)
+ - Textual annotations on classes, slots and enumerations should be written with minimal jargon, clear grammar and no misspellings
+- Include examples and counter-examples (intentionally invalid examples)
+ - Rationale: these serve as documentation and unit tests
+ - These will be used by the automated test suite
+ - All elements of the schema must be illustrated with valid and invalid data examples in src/data. New schema elements will not be merged into the main branch until examples are provided
+ - Invalid example data files should be invalid for one single reason, which should be reflected in the filename. It should be possible to render the invalid example files valid by addressing that single fault.
+- Use enums for categorical values
+ - Rationale: Open-ended string ranges encourage multiple values to represent the same entity, like “water”, “H2O” and “HOH”
+ - Any slot whose values could be constrained to a finite set should use an Enum
+ - Non-categorical values, e.g. descriptive fields like `name` or `description` fall outside of this.
+- Reuse
+ - Existing scheme elements should be reused where appropriate, rather than making duplicative elements
+ - More specific classes can be created by refinining classes using inheritance (`is_a`)
+
+[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/include-dcc/INCLUDE LinkML Data Model/issues/
+[pulls]: https://github.com/include-dcc/INCLUDE LinkML Data Model/pulls/
+
+We recommend also reading [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/)
diff --git a/Makefile b/Makefile
deleted file mode 100644
index ba8c05e1..00000000
--- a/Makefile
+++ /dev/null
@@ -1,110 +0,0 @@
-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 sh ./utils/get-value.sh name)
-SOURCE_SCHEMA_PATH = $(shell sh ./utils/get-value.sh source_schema_path)
-SRC = src
-DEST = project
-PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
-DOCDIR = docs
-
-TEMPLATEDIR = doc_templates
-
-
-# basename of a YAML file in model/
-.PHONY: all clean
-
-help: status
- @echo ""
- @echo "make all -- makes site locally"
- @echo "make install -- install dependencies"
- @echo "make setup -- initial setup"
- @echo "make test -- runs tests"
- @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)"
-
-setup: install gen-project gendoc git-init-add
-
-install:
- poetry install
-.PHONY: install
-
-all: gen-project gendoc
-%.yaml: gen-project
-deploy: all mkd-gh-deploy
-
-# generates all project files
-gen-project: $(PYMODEL)
- $(RUN) gen-project -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
-
-test:
- $(RUN) gen-project -d tmp $(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 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 $@
-
-upgrade:
- poetry add -D linkml@latest
-
-# Test documentation locally
-serve: mkd-serve
-
-# Python datamodel
-$(PYMODEL):
- mkdir -p $@
-
-
-$(DOCDIR):
- mkdir -p $@
-
-gendoc: $(DOCDIR)
- cp $(SRC)/docs/*md $(DOCDIR) ; \
- $(RUN) gen-doc -d $(DOCDIR) --template-directory $(SRC)/$(TEMPLATEDIR) $(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:
- git add .gitignore .github Makefile LICENSE *.md examples utils about.yaml mkdocs.yml poetry.lock project.Makefile pyproject.toml src/linkml/*yaml src/*/datamodel/*py src/data
- git add $(patsubst %, project/%, $(PROJECT_FOLDERS))
-git-commit:
- git commit -m 'Initial commit' -a
-git-status:
- git status
-
-clean:
- rm -rf $(DEST)
- rm -rf tmp
-
-include project.Makefile
diff --git a/config.public.mk b/config.public.mk
new file mode 100644
index 00000000..ff043a51
--- /dev/null
+++ b/config.public.mk
@@ -0,0 +1,32 @@
+# config.public.mk
+
+# This file is public in git. No sensitive info allowed.
+
+###### schema definition variables, used by justfile
+
+# Note:
+# - just works fine with quoted variables of dot-env files like this one
+LINKML_SCHEMA_NAME="include_linkml_data_model"
+LINKML_SCHEMA_AUTHOR="Eric S Torstenson "
+LINKML_SCHEMA_DESCRIPTION="TBD"
+LINKML_SCHEMA_SOURCE_DIR="src/include_linkml_data_model/schema"
+
+###### linkml generator variables, used by justfile
+
+## gen-project configuration file
+LINKML_GENERATORS_CONFIG_YAML=config.yaml
+
+## pass args if gendoc ignores config.yaml (i.e. --no-mergeimports)
+LINKML_GENERATORS_DOC_ARGS=
+
+## pass args to workaround genowl rdfs config bug (linkml#1453)
+## (i.e. --no-type-objects --no-metaclasses --metadata-profile rdfs)
+LINKML_GENERATORS_OWL_ARGS=
+
+## pass args to trigger experimental java/typescript generation
+LINKML_GENERATORS_JAVA_ARGS=
+LINKML_GENERATORS_TYPESCRIPT_ARGS=
+
+## pass args to pydantic generator which isn't supported by gen-project
+## https://github.com/linkml/linkml/issues/2537
+LINKML_GENERATORS_PYDANTIC_ARGS=
diff --git a/config.yaml b/config.yaml
new file mode 100644
index 00000000..c0382816
--- /dev/null
+++ b/config.yaml
@@ -0,0 +1,63 @@
+# Configuration of generators (defaults illustrated)
+---
+# The directory where the generated files are stored
+# directory: "tmp"
+
+# By default all generators are run. Specify here the ones to skip.
+excludes:
+ - markdown
+
+# Alternatively only specify the generators to run
+# (comment out the above "excludes" section)
+# includes:
+# - markdown
+# - excel
+
+# Set the arguments for the generators (no matter if they run or not)
+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
+ directory: "docs/elements"
+ graphql:
+ mergeimports: true
+ # gen-java is not yet supported by gen-project.
+ # https://github.com/linkml/linkml/issues/2537
+ # java:
+ # mergeimports: true
+ # metadata: true
+ jsonld:
+ mergeimports: true
+ jsonschema:
+ mergeimports: true
+ jsonldcontext:
+ mergeimports: true
+ # gen-pydantic is not yet supported by gen-project.
+ # https://github.com/linkml/linkml/issues/2537
+ # pydantic:
+ # mergeimports: true
+ python:
+ mergeimports: true
+ # head: true # Why does this not work?
+ prefixmap:
+ mergeimports: true
+ proto:
+ mergeimports: true
+ shacl:
+ mergeimports: true
+ shex:
+ mergeimports: true
+ sqlddl:
+ mergeimports: true
+ typescript:
+ mergeimports: true
+ metadata: true
+
+...
diff --git a/docs/about.md b/docs/about.md
new file mode 100644
index 00000000..5adffc90
--- /dev/null
+++ b/docs/about.md
@@ -0,0 +1,3 @@
+# About INCLUDE LinkML Data Model
+
+TBD
diff --git a/docs/elements/.gitkeep b/docs/elements/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 00000000..890955d3
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,5 @@
+# INCLUDE LinkML Data Model
+
+TBD
+
+- Auto-generated [schema documentation](elements/index.md)
diff --git a/docs/templates-linkml/README.md b/docs/templates-linkml/README.md
new file mode 100644
index 00000000..38fdc4a3
--- /dev/null
+++ b/docs/templates-linkml/README.md
@@ -0,0 +1,7 @@
+# Templates for the LinkML documentation generator
+
+Use this folder to store templates to customize the generated model documentation.
+The templates are written in Jinja2 and are used to generate the HTML documentation for the schema.
+
+The default templates are available in the [linkml repository](https://github.com/linkml/linkml/tree/main/linkml/generators/docgen).
+If you want to use these as a starting point, you can copy them into this folder and modify them as needed.
diff --git a/examples/README.md b/examples/README.md
index 2734d329..a309ae01 100644
--- a/examples/README.md
+++ b/examples/README.md
@@ -1,5 +1,9 @@
-# Examples of use of include-linkml
+# Examples of using INCLUDE LinkML Data Model
-This folder contains example data conforming to include-linkml
+This folder contains examples using the datamodel.
-The source for these is in [src/data](../src/data/examples)
\ No newline at end of file
+The source of the data used in the example is [tests/data](../tests/data/).
+
+The command `just test` creates different representations of the data in [tests/data](../tests/data/) and writes them to the subfolder `output`.
+It also generates a markdown documentation of the examples which is not very useful in its current form.
+Hence, the `output` sub-folder is git-ignored.
diff --git a/examples/include_linkml_pre.yaml b/examples/include_linkml_pre.yaml
deleted file mode 100644
index 2bfc5295..00000000
--- a/examples/include_linkml_pre.yaml
+++ /dev/null
@@ -1,761 +0,0 @@
-name: IncludePortalV1
-description: Initial Include Portal Schema
-id: https://w3id.org/include
-imports:
-- linkml:types
-prefixes:
- linkml:
- prefix_prefix: linkml
- prefix_reference: https://w3id.org/linkml/
- include:
- prefix_prefix: include
- prefix_reference: https://w3id.org/include/
- schema:
- prefix_prefix: schema
- prefix_reference: http://schema.org/
- sms:
- prefix_prefix: sms
- prefix_reference: http://sms.org/
-
-default_prefix: include
-default_range: string
-enums:
- enum_data_access:
- definition_uri: include:enum_data_access
- from_schema: https://w3id.org/include
- name: enum_data_access
- permissible_values:
- controlled:
- text: controlled
- title: Controlled
- open:
- text: open
- title: Open
- registered:
- text: registered
- title: Registered
- enum_down_syndrome_status:
- definition_uri: include:enum_down_syndrome_status
- from_schema: https://w3id.org/include
- name: enum_down_syndrome_status
- permissible_values:
- D21:
- text: D21
- title: D21
- T21:
- text: T21
- title: T21
- enum_ethnicity:
- definition_uri: include:enum_ethnicity
- from_schema: https://w3id.org/include
- name: enum_ethnicity
- permissible_values:
- asked_but_unknown:
- text: asked_but_unknown
- title: Asked but unknown
- hispanic_or_latino:
- text: hispanic_or_latino
- title: Hispanic or Latino
- not_hispanic_or_latino:
- text: not_hispanic_or_latino
- title: Not Hispanic or Latino
- enum_family_type:
- definition_uri: include:enum_family_type
- from_schema: https://w3id.org/include
- name: enum_family_type
- permissible_values:
- duo:
- text: duo
- title: Duo
- other:
- text: other
- title: Other
- proband_only:
- text: proband_only
- title: Proband-Only
- trio:
- text: trio
- title: Trio
- enum_phenotype_interpretation:
- definition_uri: include:enum_phenotype_interpretation
- from_schema: https://w3id.org/include
- name: enum_phenotype_interpretation
- permissible_values:
- not_observed:
- text: not_observed
- title: Not Observed
- observed:
- text: observed
- title: Observed
- enum_program:
- definition_uri: include:enum_program
- from_schema: https://w3id.org/include
- name: enum_program
- permissible_values:
- include:
- text: include
- title: INCLUDE
- KF:
- text: KF
- title: KF
- enum_race:
- definition_uri: include:enum_race
- from_schema: https://w3id.org/include
- name: enum_race
- permissible_values:
- american_indian_or_alaskan_native:
- text: american_indian_or_alaskan_native
- title: American Indian or Alaska Native
- asian:
- text: asian
- title: Asian
- black_or_african_american:
- text: black_or_african_american
- title: Black or African American
- more_than_one_race:
- text: more_than_one_race
- title: More than one race
- native_hawaiian_or_pacific_islander:
- text: native_hawaiian_or_pacific_islander
- title: Native Hawaiian or Other Pacific Islander
- other:
- text: other
- title: Other
- white:
- text: white
- title: White
- enum_sample_availability:
- definition_uri: include:enum_sample_availability
- from_schema: https://w3id.org/include
- name: enum_sample_availability
- permissible_values:
- available:
- text: available
- title: Available
- unavailable:
- text: unavailable
- title: Unavailable
- enum_sex:
- definition_uri: include:enum_sex
- from_schema: https://w3id.org/include
- name: enum_sex
- permissible_values:
- female:
- text: female
- title: Female
- male:
- text: male
- title: Male
- other:
- text: other
- title: Other
- unknown:
- text: unknown
- title: Unknown
- enum_study_code:
- definition_uri: include:enum_study_code
- from_schema: https://w3id.org/include
- name: enum_study_code
- permissible_values:
- DS-COG-ALL:
- text: DS-COG-ALL
- title: DS-COG-ALL
- DS-PCGC:
- text: DS-PCGC
- title: DS-PCGC
- DS360-CHD:
- text: DS360-CHD
- title: DS360-CHD
- DSC:
- text: DSC
- title: DSC
- HTP:
- text: HTP
- title: HTP
-classes:
- Biospecimen:
- name: Biospecimen
- title: Biospecimen
- definition_uri: include:Biospecimen
- description: A Biospecimen Collected from A Participant
- from_schema: https://w3id.org/include
- is_a: Thing
- annotations:
- requires_component: Study,Participant,DataFile
- required: false
- slots:
- - age_at_biospecimen_collection
- - biospecimen_storage
- - collection_id
- - collection_sample_type
- - container_id
- - has_datafile
- - has_participant
- - has_study
- - laboratory_procedure
- - parent_sample_id
- - parent_sample_type
- - sample_availability
- - sample_id
- - sample_type
- - volume
- - volume_unit
- - has_study
- DataFile:
- name: DataFile
- title: DataFile
- definition_uri: include:DataFile
- description: A DataFile Associated with a Participant or Study or Biospecimen
- from_schema: https://w3id.org/include
- is_a: Thing
- annotations:
- requires_component: Study,Participant,Biospecimen
- required: false
- slots:
- - access_url
- - collection_id
- - data_access
- - data_category
- - data_type
- - experimental_strategy
- - file_id
- - file_name
- - format
- - has_biospecimen
- - has_participant
- - has_study
- - participant_id
- - size
- Participant:
- name: Participant
- title: Participant
- definition_uri: include:Participant
- description: A Participant in a Study
- from_schema: https://w3id.org/include
- is_a: Thing
- annotations:
- requires_component: Study,DataFile
- required: false
- slots:
- - age_at_diagnosis
- - age_at_phenotype_assignment
- - age_at_the_last_vital_status
- - diagnosis_icd
- - diagnosis_mondo
- - diagnosis_ncit
- - diagnosis_source_text
- - diagnosis_type
- - down_syndrome_status
- - ethnicity
- - external_id
- - family_id
- - family_relationship
- - family_type
- - father_id
- - has_datafile
- - has_study
- - mother_id
- - outcomes_vital_status
- - participant_id
- - phenotype_hpo
- - phenotype_source_text
- - phenotype_interpretation
- - race
- - sex
- Study:
- name: Study
- title: Study
- definition_uri: include:Study
- description: A Study
- from_schema: https://w3id.org/include
- is_a: Thing
- annotations:
- required: true
- slots:
- - dbgap
- - program
- - study_code
- - study_name
- Thing:
- name: Thing
- title: Thing
- description: Highest Level Class
- definition_uri: schema:Thing
- from_schema: https://w3id.org/include
-slots:
- access_url:
- definition_uri: include:access_url
- description: Storage location for this file
- domain_of:
- - DataFile
- from_schema: https://w3id.org/include
- name: access_url
- required: false
- age_at_biospecimen_collection:
- definition_uri: include:age_at_biospecimen_collection
- description: Age in days of participant at time of biospecimen collection
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: age_at_biospecimen_collection
- required: false
- age_at_diagnosis:
- definition_uri: include:age_at_diagnosis
- description: Age in days at which phenotype was assigned
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: age_at_diagnosis
- required: false
- age_at_phenotype_assignment:
- definition_uri: include:age_at_phenotype_assignment
- description: Age in days at which phenotype was recorded
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: age_at_phenotype_assignment
- required: false
- age_at_the_last_vital_status:
- definition_uri: include:age_at_the_last_vital_status
- description: Age of last vital status
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: age_at_the_last_vital_status
- required: false
- biospecimen_storage:
- definition_uri: include:biospecimen_storage
- description: Method by which Container is stored (e.g. -80C freezer, Liquid nitrogen,
- etc.)
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: biospecimen_storage
- required: false
- collection_id:
- definition_uri: include:collection_id
- description: Identifier for the eldest sample in a lineage of processed, pooled,
- or aliquoted samples. This may be the same as Parent Sample ID or Sample ID (if
- no processing was performed).
- domain_of:
- - Biospecimen
- - DataFile
- from_schema: https://w3id.org/include
- name: collection_id
- required: false
- collection_sample_type:
- definition_uri: include:collection_sample_type
- description: Type of biological material comprising the collected sample (e.g. Whole
- blood, Bone marrow, Saliva, etc.)
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: collection_sample_type
- required: false
- container_id:
- definition_uri: include:container_id
- description: Identifier for specific container/aliquot of sample, if applicable.
- For example, distinct aliquots of a sample will have the same Sample ID but different
- Container IDs.
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: container_id
- required: false
- data_access:
- definition_uri: include:data_access
- description: Type of access control on this file, determined by DCC
- domain_of:
- - DataFile
- from_schema: https://w3id.org/include
- name: data_access
- range: enum_data_access
- required: false
- data_category:
- definition_uri: include:data_category
- description: General category of data in file (e.g. Clinical, Genomics, Proteomics,
- Metabolomics, Immune maps, Transcriptomics, etc.)
- domain_of:
- - DataFile
- from_schema: https://w3id.org/include
- name: data_category
- required: true
- data_type:
- definition_uri: include:data_type
- description: Specific type of data contained in file (e.g. Aligned reads, Unaligned
- reads, SNV, CNV, Gene fusions, Isoform expression, Gene expression quantification,
- Structural variations, Cytokine profiles, Operation reports, Pathology reports,
- Histology images, Clinical supplement, Protein expression quantification, etc.)
- domain_of:
- - DataFile
- from_schema: https://w3id.org/include
- name: data_type
- required: false
- dbgap:
- definition_uri: include:dbgap
- description: dbGaP study accession code
- domain_of:
- - Study
- from_schema: https://w3id.org/include
- name: dbgap
- required: false
- diagnosis_icd:
- definition_uri: include:diagnosis_icd
- description: ICD-10 code (annotated by data contributor or DCC)
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: diagnosis_icd
- required: false
- diagnosis_mondo:
- definition_uri: include:diagnosis_mondo
- description: Mondo disease ontology code (annotated by data contributor or DCC)
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: diagnosis_mondo
- required: false
- diagnosis_ncit:
- definition_uri: include:diagnosis_ncit
- description: NCI Thesaurus code (annotated by data contributor or DCC)
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: diagnosis_ncit
- required: false
- diagnosis_source_text:
- definition_uri: include:diagnosis_source_text
- description: Diagnosis as described by data contributor
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: diagnosis_source_text
- required: false
- diagnosis_type:
- definition_uri: include:diagnosis_type
- description: How diagnosis was assigned
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: diagnosis_type
- required: false
- down_syndrome_status:
- definition_uri: include:down_syndrome_status
- description: Down Syndrome status of participant (T21 = Trisomy 21; D21 = Disomy
- 21, euploid)
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: down_syndrome_status
- range: enum_down_syndrome_status
- required: true
- ethnicity:
- definition_uri: include:ethnicity
- description: Ethnicity of participant
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: ethnicity
- range: enum_ethnicity
- required: true
- experimental_strategy:
- definition_uri: include:experimental_strategy
- description: Experimental method used to obtain data in file (e.g. WGS, RNAseq,
- WXS, SOMAscan, Mass spec proteomics, LCMS metabolomics, Multiplex immunoassay,
- Meso Scale Discovery, etc.)
- domain_of:
- - DataFile
- from_schema: https://w3id.org/include
- name: experimental_strategy
- required: false
- external_id:
- definition_uri: include:external_id
- description: Unique identifier for the participant, assigned by data contributor
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: external_id
- required: true
- family_id:
- definition_uri: include:family_id
- description: Unique identifer for family to which Participant belongs
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: family_id
- required: false
- family_relationship:
- definition_uri: include:family_relationship
- description: Relationship of Participant to other family members
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: family_relationship
- required: false
- family_type:
- definition_uri: include:family_type
- description: 'Structure of family members participating in the study (proband-only
- = no family members participating; duo = proband + parent; trio = proband + 2
- parents; trio+ = proband + 2 parents + other relatives) '
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: family_type
- range: enum_family_type
- required: true
- father_id:
- definition_uri: include:father_id
- description: Participant ID for Participant's father
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: father_id
- required: false
- file_id:
- definition_uri: include:file_id
- description: File identifier, assigned by DCC
- domain_of:
- - DataFile
- from_schema: https://w3id.org/include
- name: file_id
- required: false
- file_name:
- definition_uri: include:file_name
- description: Synapse ID for file
- domain_of:
- - DataFile
- from_schema: https://w3id.org/include
- name: file_name
- required: false
- format:
- definition_uri: include:format
- description: Format of file (e.g. bam, cram, vcf, csv, html, png, fastq, pdf, dicom,
- etc.)
- domain_of:
- - DataFile
- from_schema: https://w3id.org/include
- name: format
- required: true
- has_biospecimen:
- definition_uri: include:has_biospecimen
- description: Link to a Biospecimen
- domain_of:
- - DataFile
- from_schema: https://w3id.org/include
- name: has_biospecimen
- range: Biospecimen
- required: false
- has_datafile:
- definition_uri: include:has_datafile
- description: Link to a DataFile
- domain_of:
- - Biospecimen
- - Participant
- from_schema: https://w3id.org/include
- name: has_datafile
- range: DataFile
- required: false
- has_participant:
- definition_uri: include:has_participant
- description: Link to a Participant
- domain_of:
- - Biospecimen
- - DataFile
- from_schema: https://w3id.org/include
- name: has_participant
- range: Participant
- required: false
- has_study:
- definition_uri: include:has_study
- description: Link to a Study
- domain_of:
- - Biospecimen
- - Biospecimen
- - DataFile
- - Participant
- from_schema: https://w3id.org/include
- name: has_study
- range: Study
- required: false
- laboratory_procedure:
- definition_uri: include:laboratory_procedure
- description: Procedure by which Sample was derived from Parent Sample (e.g. RBC
- lysis, Centrifugation, Ficoll, etc.)
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: laboratory_procedure
- required: false
- mother_id:
- definition_uri: include:mother_id
- description: Participant ID for Participant's mother
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: mother_id
- required: false
- outcomes_vital_status:
- definition_uri: include:outcomes_vital_status
- description: Whether participant is alive or dead
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: outcomes_vital_status
- required: false
- parent_sample_id:
- definition_uri: include:parent_sample_id
- description: Identifier for the direct parent from which Sample was derived, processed,
- pooled, etc. (if applicable)
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: parent_sample_id
- required: false
- parent_sample_type:
- definition_uri: include:parent_sample_type
- description: Type of biological material comprising the parent sample (e.g. Plasma,
- Serum, White blood cells, etc.)
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: parent_sample_type
- required: false
- participant_id:
- definition_uri: include:participant_id
- description: Unique identifier for the participant, assigned by DCC
- domain_of:
- - DataFile
- - Participant
- from_schema: https://w3id.org/include
- name: participant_id
- required: true
- phenotype_hpo:
- definition_uri: include:phenotype_hpo
- description: Human Phenotype Ontology code (annotated by data contributor or DCC)
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: phenotype_hpo
- required: false
- phenotype_interpretation:
- definition_uri: include:phenotype_interpretation
- description: Whether phenotype was observed or not
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: phenotype_interpretation
- range: enum_phenotype_interpretation
- required: false
- phenotype_source_text:
- definition_uri: include:phenotype_source_text
- description: Phenotype as described by data contributor
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: phenotype_source_text
- required: false
- program:
- definition_uri: include:program
- description: Funding source for the study
- domain_of:
- - Study
- from_schema: https://w3id.org/include
- name: program
- range: enum_program
- required: true
- race:
- definition_uri: include:race
- description: Race of participant
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: race
- range: enum_race
- required: true
- sample_availability:
- definition_uri: include:sample_availability
- description: Whether or not the sample is potentially available for sharing through
- the Virtual Biorepository
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: sample_availability
- range: enum_sample_availability
- required: false
- sample_id:
- definition_uri: include:sample_id
- description: Identifier for sample. A sample is a unique biological material; two
- samples with two different IDs are biologically distinct.
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: sample_id
- required: true
- sample_type:
- definition_uri: include:sample_type
- description: Type of biological material comprising the sample (e.g. Plasma, Serum,
- White blood cells, DNA, RNA, etc.)
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: sample_type
- required: true
- sex:
- definition_uri: include:sex
- description: Sex of participant
- domain_of:
- - Participant
- from_schema: https://w3id.org/include
- name: sex
- range: enum_sex
- required: true
- size:
- definition_uri: include:size
- description: Size of file
- domain_of:
- - DataFile
- from_schema: https://w3id.org/include
- name: size
- required: false
- study_code:
- definition_uri: include:study_code
- description: Unique identifer for the study, assigned by DCC
- domain_of:
- - Study
- from_schema: https://w3id.org/include
- name: study_code
- range: enum_study_code
- required: true
- study_name:
- definition_uri: include:study_name
- description: Name of the study, chosen by data contributor
- domain_of:
- - Study
- from_schema: https://w3id.org/include
- name: study_name
- required: true
- validation_rules:
- definition_uri: include:validation_rules
- description: Rules for Validation of Property Constraints and Values
- domain_of:
- - Thing
- from_schema: https://w3id.org/include
- name: validation_rules
- required: false
- title: Validation Rules
- volume:
- definition_uri: include:volume
- description: Amount of sample in container
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: volume
- required: false
- volume_unit:
- definition_uri: include:volume_unit
- description: Unit of sample volume
- domain_of:
- - Biospecimen
- from_schema: https://w3id.org/include
- name: volume_unit
- required: false
diff --git a/examples/portal_schema.jsonld b/examples/portal_schema.jsonld
deleted file mode 100644
index 7b3aa091..00000000
--- a/examples/portal_schema.jsonld
+++ /dev/null
@@ -1,4064 +0,0 @@
-{
- "@context": {
- "bts": "http://schema.biothings.io/",
- "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
- "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
- "schema": "http://schema.org/",
- "xsd": "http://www.w3.org/2001/XMLSchema#"
- },
- "@graph": [
- {
- "@id": "schema:Text",
- "@type": [
- "schema:DataType",
- "rdfs:Class"
- ],
- "rdfs:comment": "Data type: Text.",
- "rdfs:label": "Text"
- },
- {
- "@id": "schema:Number",
- "@type": [
- "schema:DataType",
- "rdfs:Class"
- ],
- "rdfs:comment": "Data type: Number.",
- "rdfs:label": "Number"
- },
- {
- "@id": "schema:Integer",
- "@type": "rdfs:Class",
- "rdfs:comment": "Data type: Integer.",
- "rdfs:label": "Integer",
- "rdfs:subClassOf": {
- "@id": "schema:Number"
- }
- },
- {
- "@id": "schema:Thing",
- "@type": "rdfs:Class",
- "rdfs:comment": "Thing",
- "rdfs:label": "Thing",
- "schema:isPartOf": {
- "@id": "http://schema.org"
- }
- },
- {
- "@id": "bts:BiologicalEntity",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "BiologicalEntity",
- "rdfs:subClassOf": {
- "@id": "schema:Thing"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:OntologyClass",
- "@type": "rdfs:Class",
- "rdfs:comment": "a concept or class in an ontology, vocabulary or thesaurus",
- "rdfs:label": "OntologyClass",
- "rdfs:subClassOf": {
- "@id": "schema:Thing"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:RelationshipType",
- "@type": "rdfs:Class",
- "rdfs:comment": "An OWL property used as an edge label",
- "rdfs:label": "RelationshipType",
- "rdfs:subClassOf": {
- "@id": "bts:OntologyClass"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:GeneOntologyClass",
- "@type": "rdfs:Class",
- "rdfs:comment": "an ontology class that describes a functional aspect of a gene, gene prodoct or complex",
- "rdfs:label": "GeneOntologyClass",
- "rdfs:subClassOf": {
- "@id": "bts:OntologyClass"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:OrganismTaxon",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "OrganismTaxon",
- "rdfs:subClassOf": {
- "@id": "bts:OntologyClass"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:OrganismalEntity",
- "@type": "rdfs:Class",
- "rdfs:comment": "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding molecular entities",
- "rdfs:label": "OrganismalEntity",
- "rdfs:subClassOf": {
- "@id": "bts:BiologicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:IndividualOrganism",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "IndividualOrganism",
- "rdfs:subClassOf": {
- "@id": "bts:OrganismalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Case",
- "@type": "rdfs:Class",
- "rdfs:comment": "An individual organism that has a patient role in some clinical context.",
- "rdfs:label": "Case",
- "rdfs:subClassOf": {
- "@id": "bts:IndividualOrganism"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:PopulationOfIndividualOrganisms",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "PopulationOfIndividualOrganisms",
- "rdfs:subClassOf": {
- "@id": "bts:OrganismalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Biosample",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "Biosample",
- "rdfs:subClassOf": {
- "@id": "bts:OrganismalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:DiseaseOrPhenotypicFeature",
- "@type": "rdfs:Class",
- "rdfs:comment": "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.",
- "rdfs:label": "DiseaseOrPhenotypicFeature",
- "rdfs:subClassOf": {
- "@id": "bts:BiologicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Disease",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "Disease",
- "rdfs:subClassOf": {
- "@id": "bts:DiseaseOrPhenotypicFeature"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:PhenotypicFeature",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "PhenotypicFeature",
- "rdfs:subClassOf": {
- "@id": "bts:DiseaseOrPhenotypicFeature"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Environment",
- "@type": "rdfs:Class",
- "rdfs:comment": "A feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes",
- "rdfs:label": "Environment",
- "rdfs:subClassOf": {
- "@id": "bts:BiologicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:InformationContentEntity",
- "@type": "rdfs:Class",
- "rdfs:comment": "a piece of information that typically describes some piece of biology or is used as support.",
- "rdfs:label": "InformationContentEntity",
- "rdfs:subClassOf": {
- "@id": "schema:Thing"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:ConfidenceLevel",
- "@type": "rdfs:Class",
- "rdfs:comment": "Level of confidence in a statement",
- "rdfs:label": "ConfidenceLevel",
- "rdfs:subClassOf": {
- "@id": "bts:InformationContentEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:EvidenceType",
- "@type": "rdfs:Class",
- "rdfs:comment": "Class of evidence that supports an association",
- "rdfs:label": "EvidenceType",
- "rdfs:subClassOf": {
- "@id": "bts:InformationContentEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Publication",
- "@type": "rdfs:Class",
- "rdfs:comment": "Any published piece of information. Can refer to a whole publication, or to a part of it (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web as well as journals.",
- "rdfs:label": "Publication",
- "rdfs:subClassOf": {
- "@id": "bts:InformationContentEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:MolecularEntity",
- "@type": "rdfs:Class",
- "rdfs:comment": "A gene, gene product, small molecule or macromolecule (including protein complex)",
- "rdfs:label": "MolecularEntity",
- "rdfs:subClassOf": {
- "@id": "bts:BiologicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:ChemicalSubstance",
- "@type": "rdfs:Class",
- "rdfs:comment": "May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part",
- "rdfs:label": "ChemicalSubstance",
- "rdfs:subClassOf": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Drug",
- "@type": "rdfs:Class",
- "rdfs:comment": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease",
- "rdfs:label": "Drug",
- "rdfs:subClassOf": {
- "@id": "bts:ChemicalSubstance"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Metabolite",
- "@type": "rdfs:Class",
- "rdfs:comment": "Any intermediate or product resulting from metabolism. Includes primary and secondary metabolites.",
- "rdfs:label": "Metabolite",
- "rdfs:subClassOf": {
- "@id": "bts:ChemicalSubstance"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:AnatomicalEntity",
- "@type": "rdfs:Class",
- "rdfs:comment": "A subcellular location, cell type or gross anatomical part",
- "rdfs:label": "AnatomicalEntity",
- "rdfs:subClassOf": {
- "@id": "bts:OrganismalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:LifeStage",
- "@type": "rdfs:Class",
- "rdfs:comment": "A stage of development or growth of an organism, including post-natal adult stages",
- "rdfs:label": "LifeStage",
- "rdfs:subClassOf": {
- "@id": "bts:OrganismalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:PlanetaryEntity",
- "@type": "rdfs:Class",
- "rdfs:comment": "Any entity or process that exists at the level of the whole planet",
- "rdfs:label": "PlanetaryEntity",
- "rdfs:subClassOf": {
- "@id": "schema:Thing"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:EnvironmentalProcess",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "EnvironmentalProcess",
- "rdfs:subClassOf": {
- "@id": "bts:PlanetaryEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:EnvironmentalFeature",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "EnvironmentalFeature",
- "rdfs:subClassOf": {
- "@id": "bts:PlanetaryEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:ClinicalEntity",
- "@type": "rdfs:Class",
- "rdfs:comment": "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities",
- "rdfs:label": "ClinicalEntity",
- "rdfs:subClassOf": {
- "@id": "schema:Thing"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:ClinicalTrial",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "ClinicalTrial",
- "rdfs:subClassOf": {
- "@id": "bts:ClinicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:ClinicalIntervention",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "ClinicalIntervention",
- "rdfs:subClassOf": {
- "@id": "bts:ClinicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Device",
- "@type": "rdfs:Class",
- "rdfs:comment": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment",
- "rdfs:label": "Device",
- "rdfs:subClassOf": {
- "@id": "schema:Thing"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:GenomicEntity",
- "@type": "rdfs:Class",
- "rdfs:comment": "an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)",
- "rdfs:label": "GenomicEntity",
- "rdfs:subClassOf": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Genome",
- "@type": "rdfs:Class",
- "rdfs:comment": "A genome is the sum of genetic material within a cell or virion.",
- "rdfs:label": "Genome",
- "rdfs:subClassOf": {
- "@id": "bts:GenomicEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Transcript",
- "@type": "rdfs:Class",
- "rdfs:comment": "An RNA synthesized on a DNA or RNA template by an RNA polymerase",
- "rdfs:label": "Transcript",
- "rdfs:subClassOf": {
- "@id": "bts:GenomicEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Exon",
- "@type": "rdfs:Class",
- "rdfs:comment": "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing",
- "rdfs:label": "Exon",
- "rdfs:subClassOf": {
- "@id": "bts:GenomicEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:CodingSequence",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "CodingSequence",
- "rdfs:subClassOf": {
- "@id": "bts:GenomicEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:MacromolecularMachine",
- "@type": "rdfs:Class",
- "rdfs:comment": "A union of gene, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.",
- "rdfs:label": "MacromolecularMachine",
- "rdfs:subClassOf": {
- "@id": "bts:GenomicEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:GeneOrGeneProduct",
- "@type": "rdfs:Class",
- "rdfs:comment": "a union of genes or gene products. Frequently an identifier for one will be used as proxy for another",
- "rdfs:label": "GeneOrGeneProduct",
- "rdfs:subClassOf": {
- "@id": "bts:MacromolecularMachine"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Gene",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "Gene",
- "rdfs:subClassOf": {
- "@id": "bts:GeneOrGeneProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:GeneProduct",
- "@type": "rdfs:Class",
- "rdfs:comment": "The functional molecular product of a single gene. Gene products are either proteins or functional RNA molecules",
- "rdfs:label": "GeneProduct",
- "rdfs:subClassOf": {
- "@id": "bts:GeneOrGeneProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Protein",
- "@type": "rdfs:Class",
- "rdfs:comment": "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA",
- "rdfs:label": "Protein",
- "rdfs:subClassOf": {
- "@id": "bts:GeneProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:GeneProductIsoform",
- "@type": "rdfs:Class",
- "rdfs:comment": "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms.",
- "rdfs:label": "GeneProductIsoform",
- "rdfs:subClassOf": {
- "@id": "bts:GeneProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:ProteinIsoform",
- "@type": "rdfs:Class",
- "rdfs:comment": "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/",
- "rdfs:label": "ProteinIsoform",
- "rdfs:subClassOf": {
- "@id": "bts:Protein"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:RnaProduct",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "RnaProduct",
- "rdfs:subClassOf": {
- "@id": "bts:GeneProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:RnaProductIsoform",
- "@type": "rdfs:Class",
- "rdfs:comment": "Represents a protein that is a specific isoform of the canonical or reference RNA",
- "rdfs:label": "RnaProductIsoform",
- "rdfs:subClassOf": {
- "@id": "bts:RnaProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:NoncodingRnaProduct",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "NoncodingRnaProduct",
- "rdfs:subClassOf": {
- "@id": "bts:RnaProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Microrna",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "Microrna",
- "rdfs:subClassOf": {
- "@id": "bts:NoncodingRnaProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:MacromolecularComplex",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "MacromolecularComplex",
- "rdfs:subClassOf": {
- "@id": "bts:MacromolecularMachine"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:GeneFamily",
- "@type": "rdfs:Class",
- "rdfs:comment": "any grouping of multiple genes or gene products related by common descent",
- "rdfs:label": "GeneFamily",
- "rdfs:subClassOf": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Genotype",
- "@type": "rdfs:Class",
- "rdfs:comment": "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some extablished background",
- "rdfs:label": "Genotype",
- "rdfs:subClassOf": {
- "@id": "bts:GenomicEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Haplotype",
- "@type": "rdfs:Class",
- "rdfs:comment": "A set of zero or more Alleles on a single instance of a Sequence[VMC]",
- "rdfs:label": "Haplotype",
- "rdfs:subClassOf": {
- "@id": "bts:GenomicEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:SequenceVariant",
- "@type": "rdfs:Class",
- "rdfs:comment": "An allele that varies in its sequence from what is considered the reference allele at that locus.",
- "rdfs:label": "SequenceVariant",
- "rdfs:subClassOf": {
- "@id": "bts:GenomicEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:DrugExposure",
- "@type": "rdfs:Class",
- "rdfs:comment": "A drug exposure is an intake of a particular chemical substance",
- "rdfs:label": "DrugExposure",
- "rdfs:subClassOf": {
- "@id": "bts:Environment"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Treatment",
- "@type": "rdfs:Class",
- "rdfs:comment": "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures'",
- "rdfs:label": "Treatment",
- "rdfs:subClassOf": {
- "@id": "bts:Environment"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:GeographicLocation",
- "@type": "rdfs:Class",
- "rdfs:comment": "a location that can be described in lat/long coordinates",
- "rdfs:label": "GeographicLocation",
- "rdfs:subClassOf": {
- "@id": "bts:PlanetaryEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:GeographicLocationAtTime",
- "@type": "rdfs:Class",
- "rdfs:comment": "a location that can be described in lat/long coordinates, for a particular time",
- "rdfs:label": "GeographicLocationAtTime",
- "rdfs:subClassOf": {
- "@id": "bts:GeographicLocation"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Occurrent",
- "@type": "rdfs:Class",
- "rdfs:comment": "A processual entity",
- "rdfs:label": "Occurrent",
- "rdfs:subClassOf": {
- "@id": "schema:Thing"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:BiologicalProcessOrActivity",
- "@type": "rdfs:Class",
- "rdfs:comment": "Either an individual molecular activity, or a collection of causally connected molecular activities",
- "rdfs:label": "BiologicalProcessOrActivity",
- "rdfs:subClassOf": {
- "@id": "bts:BiologicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:MolecularActivity",
- "@type": "rdfs:Class",
- "rdfs:comment": "An execution of a molecular function carried out by a gene product or macromolecular complex.",
- "rdfs:label": "MolecularActivity",
- "rdfs:subClassOf": {
- "@id": "bts:BiologicalProcessOrActivity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:ActivityAndBehavior",
- "@type": "rdfs:Class",
- "rdfs:comment": "Activity or behavior of any independent integral living, organization or mechanical actor in the world",
- "rdfs:label": "ActivityAndBehavior",
- "rdfs:subClassOf": {
- "@id": "bts:Occurrent"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Procedure",
- "@type": "rdfs:Class",
- "rdfs:comment": "A series of actions conducted in a certain order or manner",
- "rdfs:label": "Procedure",
- "rdfs:subClassOf": {
- "@id": "bts:Occurrent"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Phenomenon",
- "@type": "rdfs:Class",
- "rdfs:comment": "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question",
- "rdfs:label": "Phenomenon",
- "rdfs:subClassOf": {
- "@id": "bts:Occurrent"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:BiologicalProcess",
- "@type": "rdfs:Class",
- "rdfs:comment": "One or more causally connected executions of molecular functions",
- "rdfs:label": "BiologicalProcess",
- "rdfs:subClassOf": {
- "@id": "bts:BiologicalProcessOrActivity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Pathway",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "Pathway",
- "rdfs:subClassOf": {
- "@id": "bts:BiologicalProcess"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:PhysiologicalProcess",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "PhysiologicalProcess",
- "rdfs:subClassOf": {
- "@id": "bts:BiologicalProcess"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:CellularComponent",
- "@type": "rdfs:Class",
- "rdfs:comment": "A location in or around a cell",
- "rdfs:label": "CellularComponent",
- "rdfs:subClassOf": {
- "@id": "bts:AnatomicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:Cell",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "Cell",
- "rdfs:subClassOf": {
- "@id": "bts:AnatomicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:CellLine",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "CellLine",
- "rdfs:subClassOf": {
- "@id": "bts:Biosample"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:GrossAnatomicalStructure",
- "@type": "rdfs:Class",
- "rdfs:comment": null,
- "rdfs:label": "GrossAnatomicalStructure",
- "rdfs:subClassOf": {
- "@id": "bts:AnatomicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- }
- },
- {
- "@id": "bts:ensembl",
- "@type": "rdf:Property",
- "rdfs:comment": "Ensembl ID for gene, protein or transcript",
- "rdfs:label": "ensembl",
- "schema:domainIncludes": [
- {
- "@id": "bts:Transcript"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "schema:Text"
- }
- },
- {
- "@id": "bts:hgnc",
- "@type": "rdf:Property",
- "rdfs:comment": "HGNC ID for gene",
- "rdfs:label": "hgnc",
- "schema:domainIncludes": {
- "@id": "bts:Gene"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "schema:Integer"
- }
- },
- {
- "@id": "bts:entrez",
- "@type": "rdf:Property",
- "rdfs:comment": "Entrez ID for gene",
- "rdfs:label": "entrez",
- "schema:domainIncludes": {
- "@id": "bts:Gene"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "schema:Integer"
- }
- },
- {
- "@id": "bts:refseq",
- "@type": "rdf:Property",
- "rdfs:comment": "Refseq ID for gene, protein or transcript",
- "rdfs:label": "refseq",
- "schema:domainIncludes": [
- {
- "@id": "bts:Transcript"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "schema:Text"
- }
- },
- {
- "@id": "bts:omim",
- "@type": "rdf:Property",
- "rdfs:comment": "Refseq ID for gene, protein or transcript",
- "rdfs:label": "omim",
- "schema:domainIncludes": [
- {
- "@id": "bts:Disease"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "schema:Integer"
- }
- },
- {
- "@id": "bts:umls",
- "@type": "rdf:Property",
- "rdfs:comment": "Refseq ID for gene, protein or transcript",
- "rdfs:label": "umls",
- "schema:domainIncludes": {
- "@id": "bts:Disease"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "schema:Text"
- }
- },
- {
- "@id": "bts:homologousTo",
- "@type": "rdf:Property",
- "rdfs:comment": "Shared ancestry between protein or gene",
- "rdfs:label": "homologousTo",
- "schema:domainIncludes": {
- "@id": "bts:GeneOrGeneProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GeneOrGeneProduct"
- }
- },
- {
- "@id": "bts:molecularlyInteractsWith",
- "@type": "rdf:Property",
- "rdfs:comment": null,
- "rdfs:label": "molecularlyInteractsWith",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:geneticallyInteractsWith",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. Examples include epistasis and synthetic lethality.",
- "rdfs:label": "geneticallyInteractsWith",
- "schema:domainIncludes": {
- "@id": "bts:Gene"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:Gene"
- }
- },
- {
- "@id": "bts:affectsAbundanceOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the amount of the other within a system of interest",
- "rdfs:label": "affectsAbundanceOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesAbundanceOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the amount of the other within a system of interest",
- "rdfs:label": "increasesAbundanceOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesAbundanceOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the amount of the other within a system of interest",
- "rdfs:label": "decreasesAbundanceOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsActivityOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the activity of the other within a system of interest",
- "rdfs:label": "affectsActivityOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesActivityOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the activity of the other within a system of interest",
- "rdfs:label": "increasesActivityOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesActivityOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the activity of the other within a system of interest",
- "rdfs:label": "decreasesActivityOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsExpressionOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest",
- "rdfs:label": "affectsExpressionOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GenomicEntity"
- }
- },
- {
- "@id": "bts:increasesExpressionOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest",
- "rdfs:label": "increasesExpressionOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GenomicEntity"
- }
- },
- {
- "@id": "bts:decreasesExpressionOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest",
- "rdfs:label": "decreasesExpressionOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GenomicEntity"
- }
- },
- {
- "@id": "bts:affectsFoldingOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the rate or quality of folding of the other ",
- "rdfs:label": "affectsFoldingOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesFoldingOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate or quality of folding of the other ",
- "rdfs:label": "increasesFoldingOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesFoldingOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate or quality of folding of the other ",
- "rdfs:label": "decreasesFoldingOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsLocalizationOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the localization of the other within a system of interest",
- "rdfs:label": "affectsLocalizationOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesLocalizationOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the proper localization of the other within a system of interest",
- "rdfs:label": "increasesLocalizationOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesLocalizationOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the proper localization of the other within a system of interest",
- "rdfs:label": "decreasesLocalizationOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsMetabolicProcessingOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the metabolic processing of the other within a system of interest",
- "rdfs:label": "affectsMetabolicProcessingOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesMetabolicProcessingOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest",
- "rdfs:label": "increasesMetabolicProcessingOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesMetabolicProcessingOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest",
- "rdfs:label": "decreasesMetabolicProcessingOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsMolecularModificationOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one leads changes in the molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)",
- "rdfs:label": "affectsMolecularModificationOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesMolecularModificationOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)",
- "rdfs:label": "increasesMolecularModificationOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesMolecularModificationOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)",
- "rdfs:label": "decreasesMolecularModificationOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsSynthesisOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of chemical synthesis of the other",
- "rdfs:label": "affectsSynthesisOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesSynthesisOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of chemical synthesis of the other",
- "rdfs:label": "increasesSynthesisOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesSynthesisOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of chemical synthesis of the other",
- "rdfs:label": "decreasesSynthesisOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsDegradationOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of degradation of the other within a system of interest",
- "rdfs:label": "affectsDegradationOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesDegradationOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of degradation of the other within a system of interest",
- "rdfs:label": "increasesDegradationOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesDegradationOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of degradation of the other within a system of interest",
- "rdfs:label": "decreasesDegradationOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsMutationRateOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest",
- "rdfs:label": "affectsMutationRateOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GenomicEntity"
- }
- },
- {
- "@id": "bts:increasesMutationRateOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest",
- "rdfs:label": "increasesMutationRateOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GenomicEntity"
- }
- },
- {
- "@id": "bts:decreasesMutationRateOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest",
- "rdfs:label": "decreasesMutationRateOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GenomicEntity"
- }
- },
- {
- "@id": "bts:affectsResponseTo",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other",
- "rdfs:label": "affectsResponseTo",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesResponseTo",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other",
- "rdfs:label": "increasesResponseTo",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesResponseTo",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other",
- "rdfs:label": "decreasesResponseTo",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsSplicingOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity impacts the splicing of the mRNA",
- "rdfs:label": "affectsSplicingOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:Transcript"
- }
- },
- {
- "@id": "bts:increasesSplicingOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity increases the proper splicing of the mRNA",
- "rdfs:label": "increasesSplicingOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:Transcript"
- }
- },
- {
- "@id": "bts:decreasesSplicingOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity decreases the proper splicing of the mRNA",
- "rdfs:label": "decreasesSplicingOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:Transcript"
- }
- },
- {
- "@id": "bts:affectsStabilityOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the stability of the other within a system of interest",
- "rdfs:label": "affectsStabilityOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesStabilityOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the stability of the other within a system of interest",
- "rdfs:label": "increasesStabilityOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesStabilityOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the stability of the other within a system of interest",
- "rdfs:label": "decreasesStabilityOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsTransportOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest",
- "rdfs:label": "affectsTransportOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesTransportOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest",
- "rdfs:label": "increasesTransportOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesTransportOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest",
- "rdfs:label": "decreasesTransportOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsSecretionOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of secretion of the other out of a cell, gland, or organ",
- "rdfs:label": "affectsSecretionOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesSecretionOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ",
- "rdfs:label": "increasesSecretionOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesSecretionOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ",
- "rdfs:label": "decreasesSecretionOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:affectsUptakeOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of uptake of the other into of a cell, gland, or organ",
- "rdfs:label": "affectsUptakeOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:increasesUptakeOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ",
- "rdfs:label": "increasesUptakeOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:decreasesUptakeOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ",
- "rdfs:label": "decreasesUptakeOf",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:regulates,ProcessToProcess",
- "@type": "rdf:Property",
- "rdfs:comment": null,
- "rdfs:label": "regulates,ProcessToProcess",
- "schema:domainIncludes": {
- "@id": "bts:Occurrent"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:Occurrent"
- }
- },
- {
- "@id": "bts:regulates,EntityToEntity",
- "@type": "rdf:Property",
- "rdfs:comment": null,
- "rdfs:label": "regulates,EntityToEntity",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:hasGeneProduct",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a gene and a transcribed and/or translated product generated from it",
- "rdfs:label": "hasGeneProduct",
- "schema:domainIncludes": {
- "@id": "bts:Gene"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GeneProduct"
- }
- },
- {
- "@id": "bts:inPathwayWith",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two genes or gene products that are part of in the same biological pathway",
- "rdfs:label": "inPathwayWith",
- "schema:domainIncludes": {
- "@id": "bts:GeneOrGeneProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GeneOrGeneProduct"
- }
- },
- {
- "@id": "bts:inComplexWith",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex",
- "rdfs:label": "inComplexWith",
- "schema:domainIncludes": {
- "@id": "bts:GeneOrGeneProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GeneOrGeneProduct"
- }
- },
- {
- "@id": "bts:inCellPopulationWith",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two genes or gene products that are expressed in the same cell type or population ",
- "rdfs:label": "inCellPopulationWith",
- "schema:domainIncludes": {
- "@id": "bts:GeneOrGeneProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GeneOrGeneProduct"
- }
- },
- {
- "@id": "bts:geneAssociatedWithCondition",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with",
- "rdfs:label": "geneAssociatedWithCondition",
- "schema:domainIncludes": {
- "@id": "bts:Gene"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:DiseaseOrPhenotypicFeature"
- }
- },
- {
- "@id": "bts:treats",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature that it is used to treat",
- "rdfs:label": "treats",
- "schema:domainIncludes": {
- "@id": "bts:Treatment"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:DiseaseOrPhenotypicFeature"
- }
- },
- {
- "@id": "bts:correlatedWith",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.",
- "rdfs:label": "correlatedWith",
- "schema:domainIncludes": {
- "@id": "bts:DiseaseOrPhenotypicFeature"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:hasBiomarker",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.",
- "rdfs:label": "hasBiomarker",
- "schema:domainIncludes": {
- "@id": "bts:DiseaseOrPhenotypicFeature"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:MolecularEntity"
- }
- },
- {
- "@id": "bts:biomarkerFor",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a measurable molecular entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.",
- "rdfs:label": "biomarkerFor",
- "schema:domainIncludes": {
- "@id": "bts:MolecularEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:DiseaseOrPhenotypicFeature"
- }
- },
- {
- "@id": "bts:expressedIn",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a gene or gene product and an anatomical entity in which it is expressed",
- "rdfs:label": "expressedIn",
- "schema:domainIncludes": {
- "@id": "bts:GeneOrGeneProduct"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:AnatomicalEntity"
- }
- },
- {
- "@id": "bts:expresses",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between an anatomical entity and gene or gene product that is expressed there",
- "rdfs:label": "expresses",
- "schema:domainIncludes": {
- "@id": "bts:AnatomicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:GeneOrGeneProduct"
- }
- },
- {
- "@id": "bts:hasPhenotype",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). ",
- "rdfs:label": "hasPhenotype",
- "schema:domainIncludes": {
- "@id": "bts:BiologicalEntity"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:DiseaseOrPhenotypicFeature"
- }
- },
- {
- "@id": "bts:precedes",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two processes, where one completes before the other begins",
- "rdfs:label": "precedes",
- "schema:domainIncludes": {
- "@id": "bts:Occurrent"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:Occurrent"
- }
- },
- {
- "@id": "bts:subclassOf",
- "@type": "rdf:Property",
- "rdfs:comment": "holds between two classes where the domain class is a specialization of the range class",
- "rdfs:label": "subclassOf",
- "schema:domainIncludes": {
- "@id": "bts:OntologyClass"
- },
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": {
- "@id": "bts:OntologyClass"
- }
- },
- {
- "@id": "bts:Study",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Study",
- "rdfs:subClassOf": [
- {
- "@id": "schema:Thing"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Study",
- "sms:required": "sms:true",
- "sms:requiresDependency": [
- {
- "@id": "bts:StudyCode"
- },
- {
- "@id": "bts:StudyName"
- },
- {
- "@id": "bts:Program"
- },
- {
- "@id": "bts:DbGaP"
- }
- ],
- "sms:validationRules": []
- },
- {
- "@id": "bts:StudyCode",
- "@type": "rdfs:Class",
- "rdfs:comment": "Unique identifer for the study, assigned by DCC",
- "rdfs:label": "StudyCode",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Study"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": [
- {
- "@id": "bts:ABC-DS"
- },
- {
- "@id": "bts:ADS"
- },
- {
- "@id": "bts:DS-Brain"
- },
- {
- "@id": "bts:DS-COG-ALL"
- },
- {
- "@id": "bts:DS-COG-AML"
- },
- {
- "@id": "bts:DS-Immune"
- },
- {
- "@id": "bts:DS-ISP"
- },
- {
- "@id": "bts:DS-PALS"
- },
- {
- "@id": "bts:DS-PCGC"
- },
- {
- "@id": "bts:DS-Sleep"
- },
- {
- "@id": "bts:DS360-CHD"
- },
- {
- "@id": "bts:DSC"
- },
- {
- "@id": "bts:ECODS"
- },
- {
- "@id": "bts:ExCEEDS"
- },
- {
- "@id": "bts:HTP"
- },
- {
- "@id": "bts:TRC-DS"
- },
- {
- "@id": "bts:X01-DeSmith"
- },
- {
- "@id": "bts:X01-Hakon"
- }
- ],
- "sms:displayName": "Study Code",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:StudyName",
- "@type": "rdfs:Class",
- "rdfs:comment": "Name of the study, chosen by data contributor",
- "rdfs:label": "StudyName",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Study"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Study Name",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Program",
- "@type": "rdfs:Class",
- "rdfs:comment": "Funding source for the study",
- "rdfs:label": "Program",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Study"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": [
- {
- "@id": "bts:INCLUDE"
- },
- {
- "@id": "bts:KF"
- }
- ],
- "sms:displayName": "Program",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:DbGaP",
- "@type": "rdfs:Class",
- "rdfs:comment": "dbGaP study accession code",
- "rdfs:label": "DbGaP",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Study"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "dbGaP",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Participant",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Participant",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Thing"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Participant",
- "sms:required": "sms:false",
- "sms:requiresComponent": [
- {
- "@id": "bts:Study"
- },
- {
- "@id": "bts:DataFile"
- }
- ],
- "sms:requiresDependency": [
- {
- "@id": "bts:ParticipantID"
- },
- {
- "@id": "bts:ExternalID"
- },
- {
- "@id": "bts:FamilyID"
- },
- {
- "@id": "bts:FamilyType"
- },
- {
- "@id": "bts:FatherID"
- },
- {
- "@id": "bts:MotherID"
- },
- {
- "@id": "bts:FamilyRelationship"
- },
- {
- "@id": "bts:StudyCode"
- },
- {
- "@id": "bts:Sex"
- },
- {
- "@id": "bts:Race"
- },
- {
- "@id": "bts:Ethnicity"
- },
- {
- "@id": "bts:DownSyndromeStatus"
- },
- {
- "@id": "bts:OutcomesVitalStatus"
- },
- {
- "@id": "bts:AgeatLastVitalStatus"
- },
- {
- "@id": "bts:PhenotypeHPO"
- },
- {
- "@id": "bts:PhenotypeSourceText"
- },
- {
- "@id": "bts:PhenotypeInterpretation"
- },
- {
- "@id": "bts:AgeatPhenotypeAssignment"
- },
- {
- "@id": "bts:DiagnosisType"
- },
- {
- "@id": "bts:DiagnosisMONDO"
- },
- {
- "@id": "bts:DiagnosisNCIT"
- },
- {
- "@id": "bts:DiagnosisICD"
- },
- {
- "@id": "bts:DiagnosisSourceText"
- },
- {
- "@id": "bts:AgeatDiagnosis"
- }
- ],
- "sms:validationRules": []
- },
- {
- "@id": "bts:ParticipantID",
- "@type": "rdfs:Class",
- "rdfs:comment": "Unique identifier for the participant, assigned by DCC",
- "rdfs:label": "ParticipantID",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Participant ID",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:ExternalID",
- "@type": "rdfs:Class",
- "rdfs:comment": "Unique identifier for the participant, assigned by data contributor",
- "rdfs:label": "ExternalID",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "External ID",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:FamilyID",
- "@type": "rdfs:Class",
- "rdfs:comment": "Unique identifer for family to which Participant belongs",
- "rdfs:label": "FamilyID",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Family ID",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:FamilyType",
- "@type": "rdfs:Class",
- "rdfs:comment": "Structure of family members participating in the study (proband-only = no family members participating; duo = proband + parent; trio = proband + 2 parents; trio+ = proband + 2 parents + other relatives) ",
- "rdfs:label": "FamilyType",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": [
- {
- "@id": "bts:Proband-only"
- },
- {
- "@id": "bts:Trio"
- },
- {
- "@id": "bts:Trio+"
- },
- {
- "@id": "bts:Duo"
- },
- {
- "@id": "bts:Other"
- }
- ],
- "sms:displayName": "Family Type",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:FatherID",
- "@type": "rdfs:Class",
- "rdfs:comment": "Participant ID for Participant's father",
- "rdfs:label": "FatherID",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Father ID",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:MotherID",
- "@type": "rdfs:Class",
- "rdfs:comment": "Participant ID for Participant's mother",
- "rdfs:label": "MotherID",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Mother ID",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:FamilyRelationship",
- "@type": "rdfs:Class",
- "rdfs:comment": "Relationship of Participant to other family members",
- "rdfs:label": "FamilyRelationship",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Family Relationship",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Sex",
- "@type": "rdfs:Class",
- "rdfs:comment": "Sex of participant",
- "rdfs:label": "Sex",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": [
- {
- "@id": "bts:Male"
- },
- {
- "@id": "bts:Female"
- },
- {
- "@id": "bts:Other"
- },
- {
- "@id": "bts:Unknown"
- }
- ],
- "sms:displayName": "Sex",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Race",
- "@type": "rdfs:Class",
- "rdfs:comment": "Race of participant",
- "rdfs:label": "Race",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": [
- {
- "@id": "bts:White"
- },
- {
- "@id": "bts:BlackorAfricanAmerican"
- },
- {
- "@id": "bts:Asian"
- },
- {
- "@id": "bts:Morethanonerace"
- },
- {
- "@id": "bts:AmericanIndianorAlaskaNative"
- },
- {
- "@id": "bts:NativeHawaiianorOtherPacificIslander"
- },
- {
- "@id": "bts:Other"
- },
- {
- "@id": "bts:Prefernottoanswer"
- },
- {
- "@id": "bts:Unknown"
- }
- ],
- "sms:displayName": "Race",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Ethnicity",
- "@type": "rdfs:Class",
- "rdfs:comment": "Ethnicity of participant",
- "rdfs:label": "Ethnicity",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": [
- {
- "@id": "bts:NotHispanicorLatino"
- },
- {
- "@id": "bts:HispanicorLatino"
- },
- {
- "@id": "bts:Prefernottoanswer"
- },
- {
- "@id": "bts:Unknown"
- }
- ],
- "sms:displayName": "Ethnicity",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:DownSyndromeStatus",
- "@type": "rdfs:Class",
- "rdfs:comment": "Down Syndrome status of participant (T21 = Trisomy 21; D21 = Disomy 21, euploid)",
- "rdfs:label": "DownSyndromeStatus",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": [
- {
- "@id": "bts:T21"
- },
- {
- "@id": "bts:D21"
- }
- ],
- "sms:displayName": "Down Syndrome Status",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:OutcomesVitalStatus",
- "@type": "rdfs:Class",
- "rdfs:comment": "Whether participant is alive or dead",
- "rdfs:label": "OutcomesVitalStatus",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Outcomes Vital Status",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:AgeatLastVitalStatus",
- "@type": "rdfs:Class",
- "rdfs:comment": "Age in days when participant's vital status was last recorded",
- "rdfs:label": "AgeatLastVitalStatus",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Age at Last Vital Status",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:PhenotypeHPO",
- "@type": "rdfs:Class",
- "rdfs:comment": "Human Phenotype Ontology code (annotated by data contributor or DCC)",
- "rdfs:label": "PhenotypeHPO",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Phenotype HPO",
- "sms:required": "sms:false",
- "sms:validationRules": [
- "list"
- ]
- },
- {
- "@id": "bts:PhenotypeSourceText",
- "@type": "rdfs:Class",
- "rdfs:comment": "Phenotype as described by data contributor",
- "rdfs:label": "PhenotypeSourceText",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Phenotype Source Text",
- "sms:required": "sms:false",
- "sms:validationRules": [
- "list"
- ]
- },
- {
- "@id": "bts:PhenotypeInterpretation",
- "@type": "rdfs:Class",
- "rdfs:comment": "Whether phenotype was observed or not",
- "rdfs:label": "PhenotypeInterpretation",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": [
- {
- "@id": "bts:Observed"
- },
- {
- "@id": "bts:NotObserved"
- }
- ],
- "sms:displayName": "Phenotype Interpretation",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:AgeatPhenotypeAssignment",
- "@type": "rdfs:Class",
- "rdfs:comment": "Age in days at which phenotype was recorded",
- "rdfs:label": "AgeatPhenotypeAssignment",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Age at Phenotype Assignment",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:DiagnosisType",
- "@type": "rdfs:Class",
- "rdfs:comment": "How diagnosis was assigned",
- "rdfs:label": "DiagnosisType",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Diagnosis Type",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:DiagnosisMONDO",
- "@type": "rdfs:Class",
- "rdfs:comment": "Mondo disease ontology code (annotated by data contributor or DCC)",
- "rdfs:label": "DiagnosisMONDO",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Diagnosis MONDO",
- "sms:required": "sms:false",
- "sms:validationRules": [
- "list"
- ]
- },
- {
- "@id": "bts:DiagnosisNCIT",
- "@type": "rdfs:Class",
- "rdfs:comment": "NCI Thesaurus code (annotated by data contributor or DCC)",
- "rdfs:label": "DiagnosisNCIT",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Diagnosis NCIT",
- "sms:required": "sms:false",
- "sms:validationRules": [
- "list"
- ]
- },
- {
- "@id": "bts:DiagnosisICD",
- "@type": "rdfs:Class",
- "rdfs:comment": "ICD-10 code (annotated by data contributor or DCC)",
- "rdfs:label": "DiagnosisICD",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Diagnosis ICD",
- "sms:required": "sms:false",
- "sms:validationRules": [
- "list"
- ]
- },
- {
- "@id": "bts:DiagnosisSourceText",
- "@type": "rdfs:Class",
- "rdfs:comment": "Diagnosis as described by data contributor",
- "rdfs:label": "DiagnosisSourceText",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Diagnosis Source Text",
- "sms:required": "sms:false",
- "sms:validationRules": [
- "list"
- ]
- },
- {
- "@id": "bts:AgeatDiagnosis",
- "@type": "rdfs:Class",
- "rdfs:comment": "Age in days at which phenotype was assigned",
- "rdfs:label": "AgeatDiagnosis",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Participant"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Age at Diagnosis",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Biospecimen",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Biospecimen",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Thing"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Biospecimen",
- "sms:required": "sms:false",
- "sms:requiresComponent": [
- {
- "@id": "bts:Study"
- },
- {
- "@id": "bts:Participant"
- },
- {
- "@id": "bts:DataFile"
- }
- ],
- "sms:requiresDependency": [
- {
- "@id": "bts:ParticipantID"
- },
- {
- "@id": "bts:CollectionID"
- },
- {
- "@id": "bts:CollectionSampleType"
- },
- {
- "@id": "bts:SampleID"
- },
- {
- "@id": "bts:ContainerID"
- },
- {
- "@id": "bts:SampleType"
- },
- {
- "@id": "bts:ParentSampleID"
- },
- {
- "@id": "bts:ParentSampleType"
- },
- {
- "@id": "bts:AgeAtBiospecimenCollection"
- },
- {
- "@id": "bts:SampleAvailability"
- },
- {
- "@id": "bts:Volume"
- },
- {
- "@id": "bts:VolumeUnit"
- },
- {
- "@id": "bts:LaboratoryProcedure"
- },
- {
- "@id": "bts:BiospecimenStorage"
- }
- ],
- "sms:validationRules": []
- },
- {
- "@id": "bts:CollectionID",
- "@type": "rdfs:Class",
- "rdfs:comment": "Identifier for the eldest sample in a lineage of processed, pooled, or aliquoted samples. This may be the same as Parent Sample ID or Sample ID (if no processing was performed).",
- "rdfs:label": "CollectionID",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Biospecimen"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Collection ID",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:CollectionSampleType",
- "@type": "rdfs:Class",
- "rdfs:comment": "Type of biological material comprising the collected sample (e.g. Whole blood, Bone marrow, Saliva, etc.)",
- "rdfs:label": "CollectionSampleType",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Biospecimen"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Collection Sample Type",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:SampleID",
- "@type": "rdfs:Class",
- "rdfs:comment": "Identifier for sample. A sample is a unique biological material; two samples with two different IDs are biologically distinct.",
- "rdfs:label": "SampleID",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Biospecimen"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Sample ID",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:ContainerID",
- "@type": "rdfs:Class",
- "rdfs:comment": "Identifier for specific container/aliquot of sample, if applicable. For example, distinct aliquots of a sample will have the same Sample ID but different Container IDs.",
- "rdfs:label": "ContainerID",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Biospecimen"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Container ID",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:SampleType",
- "@type": "rdfs:Class",
- "rdfs:comment": "Type of biological material comprising the sample (e.g. Plasma, Serum, White blood cells, DNA, RNA, etc.)",
- "rdfs:label": "SampleType",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Biospecimen"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Sample Type",
- "sms:required": "sms:true",
- "sms:validationRules": []
- },
- {
- "@id": "bts:ParentSampleID",
- "@type": "rdfs:Class",
- "rdfs:comment": "Identifier for the direct parent from which Sample was derived, processed, pooled, etc. (if applicable)",
- "rdfs:label": "ParentSampleID",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Biospecimen"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Parent Sample ID",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:ParentSampleType",
- "@type": "rdfs:Class",
- "rdfs:comment": "Type of biological material comprising the parent sample (e.g. Plasma, Serum, White blood cells, etc.)",
- "rdfs:label": "ParentSampleType",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Biospecimen"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Parent Sample Type",
- "sms:required": "sms:false",
- "sms:requiresDependency": [
- {
- "@id": "bts:ParentSampleID"
- }
- ],
- "sms:validationRules": []
- },
- {
- "@id": "bts:AgeAtBiospecimenCollection",
- "@type": "rdfs:Class",
- "rdfs:comment": "Age in days of participant at time of biospecimen collection",
- "rdfs:label": "AgeAtBiospecimenCollection",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Biospecimen"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Age At Biospecimen Collection",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:SampleAvailability",
- "@type": "rdfs:Class",
- "rdfs:comment": "Whether or not the sample is potentially available for sharing through the Virtual Biorepository",
- "rdfs:label": "SampleAvailability",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Biospecimen"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "schema:rangeIncludes": [
- {
- "@id": "bts:Available"
- },
- {
- "@id": "bts:Unavailable"
- }
- ],
- "sms:displayName": "Sample Availability",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Volume",
- "@type": "rdfs:Class",
- "rdfs:comment": "Amount of sample in container",
- "rdfs:label": "Volume",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Biospecimen"
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- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Black or African American",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Asian",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Asian",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Race"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Asian",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Morethanonerace",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Morethanonerace",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Race"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "More than one race",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:AmericanIndianorAlaskaNative",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "AmericanIndianorAlaskaNative",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Race"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "American Indian or Alaska Native",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:NativeHawaiianorOtherPacificIslander",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "NativeHawaiianorOtherPacificIslander",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Race"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Native Hawaiian or Other Pacific Islander",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Prefernottoanswer",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Prefernottoanswer",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Race"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Prefer not to answer",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:NotHispanicorLatino",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "NotHispanicorLatino",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Ethnicity"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Not Hispanic or Latino",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:HispanicorLatino",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "HispanicorLatino",
- "rdfs:subClassOf": [
- {
- "@id": "bts:Ethnicity"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Hispanic or Latino",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:T21",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "T21",
- "rdfs:subClassOf": [
- {
- "@id": "bts:DownSyndromeStatus"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "T21",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:D21",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "D21",
- "rdfs:subClassOf": [
- {
- "@id": "bts:DownSyndromeStatus"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "D21",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Observed",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Observed",
- "rdfs:subClassOf": [
- {
- "@id": "bts:PhenotypeInterpretation"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Observed",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:NotObserved",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "NotObserved",
- "rdfs:subClassOf": [
- {
- "@id": "bts:PhenotypeInterpretation"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Not Observed",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Available",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Available",
- "rdfs:subClassOf": [
- {
- "@id": "bts:SampleAvailability"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Available",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Unavailable",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Unavailable",
- "rdfs:subClassOf": [
- {
- "@id": "bts:SampleAvailability"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Unavailable",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Controlled",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Controlled",
- "rdfs:subClassOf": [
- {
- "@id": "bts:DataAccess"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Controlled",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Registered",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Registered",
- "rdfs:subClassOf": [
- {
- "@id": "bts:DataAccess"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Registered",
- "sms:required": "sms:false",
- "sms:validationRules": []
- },
- {
- "@id": "bts:Open",
- "@type": "rdfs:Class",
- "rdfs:comment": "TBD",
- "rdfs:label": "Open",
- "rdfs:subClassOf": [
- {
- "@id": "bts:DataAccess"
- }
- ],
- "schema:isPartOf": {
- "@id": "http://schema.biothings.io"
- },
- "sms:displayName": "Open",
- "sms:required": "sms:false",
- "sms:validationRules": []
- }
- ],
- "@id": "http://schema.biothings.io/#0.1"
-}
\ No newline at end of file
diff --git a/justfile b/justfile
new file mode 100644
index 00000000..d032c636
--- /dev/null
+++ b/justfile
@@ -0,0 +1,249 @@
+# ============ Hint for for Windows Users ============
+
+# On Windows the "sh" shell that comes with Git for Windows should be used.
+# If it is not on path, provide the path to the executable in the following line.
+#set windows-shell := ["C:/Program Files/Git/usr/bin/sh", "-cu"]
+
+# ============ Variables used in recipes ============
+
+# Load environment variables from config.public.mk or specified file
+set dotenv-load := true
+# set dotenv-filename := env_var_or_default("LINKML_ENVIRONMENT_FILENAME", "config.public.mk")
+set dotenv-filename := x'${LINKML_ENVIRONMENT_FILENAME:-config.public.mk}'
+
+# Set shebang line for cross-platform Python recipes (assumes presence of launcher on Windows)
+shebang := if os() == 'windows' {
+ 'py'
+} else {
+ '/usr/bin/env python3'
+}
+
+# Environment variables with defaults
+schema_name := env_var_or_default("LINKML_SCHEMA_NAME", "_no_schema_given_")
+source_schema_dir := env_var_or_default("LINKML_SCHEMA_SOURCE_DIR", "")
+config_yaml := if env_var_or_default("LINKML_GENERATORS_CONFIG_YAML", "") != "" {
+ "--config-file " + env_var_or_default("LINKML_GENERATORS_CONFIG_YAML", "")
+} else {
+ ""
+}
+gen_doc_args := env_var_or_default("LINKML_GENERATORS_DOC_ARGS", "")
+gen_java_args := env_var_or_default("LINKML_GENERATORS_JAVA_ARGS", "")
+gen_owl_args := env_var_or_default("LINKML_GENERATORS_OWL_ARGS", "")
+gen_pydantic_args := env_var_or_default("LINKML_GENERATORS_PYDANTIC_ARGS", "")
+gen_ts_args := env_var_or_default("LINKML_GENERATORS_TYPESCRIPT_ARGS", "")
+
+# Directory variables
+src := "src"
+dest := "project"
+pymodel := src / schema_name / "datamodel"
+source_schema_path := source_schema_dir / schema_name + ".yaml"
+docdir := "docs/elements" # Directory for generated documentation
+merged_schema_path := "docs/schema" / schema_name + ".yaml"
+
+# ============== Project recipes ==============
+
+# List all commands as default command. The prefix "_" hides the command.
+_default: _status
+ @just --list
+
+# Initialize a new project (use this for projects not yet under version control)
+[group('project management')]
+setup: _check-config _git-init install _git-add && _setup_part2
+ git commit -m "Initialise git with minimal project" -a
+
+_setup_part2: gen-project gen-doc
+ @echo
+ @echo '=== Setup completed! ==='
+ @echo 'Various model representations have been created under directory "project". By default'
+ @echo 'they are ignored by git. You decide whether you want to add them to git tracking or'
+ @echo 'continue to git-ignore them as they can be regenerated if needed.'
+ @echo 'For tracking specific subfolders, add !project/[foldername]/* line(s) to ".gitignore".'
+
+# Install project dependencies
+[group('project management')]
+install:
+ uv sync --group dev
+
+# Updates project template and LinkML package
+[group('project management')]
+update: _update-template _update-linkml
+
+# Clean all generated files
+[group('project management')]
+clean: _clean_project
+ rm -rf tmp
+ rm -rf {{docdir}}/*.md
+
+# (Re-)Generate project and documentation locally
+[group('model development')]
+site: gen-project gen-doc
+
+# Deploy documentation site to Github Pages
+[group('deployment')]
+deploy: site
+ mkd-gh-deploy
+
+# Run all tests
+[group('model development')]
+test: _test-schema _test-python _test-examples
+
+# Run linting
+[group('model development')]
+lint:
+ uv run linkml-lint {{source_schema_dir}}
+
+# Generate md documentation for the schema
+[group('model development')]
+gen-doc: _gen-yaml
+ uv run gen-doc {{gen_doc_args}} -d {{docdir}} {{source_schema_path}}
+
+# Build docs and run test server
+[group('model development')]
+testdoc: gen-doc _serve
+
+# Generate the Python data models (dataclasses & pydantic)
+gen-python:
+ uv run gen-project -d {{pymodel}} -I python {{source_schema_path}}
+ uv run gen-pydantic {{gen_pydantic_args}} {{source_schema_path}} > {{pymodel}}/{{schema_name}}_pydantic.py
+
+# Generate project files including Python data model
+[group('model development')]
+gen-project:
+ uv run gen-project {{config_yaml}} -d {{dest}} {{source_schema_path}}
+ mv {{dest}}/*.py {{pymodel}}
+ uv run gen-pydantic {{gen_pydantic_args}} {{source_schema_path}} > {{pymodel}}/{{schema_name}}_pydantic.py
+ uv run gen-java {{gen_java_args}} --output-directory {{dest}}/java/ {{source_schema_path}}
+ @if [ ! ${{gen_owl_args}} ]; then \
+ mkdir -p {{dest}}/owl && \
+ uv run gen-owl {{gen_owl_args}} {{source_schema_path}} > {{dest}}/owl/{{schema_name}}.owl.ttl || true ; \
+ fi
+ @if [ ! ${{gen_ts_args}} ]; then \
+ uv run gen-typescript {{gen_ts_args}} {{source_schema_path}} > {{dest}}/typescript/{{schema_name}}.ts || true ; \
+ fi
+
+# ============== Migrations recipes for Copier ==============
+
+# Hidden command to adjust the directory layout on upgrading a project
+# created with linkml-project-copier v0.1.x to v0.2.0 or newer.
+# Use with care! - It may not work for customized projects.
+_post_upgrade_v020: && _post_upgrade_v020py
+ mv docs/*.md docs/elements
+
+_post_upgrade_v020py:
+ #!{{shebang}}
+ import subprocess
+ from pathlib import Path
+ # Git move files from folder src to folder dest
+ tasks = [
+ (Path("src/docs/files"), Path("docs")),
+ (Path("src/docs/templates"), Path("docs/templates-linkml")),
+ (Path("src/data/examples"), Path("tests/data/")),
+ ]
+ for src, dest in tasks:
+ for path_obj in src.rglob("*"):
+ if not path_obj.is_file():
+ continue
+ file_dest = dest / path_obj.relative_to(src)
+ if not file_dest.parent.exists():
+ file_dest.parent.mkdir(parents=True)
+ print(f"Moving {path_obj} --> {file_dest}")
+ subprocess.run(["git", "mv", str(path_obj), str(file_dest)])
+ print(
+ "Migration to v0.2.x completed! Check the changes carefully before committing."
+ )
+
+# ============== Hidden internal recipes ==============
+
+# Show current project status
+_status: _check-config
+ @echo "Project: {{schema_name}}"
+ @echo "Source: {{source_schema_path}}"
+
+# Check project configuration
+_check-config:
+ #!{{shebang}}
+ import os
+ schema_name = os.getenv('LINKML_SCHEMA_NAME')
+ if not schema_name:
+ print('**Project not configured**:\n - See \'.env.public\'')
+ exit(1)
+ print('Project-status: Ok')
+
+# Update project template
+_update-template:
+ copier update --trust --skip-answered
+
+# Update LinkML to latest version
+_update-linkml:
+ uv add linkml --upgrade-package linkml
+
+# Test schema generation
+_test-schema:
+ uv run gen-project {{config_yaml}} -d tmp {{source_schema_path}}
+
+# Run Python unit tests with pytest
+_test-python: gen-python
+ uv run python -m pytest
+
+# Run example tests
+_test-examples: _ensure_examples_output
+ uv run linkml-run-examples \
+ --input-formats json \
+ --input-formats yaml \
+ --output-formats json \
+ --output-formats yaml \
+ --counter-example-input-directory tests/data/invalid \
+ --input-directory tests/data/valid \
+ --output-directory examples/output \
+ --schema {{source_schema_path}} > examples/output/README.md
+
+# Generate merged model
+_gen-yaml:
+ -mkdir -p docs/schema
+ uv run gen-yaml {{source_schema_path}} > {{merged_schema_path}}
+
+# Run documentation server
+_serve:
+ uv run mkdocs serve
+
+# Initialize git repository
+_git-init:
+ git init
+
+# Add files to git
+_git-add:
+ git add .
+
+# Commit files to git
+_git-commit:
+ git commit -m 'chore: just setup was run' -a
+
+# Show git status
+_git-status:
+ git status
+
+_clean_project:
+ #!{{shebang}}
+ import shutil, pathlib
+ # remove the generated project files
+ for d in pathlib.Path("{{dest}}").iterdir():
+ if d.is_dir():
+ print(f'removing "{d}"')
+ shutil.rmtree(d, ignore_errors=True)
+ # remove the generated python data model
+ for d in pathlib.Path("{{pymodel}}").iterdir():
+ if d.name == "__init__.py":
+ continue
+ print(f'removing "{d}"')
+ if d.is_dir():
+ shutil.rmtree(d, ignore_errors=True)
+ else:
+ d.unlink()
+
+_ensure_examples_output: # Ensure a clean examples/output directory exists
+ -mkdir -p examples/output
+ -rm -rf examples/output/*.*
+
+# ============== Include project-specific recipes ==============
+
+import "project.justfile"
diff --git a/mkdocs.yml b/mkdocs.yml
index 70ab7edc..f06811bc 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,32 +1,43 @@
-site_name: "INCLUDE Data Model"
+---
+site_name: "INCLUDE LinkML Data Model"
theme:
name: material
- analytics:
- gtag: G-2SYBSJVZ23
- palette:
- - media: '(prefers-color-scheme: light)'
- scheme: default
- primary: teal
- accent: amber
- toggle:
- icon: material/lightbulb
- name: Switch to light mode
- - media: '(prefers-color-scheme: light)'
- scheme: slate
- primary: teal
- accent: amber
- toggle:
- icon: material/lightbulb-outline
- name: Switch to dark mode
+ # palette:
+ # scheme: slate
+ # primary: cyan
+ features:
+ - content.tabs.link
+
+# for adding extra css/js see https://www.mkdocs.org/user-guide/customizing-your-theme/
+
plugins:
- search
+ - mknotebooks:
+ execute: false
- mermaid2:
- version: 10.9.0
+ version: 11.4.1
+ # TODO rebuild docs on schema change (https://github.com/dalito/linkml-project-copier/issues/39)
+ # - gen-files:
+ # scripts:
+ # - gen_pages.py # or any other name or path
+
+watch:
+ - src/include_linkml_data_model/schema
nav:
- - Index: index.md
+ - Home: index.md
+ - Schema: elements/index.md
- About: about.md
- - ER Diagram: erdiagram.md
-site_url: https://include-dcc.github.io/include-linkml/
-repo_url: https://github.com/include-dcc/include-linkml/
+exclude_docs: |
+ /templates-linkml/
+
+site_url: https://include-dcc.github.io/INCLUDE LinkML Data Model
+repo_url: https://github.com/include-dcc/INCLUDE LinkML Data Model
+
+# Uncomment this block to enable use of Google Analytics.
+# Replace the property value with your own ID.
+# extra:
+# analytics:
+# provider: google
+# property: G-XXXXXXXXXX
diff --git a/project.Makefile b/project.Makefile
deleted file mode 100644
index 7ba952ac..00000000
--- a/project.Makefile
+++ /dev/null
@@ -1,31 +0,0 @@
-template_dir = src/data/sheets
-output_dir = src/data/output
-
-# ls -1 src/data/sheets/*.tsv
- #src/data/sheets/INCLUDE_Portal_V1_LinkML_Schema_Classes_Slots.tsv
- #src/data/sheets/INCLUDE_Portal_V1_LinkML_Schema_Enums.tsv
- #src/data/sheets/INCLUDE_Portal_V1_LinkML_Schema_Prefixes.tsv
- #src/data/sheets/INCLUDE_Portal_V1_LinkML_Schema_Schema.tsv
- #src/data/sheets/INCLUDE_Portal_V1_LinkML_Schema_Types.tsv
-
- # ValueError: dict contains fields not in fieldnames: 'desc', 'slot'
- # when last arg is src/data/sheets/*.tsv
- # but each of the templates complies OK on its own
-
-.PHONY: individually_all linkml2sheets_clean individually
-
-individually_all: linkml2sheets_clean individually
-
-linkml2sheets_clean:
- rm -rf $(output_dir)/*
-
-src/data/output/%.tsv:
- poetry run linkml2sheets \
- --schema src/linkml/include_linkml.yaml \
- --output-directory $(output_dir) \
- --overwrite $(subst $(output_dir),$(template_dir),$@)
-
-individually: src/data/output/INCLUDE_Portal_V1_LinkML_Schema_Classes_Slots.tsv \
-src/data/output/INCLUDE_Portal_V1_LinkML_Schema_Enums.tsv \
-src/data/output/INCLUDE_Portal_V1_LinkML_Schema_Prefixes.tsv \
-src/data/output/INCLUDE_Portal_V1_LinkML_Schema_Schema.tsv
diff --git a/project.justfile b/project.justfile
new file mode 100644
index 00000000..bf84fbcc
--- /dev/null
+++ b/project.justfile
@@ -0,0 +1 @@
+## Add your own just recipes here. This is imported by the main justfile.
diff --git a/project/excel/include_schema.xlsx b/project/excel/include_schema.xlsx
deleted file mode 100644
index e406582d..00000000
Binary files a/project/excel/include_schema.xlsx and /dev/null differ
diff --git a/project/graphql/include_schema.graphql b/project/graphql/include_schema.graphql
deleted file mode 100644
index ccd3f9ee..00000000
--- a/project/graphql/include_schema.graphql
+++ /dev/null
@@ -1,98 +0,0 @@
-type Biospecimen
- {
- hasStudy: Study
- hasParticipant: Participant
- sampleId: String!
- sampleType: String!
- ageAtBiospecimenCollection: Integer
- parentSampleId: String
- parentSampleType: String
- collectionId: String
- collectionSampleType: String
- containerId: String
- volume: Float
- volumeUnit: String
- laboratoryProcedure: String
- biospecimenStorage: String
- sampleAvailability: EnumSampleAvailability
- }
-
-type Condition
- {
- hasStudy: Study
- hasParticipant: Participant
- eventId: String
- eventType: String
- conditionSourceText: String
- ageAtConditionObservation: Integer
- conditionInterpretation: EnumConditionInterpretation
- conditionStatus: EnumConditionStatus
- conditionDataSource: EnumConditionDataSource
- hpoLabel: String
- hpoCode: String
- mondoLabel: String
- mondoCode: String
- maxoLabel: String
- maxoCode: String
- otherLabel: String
- otherCode: String
- measureType: String
- measureValue: Integer
- measureUnit: String
- ageAtMeasurement: Integer
- }
-
-type DataFile
- {
- hasStudy: Study
- hasParticipant: Participant
- hasBiospecimen: Biospecimen
- fileId: String
- fileName: String!
- fileHash: String
- dataAccess: EnumDataAccess
- dataCategory: String!
- dataType: String
- experimentalStrategy: String
- experimentalPlatform: String
- fileFormat: String!
- fileSize: Integer
- fileSizeUnit: String
- accessUrl: Uriorcurie
- publicationDoi: String
- }
-
-type Participant
- {
- hasStudy: Study
- participantId: String
- participantExternalId: String!
- familyId: String
- familyType: EnumFamilyType!
- fatherId: String
- motherId: String
- siblingId: String
- otherFamilyMemberId: String
- familyRelationship: EnumFamilyRelationship
- sex: EnumSex!
- race: EnumRace!
- ethnicity: EnumEthnicity!
- downSyndromeStatus: EnumDownSyndromeStatus!
- ageAtFirstPatientEngagement: Integer!
- firstPatientEngagementEvent: String!
- outcomesVitalStatus: EnumVitalStatus
- ageAtLastVitalStatus: Integer
- }
-
-type Study
- {
- studyCode: EnumStudyCode!
- studyName: String!
- program: EnumProgram!
- dbgap: String
- }
-
-type Thing
- {
- }
-
diff --git a/project/jsonld/include_schema.context.jsonld b/project/jsonld/include_schema.context.jsonld
deleted file mode 100644
index 5b8a83fe..00000000
--- a/project/jsonld/include_schema.context.jsonld
+++ /dev/null
@@ -1,162 +0,0 @@
-{
- "comments": {
- "description": "Auto generated by LinkML jsonld context generator",
- "generation_date": "2023-03-03T10:38:26",
- "source": "include_schema.yaml"
- },
- "@context": {
- "include": "https://w3id.org/include/",
- "linkml": "https://w3id.org/linkml/",
- "schema": "http://schema.org/",
- "skos": "http://www.w3.org/2004/02/skos/core#",
- "@vocab": "https://w3id.org/include/",
- "accessUrl": {
- "@type": "@id"
- },
- "ageAtBiospecimenCollection": {
- "@type": "xsd:integer"
- },
- "ageAtConditionObservation": {
- "@type": "xsd:integer"
- },
- "ageAtFirstPatientEngagement": {
- "@type": "xsd:integer"
- },
- "ageAtLastVitalStatus": {
- "@type": "xsd:integer"
- },
- "ageAtMeasurement": {
- "@type": "xsd:integer"
- },
- "conditionDataSource": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "conditionInterpretation": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "conditionStatus": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "dataAccess": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "downSyndromeStatus": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "ethnicity": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "familyRelationship": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "familyType": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "fileSize": {
- "@type": "xsd:integer"
- },
- "hasBiospecimen": {
- "@type": "@id"
- },
- "hasParticipant": {
- "@type": "@id"
- },
- "hasStudy": {
- "@type": "@id"
- },
- "measureValue": {
- "@type": "xsd:integer"
- },
- "outcomesVitalStatus": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "program": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "race": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "sampleAvailability": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "sex": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "studyCode": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
- "volume": {
- "@type": "xsd:float"
- }
- }
-}
diff --git a/project/jsonld/include_schema.jsonld b/project/jsonld/include_schema.jsonld
deleted file mode 100644
index 6bb765c3..00000000
--- a/project/jsonld/include_schema.jsonld
+++ /dev/null
@@ -1,1921 +0,0 @@
-{
- "name": "include-schema",
- "id": "https://w3id.org/include",
- "imports": [
- "linkml:types",
- "include_core",
- "include_assay",
- "include_participant",
- "include_study"
- ],
- "license": "https://creativecommons.org/publicdomain/zero/1.0/",
- "prefixes": [
- {
- "prefix_prefix": "include",
- "prefix_reference": "https://w3id.org/include/"
- },
- {
- "prefix_prefix": "linkml",
- "prefix_reference": "https://w3id.org/linkml/"
- },
- {
- "prefix_prefix": "schema",
- "prefix_reference": "http://schema.org/"
- }
- ],
- "default_prefix": "include",
- "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#dateTime",
- "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 inheritence 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"
- }
- ],
- "enums": [
- {
- "name": "enum_dataAccess",
- "definition_uri": "https://w3id.org/include/assay/EnumDataAccess",
- "from_schema": "https://w3id.org/include/assay",
- "permissible_values": [
- {
- "text": "controlled",
- "title": "Controlled"
- },
- {
- "text": "open",
- "title": "Open"
- },
- {
- "text": "registered",
- "title": "Registered"
- }
- ]
- },
- {
- "name": "enum_sampleAvailability",
- "definition_uri": "https://w3id.org/include/assay/EnumSampleAvailability",
- "from_schema": "https://w3id.org/include/assay",
- "permissible_values": [
- {
- "text": "available",
- "title": "Available"
- },
- {
- "text": "unavailable",
- "title": "Unavailable"
- }
- ]
- },
- {
- "name": "enum_conditionInterpretation",
- "definition_uri": "https://w3id.org/include/participant/EnumConditionInterpretation",
- "from_schema": "https://w3id.org/include/participant",
- "permissible_values": [
- {
- "text": "observed",
- "description": "Condition was observed or reported (this will be the case for most conditions)",
- "title": "Observed"
- },
- {
- "text": "not_observed",
- "description": "Participant was specifically examined or medical record queried for condition and found to be negative",
- "title": "Not Observed"
- }
- ]
- },
- {
- "name": "enum_conditionDataSource",
- "definition_uri": "https://w3id.org/include/participant/EnumConditionDataSource",
- "from_schema": "https://w3id.org/include/participant",
- "permissible_values": [
- {
- "text": "clinical",
- "description": "Information about condition was obtained from medical records or reported by investigator",
- "title": "Clinical"
- },
- {
- "text": "self_reported",
- "description": "Information about condition was reported by participant or family member",
- "title": "Self-reported"
- }
- ]
- },
- {
- "name": "enum_conditionStatus",
- "definition_uri": "https://w3id.org/include/participant/EnumConditionStatus",
- "from_schema": "https://w3id.org/include/participant",
- "permissible_values": [
- {
- "text": "current",
- "description": "Condition is ongoing",
- "title": "Current"
- },
- {
- "text": "resolved",
- "description": "Condition has been resolved",
- "title": "Resolved"
- },
- {
- "text": "history_of",
- "description": "This is a general history of the condition, without known dates",
- "title": "History Of"
- }
- ]
- },
- {
- "name": "enum_downSyndromeStatus",
- "definition_uri": "https://w3id.org/include/participant/EnumDownSyndromeStatus",
- "from_schema": "https://w3id.org/include/participant",
- "permissible_values": [
- {
- "text": "d21",
- "description": "Disomy 21 (euploid)",
- "title": "D21"
- },
- {
- "text": "t21",
- "description": "Trisomy 21 (Down syndrome)",
- "meaning": "MONDO:0008608",
- "title": "T21"
- }
- ]
- },
- {
- "name": "enum_ethnicity",
- "definition_uri": "https://w3id.org/include/participant/EnumEthnicity",
- "from_schema": "https://w3id.org/include/participant",
- "permissible_values": [
- {
- "text": "hispanic_or_latino",
- "meaning": "NCIT:C17459",
- "title": "Hispanic or Latino"
- },
- {
- "text": "not_hispanic_or_latino",
- "meaning": "NCIT:C41222",
- "title": "Not Hispanic or Latino"
- },
- {
- "text": "prefer_not_to_answer",
- "meaning": "NCIT:C132222",
- "title": "Prefer not to answer"
- },
- {
- "text": "unknown",
- "meaning": "NCIT:C17998",
- "title": "Unknown"
- }
- ]
- },
- {
- "name": "enum_familyRelationship",
- "definition_uri": "https://w3id.org/include/participant/EnumFamilyRelationship",
- "from_schema": "https://w3id.org/include/participant",
- "permissible_values": [
- {
- "text": "proband",
- "description": "The first affected family member to join the study",
- "meaning": "NCIT:C64435",
- "title": "Proband"
- },
- {
- "text": "father",
- "meaning": "NCIT:C25174",
- "title": "Father"
- },
- {
- "text": "mother",
- "meaning": "NCIT:C25189",
- "title": "Mother"
- },
- {
- "text": "sibling",
- "meaning": "NCIT:C25204",
- "title": "Sibling"
- },
- {
- "text": "other_relative",
- "meaning": "NCIT:C21480",
- "title": "Other relative"
- },
- {
- "text": "unrelated_control",
- "meaning": "NCIT:C25328",
- "title": "Unrelated control"
- }
- ]
- },
- {
- "name": "enum_familyType",
- "definition_uri": "https://w3id.org/include/participant/EnumFamilyType",
- "from_schema": "https://w3id.org/include/participant",
- "permissible_values": [
- {
- "text": "control_only",
- "description": "Unrelated control, no Down syndrome family members",
- "title": "Control-only"
- },
- {
- "text": "duo",
- "description": "Proband + one parent",
- "title": "Duo"
- },
- {
- "text": "other",
- "description": "Other family structure, e.g. one parent + twins",
- "title": "Other"
- },
- {
- "text": "proband_only",
- "description": "Proband only, no family members participating in study",
- "title": "Proband-only"
- },
- {
- "text": "trio",
- "description": "Proband + two parents",
- "title": "Trio"
- },
- {
- "text": "trio_plus",
- "description": "Proband + two parents + other relatives",
- "title": "Trio+"
- }
- ]
- },
- {
- "name": "enum_race",
- "definition_uri": "https://w3id.org/include/participant/EnumRace",
- "from_schema": "https://w3id.org/include/participant",
- "permissible_values": [
- {
- "text": "american_indian_or_alaskan_native",
- "meaning": "NCIT:C41259",
- "title": "American Indian or Alaska Native"
- },
- {
- "text": "asian",
- "meaning": "NCIT:C41260",
- "title": "Asian"
- },
- {
- "text": "black_or_african_american",
- "meaning": "NCIT:C16352",
- "title": "Black or African American"
- },
- {
- "text": "more_than_one_race",
- "meaning": "NCIT:C67109",
- "title": "More than one race"
- },
- {
- "text": "native_hawaiian_or_other_pacific_islander",
- "meaning": "NCIT:C41219",
- "title": "Native Hawaiian or Other Pacific Islander"
- },
- {
- "text": "other",
- "meaning": "NCIT:C17649",
- "title": "Other"
- },
- {
- "text": "white",
- "meaning": "NCIT:C41261",
- "title": "White"
- },
- {
- "text": "prefer_not_to_answer",
- "meaning": "NCIT:C132222",
- "title": "Prefer not to answer"
- },
- {
- "text": "unknown",
- "meaning": "NCIT:C17998",
- "title": "Unknown"
- },
- {
- "text": "east_asian",
- "description": "UK only; do not use for US data",
- "meaning": "NCIT:C161419",
- "title": "East Asian"
- },
- {
- "text": "latin_american",
- "description": "UK only; do not use for US data",
- "meaning": "NCIT:C126531",
- "title": "Latin American"
- },
- {
- "text": "middle_eastern_or_north_african",
- "description": "UK only; do not use for US data",
- "meaning": "NCIT:C43866",
- "title": "Middle Eastern or North African"
- },
- {
- "text": "south_asian",
- "description": "UK only; do not use for US data",
- "meaning": "NCIT:C41263",
- "title": "South Asian"
- }
- ]
- },
- {
- "name": "enum_sex",
- "definition_uri": "https://w3id.org/include/participant/EnumSex",
- "from_schema": "https://w3id.org/include/participant",
- "permissible_values": [
- {
- "text": "female",
- "meaning": "NCIT:C16576",
- "title": "Female"
- },
- {
- "text": "male",
- "meaning": "NCIT:C20197",
- "title": "Male"
- },
- {
- "text": "other",
- "meaning": "NCIT:C17649",
- "title": "Other"
- },
- {
- "text": "unknown",
- "meaning": "NCIT:C17998",
- "title": "Unknown"
- }
- ]
- },
- {
- "name": "enum_vital_status",
- "definition_uri": "https://w3id.org/include/participant/EnumVitalStatus",
- "from_schema": "https://w3id.org/include/participant",
- "permissible_values": [
- {
- "text": "dead",
- "meaning": "NCIT:C28554",
- "title": "Dead"
- },
- {
- "text": "alive",
- "meaning": "NCIT:C37987",
- "title": "Alive"
- },
- {
- "text": "unknown_or_not_available",
- "meaning": "NCIT:C17998",
- "title": "Unknown or not available"
- }
- ]
- },
- {
- "name": "enum_program",
- "definition_uri": "https://w3id.org/include/study/EnumProgram",
- "from_schema": "https://w3id.org/include/study",
- "permissible_values": [
- {
- "text": "include",
- "title": "INCLUDE"
- },
- {
- "text": "kf",
- "title": "KF"
- }
- ]
- },
- {
- "name": "enum_studyCode",
- "definition_uri": "https://w3id.org/include/study/EnumStudyCode",
- "from_schema": "https://w3id.org/include/study",
- "permissible_values": [
- {
- "text": "abcds",
- "title": "ABC-DS"
- },
- {
- "text": "ads",
- "title": "ADS"
- },
- {
- "text": "aecom_ds",
- "title": "AECOM-DS"
- },
- {
- "text": "brainpower",
- "title": "BrainPower"
- },
- {
- "text": "bri_dsr",
- "title": "BRI-DSR"
- },
- {
- "text": "charge_ds",
- "title": "CHARGE-DS"
- },
- {
- "text": "ds_brain",
- "title": "DS-Brain"
- },
- {
- "text": "ds_cog_all",
- "title": "DS-COG-ALL"
- },
- {
- "text": "ds_cog_aml",
- "title": "DS-COG-AML"
- },
- {
- "text": "ds_determined",
- "title": "DS-DETERMINED"
- },
- {
- "text": "ds_hsat",
- "title": "DS-HSAT"
- },
- {
- "text": "ds_isp",
- "title": "DS-ISP"
- },
- {
- "text": "ds_nexus",
- "title": "DS-Nexus"
- },
- {
- "text": "ds_pals",
- "title": "DS-PALS"
- },
- {
- "text": "ds_pcgc",
- "title": "DS-PCGC"
- },
- {
- "text": "ds_sleep",
- "title": "DS-Sleep"
- },
- {
- "text": "ds360_chd",
- "title": "DS360-CHD"
- },
- {
- "text": "dsc",
- "title": "DSC"
- },
- {
- "text": "ecods",
- "title": "ECODS"
- },
- {
- "text": "exceeds",
- "title": "ExCEEDS"
- },
- {
- "text": "htp",
- "title": "HTP"
- },
- {
- "text": "trc_ds",
- "title": "TRC-DS"
- },
- {
- "text": "x01_desmith",
- "title": "X01-deSmith"
- },
- {
- "text": "x01_hakon",
- "title": "X01-Hakon"
- }
- ]
- }
- ],
- "slots": [
- {
- "name": "sampleId",
- "definition_uri": "https://w3id.org/include/assay/sampleId",
- "description": "Identifier for sample. A sample is a unique biological material; two samples with two different IDs are biologically distinct.",
- "title": "Sample ID",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/sampleId",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "string",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "sampleType",
- "definition_uri": "https://w3id.org/include/assay/sampleType",
- "description": "Type of biological material comprising the Sample (e.g. Plasma, White blood cells, Red blood cells, DNA, RNA, Peripheral blood mononuclear cells, CD4+ Tconv cells, NK cells, Monocytes, CD8+ T cells, B cells, Granulocytes, Treg cells)",
- "title": "Sample Type",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/sampleType",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "string",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "ageAtBiospecimenCollection",
- "definition_uri": "https://w3id.org/include/assay/ageAtBiospecimenCollection",
- "description": "Age in days of participant at time of biospecimen collection",
- "title": "Age At Biospecimen Collection",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/ageAtBiospecimenCollection",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "integer",
- "@type": "SlotDefinition"
- },
- {
- "name": "parentSampleId",
- "definition_uri": "https://w3id.org/include/assay/parentSampleId",
- "description": "Identifier for the direct parent from which Sample was derived, processed, pooled, etc. (if applicable)",
- "title": "Parent Sample Id",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/parentSampleId",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "parentSampleType",
- "definition_uri": "https://w3id.org/include/assay/parentSampleType",
- "description": "Type of biological material comprising the Parent Sample (e.g. Peripheral Whole Blood, Derived Cell Line, Saliva, Whole blood, WBCs)",
- "title": "Parent Sample Type",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/parentSampleType",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "collectionId",
- "definition_uri": "https://w3id.org/include/assay/collectionId",
- "description": "Identifier for the eldest sample in a lineage of processed, pooled, or aliquoted samples - typically the material actually collected from the Participant. This may be the same as Parent Sample ID or Sample ID (if no processing was performed).",
- "title": "Collection ID",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/collectionId",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "collectionSampleType",
- "definition_uri": "https://w3id.org/include/assay/collectionSampleType",
- "description": "Type of biological material comprising the Collected Sample (e.g. Whole blood, Not reported, Saliva, Derived cell line)",
- "title": "Collection Sample Type",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/collectionSampleType",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "containerId",
- "definition_uri": "https://w3id.org/include/assay/containerId",
- "description": "Identifier for specific container/aliquot of sample, if applicable. For example, distinct aliquots of a sample will have the same Sample ID but different Container IDs.",
- "title": "Container ID",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/containerId",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "volume",
- "definition_uri": "https://w3id.org/include/assay/volume",
- "description": "Amount of sample in container",
- "title": "Volume",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/volume",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "float",
- "@type": "SlotDefinition"
- },
- {
- "name": "volumeUnit",
- "definition_uri": "https://w3id.org/include/assay/volumeUnit",
- "description": "Unit of sample volume",
- "title": "Volume Unit",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/volumeUnit",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "laboratoryProcedure",
- "definition_uri": "https://w3id.org/include/assay/laboratoryProcedure",
- "description": "Procedure by which Sample was derived from Parent Sample (e.g. Centrifugation, RBC lysis, Lyse/fix buffer, FACS, PAXgene DNA, PAXgene RNA, Qiagen Allprep, Ficoll)",
- "title": "Laboratory Procedure",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/laboratoryProcedure",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "biospecimenStorage",
- "definition_uri": "https://w3id.org/include/assay/biospecimenStorage",
- "description": "Method by which Container is stored (e.g. Minus 80 degrees Celsius, Liquid nitrogen storage)",
- "title": "Biospecimen Storage",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/biospecimenStorage",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "sampleAvailability",
- "definition_uri": "https://w3id.org/include/assay/sampleAvailability",
- "description": "Whether or not the sample is potentially available for sharing through the Virtual Biorepository",
- "title": "Sample Availability",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/sampleAvailability",
- "owner": "Biospecimen",
- "domain_of": [
- "Biospecimen"
- ],
- "range": "enum_sampleAvailability",
- "@type": "SlotDefinition"
- },
- {
- "name": "hasParticipant",
- "definition_uri": "https://w3id.org/include/assay/hasParticipant",
- "description": "Link to a Participant",
- "title": "Has Participant",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/hasParticipant",
- "owner": "Condition",
- "domain_of": [
- "Biospecimen",
- "DataFile",
- "Condition"
- ],
- "range": "Participant",
- "inlined": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "fileId",
- "definition_uri": "https://w3id.org/include/assay/fileId",
- "description": "File identifier, assigned by DCC",
- "title": "File ID",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/fileId",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "fileName",
- "definition_uri": "https://w3id.org/include/assay/fileName",
- "description": "Name of file, assigned by data contributor",
- "title": "File Name",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/fileName",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "string",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "fileHash",
- "definition_uri": "https://w3id.org/include/assay/fileHash",
- "description": "md5 hash of this file for validation (if known)",
- "title": "File Hash",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/fileHash",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "dataAccess",
- "definition_uri": "https://w3id.org/include/assay/dataAccess",
- "description": "Type of access control on this file, determined by DCC",
- "title": "Data Access",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/dataAccess",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "enum_dataAccess",
- "@type": "SlotDefinition"
- },
- {
- "name": "dataCategory",
- "definition_uri": "https://w3id.org/include/assay/dataCategory",
- "description": "General category of data in file (e.g. Clinical, Genomics, Proteomics, Metabolomics, Immune profiling, Transcriptomics)",
- "title": "Data Category",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/dataCategory",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "string",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "dataType",
- "definition_uri": "https://w3id.org/include/assay/dataType",
- "description": "Specific type of data contained in file (e.g. Preprocessed metabolite relative abundance, Absolute protein concentration, Aligned reads, Simple nucleotide variations, GVCF, Gene expression quantifications, Gene fusions, Somatic copy number variations, Somatic structural variations)",
- "title": "Data Type",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/dataType",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "experimentalStrategy",
- "definition_uri": "https://w3id.org/include/assay/experimentalStrategy",
- "description": "Experimental method used to obtain data in file (e.g. Whole genome sequencing, RNAseq, Multiplex immunoassay, Mass spec metabolomics)",
- "title": "Experimental Strategy",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/experimentalStrategy",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "experimentalPlatform",
- "definition_uri": "https://w3id.org/include/assay/experimentalPlatform",
- "description": "Specific platform used to perform experiment (e.g. SOMAscan, MSD, Luminex, Illumina)",
- "title": "Experimental Platform",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/experimentalPlatform",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "fileFormat",
- "definition_uri": "https://w3id.org/include/assay/fileFormat",
- "description": "Format of file (e.g. tsv, cram, gvcf, vcf, maf, txt, pdf, html, png)",
- "title": "File Format",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/fileFormat",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "string",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "fileSize",
- "definition_uri": "https://w3id.org/include/assay/fileSize",
- "description": "Size of file, if known (mainly important if large)",
- "title": "File Size",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/fileSize",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "integer",
- "@type": "SlotDefinition"
- },
- {
- "name": "fileSizeUnit",
- "definition_uri": "https://w3id.org/include/assay/fileSizeUnit",
- "description": "Unit of file size",
- "title": "File Size Unit",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/fileSizeUnit",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "accessUrl",
- "definition_uri": "https://w3id.org/include/assay/accessUrl",
- "description": "URL/URI to file repository location",
- "title": "Access URL",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/accessUrl",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "uriorcurie",
- "@type": "SlotDefinition"
- },
- {
- "name": "publicationDoi",
- "definition_uri": "https://w3id.org/include/assay/publicationDoi",
- "description": "DOI of publication associated with this file, if published",
- "title": "Publication DOI",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/publicationDoi",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "hasBiospecimen",
- "definition_uri": "https://w3id.org/include/assay/hasBiospecimen",
- "description": "Link to a Biospecimen",
- "title": "Has Biospecimen",
- "from_schema": "https://w3id.org/include/assay",
- "slot_uri": "https://w3id.org/include/assay/hasBiospecimen",
- "owner": "DataFile",
- "domain_of": [
- "DataFile"
- ],
- "range": "Biospecimen",
- "inlined": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "participantId",
- "definition_uri": "https://w3id.org/include/participant/participantId",
- "description": "Unique identifier for the participant, assigned by DCC",
- "title": "Participant ID",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/participantId",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "participantExternalId",
- "definition_uri": "https://w3id.org/include/participant/participantExternalId",
- "description": "Unique, de-identified identifier for the participant, assigned by data contributor. External IDs must be two steps removed from personal information in the study records.",
- "title": "Participant External ID",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/participantExternalId",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "string",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "familyId",
- "definition_uri": "https://w3id.org/include/participant/familyId",
- "description": "Unique identifer for family to which Participant belongs, assigned by data contributor",
- "title": "Family ID",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/familyId",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "familyType",
- "definition_uri": "https://w3id.org/include/participant/familyType",
- "description": "Structure of family members participating in the study",
- "title": "Family Type",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/familyType",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "enum_familyType",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "fatherId",
- "definition_uri": "https://w3id.org/include/participant/fatherId",
- "description": "Participant External ID for Participant's father (NA if Participant is not the proband)",
- "title": "Father ID",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/fatherId",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "motherId",
- "definition_uri": "https://w3id.org/include/participant/motherId",
- "description": "Participant External ID for Participant's mother (NA if Participant is not the proband)",
- "title": "Mother ID",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/motherId",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "siblingId",
- "definition_uri": "https://w3id.org/include/participant/siblingId",
- "description": "Participant External ID for Participant's sibling(s) (NA if Participant is not the proband)",
- "title": "Sibling ID",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/siblingId",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "otherFamilyMemberId",
- "definition_uri": "https://w3id.org/include/participant/otherFamilyMemberId",
- "description": "Participant External ID for Participant's other family members (NA if Participant is not the proband)",
- "title": "Other Family Member ID",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/otherFamilyMemberId",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "familyRelationship",
- "definition_uri": "https://w3id.org/include/participant/familyRelationship",
- "description": "Relationship of Participant to proband",
- "title": "Family Relationship",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/familyRelationship",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "enum_familyRelationship",
- "@type": "SlotDefinition"
- },
- {
- "name": "sex",
- "definition_uri": "https://w3id.org/include/participant/sex",
- "description": "Sex of Participant",
- "title": "sex",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/sex",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "enum_sex",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "race",
- "definition_uri": "https://w3id.org/include/participant/race",
- "description": "Race of Participant",
- "title": "Race",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/race",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "enum_race",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "ethnicity",
- "definition_uri": "https://w3id.org/include/participant/ethnicity",
- "description": "Ethnicity of Participant",
- "title": "Ethnicity",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/ethnicity",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "enum_ethnicity",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "downSyndromeStatus",
- "definition_uri": "https://w3id.org/include/participant/downSyndromeStatus",
- "description": "Down Syndrome status of participant",
- "title": "Down Syndrome Status",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/downSyndromeStatus",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "enum_downSyndromeStatus",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "ageAtFirstPatientEngagement",
- "definition_uri": "https://w3id.org/include/participant/ageAtFirstPatientEngagement",
- "description": "Age in days of Participant at first recorded study event (registration/enrollment, visit, observation, sample collection, survey completion, etc.). Age at registration/enrollment is preferred, if available.",
- "title": "Age at First Patient Engagement",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/ageAtFirstPatientEngagement",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "integer",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "firstPatientEngagementEvent",
- "definition_uri": "https://w3id.org/include/participant/firstPatientEngagementEvent",
- "description": "Event for which Age at First Patient Engagement is given (registration/enrollment, visit, observation, sample collection, survey completion, etc.). Age at registration/enrollment is preferred, if available.",
- "title": "First Patient Engagement Event",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/firstPatientEngagementEvent",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "string",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "outcomesVitalStatus",
- "definition_uri": "https://w3id.org/include/participant/outcomesVitalStatus",
- "description": "Whether participant is alive or dead",
- "title": "Outcomes Vital Status",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/outcomesVitalStatus",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "enum_vital_status",
- "@type": "SlotDefinition"
- },
- {
- "name": "ageAtLastVitalStatus",
- "definition_uri": "https://w3id.org/include/participant/ageAtLastVitalStatus",
- "description": "Age in days when participant's vital status was last recorded",
- "title": "Age at Last Vital Status",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/ageAtLastVitalStatus",
- "owner": "Participant",
- "domain_of": [
- "Participant"
- ],
- "range": "integer",
- "@type": "SlotDefinition"
- },
- {
- "name": "hasStudy",
- "definition_uri": "https://w3id.org/include/participant/hasStudy",
- "description": "Link to a Study",
- "title": "Has Study",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/hasStudy",
- "owner": "Condition",
- "domain_of": [
- "Biospecimen",
- "DataFile",
- "Participant",
- "Condition"
- ],
- "range": "Study",
- "inlined": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "eventId",
- "definition_uri": "https://w3id.org/include/participant/eventId",
- "description": "Identifier for event (Visit, Survey completion, Sample collection, etc.) to which the Condition data are linked, if applicable. There may be multiple events linked to a Participant.",
- "title": "Event Id",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/eventId",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "eventType",
- "definition_uri": "https://w3id.org/include/participant/eventType",
- "description": "Type of event for which Event ID is given (Visit, Survey completion, Sample collection, etc.)",
- "title": "Event Type",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/eventType",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "conditionSourceText",
- "definition_uri": "https://w3id.org/include/participant/conditionSourceText",
- "description": "Phenotype or diagnosis, as described by data contributor. The Down Syndrome Genetic Diagnosis will be rolled into this field.",
- "title": "Condition Source Text",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/conditionSourceText",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "ageAtConditionObservation",
- "definition_uri": "https://w3id.org/include/participant/ageAtConditionObservation",
- "description": "Age in days at which condition was observed, recorded, or diagnosed",
- "title": "Age At Condition Observation",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/ageAtConditionObservation",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "integer",
- "@type": "SlotDefinition"
- },
- {
- "name": "conditionInterpretation",
- "definition_uri": "https://w3id.org/include/participant/conditionInterpretation",
- "description": "Whether condition was observed or not",
- "title": "Condition Interpretation",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/conditionInterpretation",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "enum_conditionInterpretation",
- "@type": "SlotDefinition"
- },
- {
- "name": "conditionStatus",
- "definition_uri": "https://w3id.org/include/participant/conditionStatus",
- "description": "Whether the Condition is ongoing, has been resolved, or this is a general history of the condition without known dates",
- "title": "Condition Status",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/conditionStatus",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "enum_conditionStatus",
- "@type": "SlotDefinition"
- },
- {
- "name": "conditionDataSource",
- "definition_uri": "https://w3id.org/include/participant/conditionDataSource",
- "description": "Whether condition information was obtained from medical records or reported by participant/family member",
- "title": "Condition Data Source",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/conditionDataSource",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "enum_conditionDataSource",
- "@type": "SlotDefinition"
- },
- {
- "name": "hpoLabel",
- "definition_uri": "https://w3id.org/include/participant/hpoLabel",
- "description": "Label for condition in the Human Phenotype Ontology (HPO)",
- "title": "Hpo Label",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/hpoLabel",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "hpoCode",
- "definition_uri": "https://w3id.org/include/participant/hpoCode",
- "description": "Code for condition in the Human Phenotype Ontology (HPO)",
- "title": "Hpo Code",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/hpoCode",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "mondoLabel",
- "definition_uri": "https://w3id.org/include/participant/mondoLabel",
- "description": "Label for condition in the Mondo Disease Ontology (MONDO)",
- "title": "Mondo Label",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/mondoLabel",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "mondoCode",
- "definition_uri": "https://w3id.org/include/participant/mondoCode",
- "description": "Code for condition in the Mondo Disease Ontology (Mondo)",
- "title": "Mondo Code",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/mondoCode",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "maxoLabel",
- "definition_uri": "https://w3id.org/include/participant/maxoLabel",
- "description": "Label for condition in the Medical Action Ontology (MAXO)",
- "title": "Maxo Label",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/maxoLabel",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "maxoCode",
- "definition_uri": "https://w3id.org/include/participant/maxoCode",
- "description": "Code for condition in the Medical Action Ontology (MAXO)",
- "title": "Maxo Code",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/maxoCode",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "otherLabel",
- "definition_uri": "https://w3id.org/include/participant/otherLabel",
- "description": "Label for condition in another ontology (if no match in HPO, MONDO, or MAXO)",
- "title": "Other Label",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/otherLabel",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "otherCode",
- "definition_uri": "https://w3id.org/include/participant/otherCode",
- "description": "Code for condition in another ontology (if no match in HPO, MONDO, or MAXO)",
- "title": "Other Code",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/otherCode",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "measureType",
- "definition_uri": "https://w3id.org/include/participant/measureType",
- "description": "Type of measure. A Measure is an observation with a numeric value, e.g. Weight, Height, BMI, Blood glucose, Bone density, Blast percentage, etc.",
- "title": "Measure Type",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/measureType",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "measureValue",
- "definition_uri": "https://w3id.org/include/participant/measureValue",
- "description": "Numeric value of Measure",
- "title": "Measure Value",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/measureValue",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "integer",
- "@type": "SlotDefinition"
- },
- {
- "name": "measureUnit",
- "definition_uri": "https://w3id.org/include/participant/measureUnit",
- "description": "Unit that is associated with Measure Value (e.g. kg, cm, %, x10^9/L, etc.)",
- "title": "Measure Unit",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/measureUnit",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- },
- {
- "name": "ageAtMeasurement",
- "definition_uri": "https://w3id.org/include/participant/ageAtMeasurement",
- "description": "Age in days at which measurement was performed",
- "title": "Age At Measurement",
- "from_schema": "https://w3id.org/include/participant",
- "slot_uri": "https://w3id.org/include/participant/ageAtMeasurement",
- "owner": "Condition",
- "domain_of": [
- "Condition"
- ],
- "range": "integer",
- "@type": "SlotDefinition"
- },
- {
- "name": "studyCode",
- "definition_uri": "https://w3id.org/include/study/studyCode",
- "description": "Unique identifer for the study, assigned by DCC",
- "title": "Study Code",
- "from_schema": "https://w3id.org/include/study",
- "slot_uri": "https://w3id.org/include/study/studyCode",
- "owner": "Study",
- "domain_of": [
- "Study"
- ],
- "range": "enum_studyCode",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "studyName",
- "definition_uri": "https://w3id.org/include/study/studyName",
- "description": "Full name of the study, chosen by data contributor",
- "title": "Study Name",
- "from_schema": "https://w3id.org/include/study",
- "slot_uri": "https://w3id.org/include/study/studyName",
- "owner": "Study",
- "domain_of": [
- "Study"
- ],
- "range": "string",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "program",
- "definition_uri": "https://w3id.org/include/study/program",
- "description": "Funding source for the study",
- "title": "Program",
- "from_schema": "https://w3id.org/include/study",
- "slot_uri": "https://w3id.org/include/study/program",
- "owner": "Study",
- "domain_of": [
- "Study"
- ],
- "range": "enum_program",
- "required": true,
- "@type": "SlotDefinition"
- },
- {
- "name": "dbgap",
- "definition_uri": "https://w3id.org/include/study/dbgap",
- "description": "dbGaP study accession code",
- "title": "dbGaP",
- "from_schema": "https://w3id.org/include/study",
- "slot_uri": "https://w3id.org/include/study/dbgap",
- "owner": "Study",
- "domain_of": [
- "Study"
- ],
- "range": "string",
- "@type": "SlotDefinition"
- }
- ],
- "classes": [
- {
- "name": "Thing",
- "definition_uri": "https://w3id.org/include/core/Thing",
- "annotations": [
- {
- "tag": "required",
- "value": "False",
- "@type": "Annotation"
- }
- ],
- "description": "Highest Level Class",
- "title": "Thing",
- "from_schema": "https://w3id.org/include/core",
- "slot_usage": {},
- "class_uri": "https://w3id.org/include/core/Thing",
- "@type": "ClassDefinition"
- },
- {
- "name": "Biospecimen",
- "definition_uri": "https://w3id.org/include/assay/Biospecimen",
- "annotations": [
- {
- "tag": "required",
- "value": "True",
- "@type": "Annotation"
- },
- {
- "tag": "requires_component",
- "value": "Study,Participant,DataFile",
- "@type": "Annotation"
- }
- ],
- "description": "A Biospecimen Collected from A Participant",
- "title": "Biospecimen",
- "from_schema": "https://w3id.org/include/assay",
- "is_a": "Thing",
- "slots": [
- "hasStudy",
- "hasParticipant",
- "sampleId",
- "sampleType",
- "ageAtBiospecimenCollection",
- "parentSampleId",
- "parentSampleType",
- "collectionId",
- "collectionSampleType",
- "containerId",
- "volume",
- "volumeUnit",
- "laboratoryProcedure",
- "biospecimenStorage",
- "sampleAvailability"
- ],
- "slot_usage": {},
- "class_uri": "https://w3id.org/include/assay/Biospecimen",
- "@type": "ClassDefinition"
- },
- {
- "name": "DataFile",
- "definition_uri": "https://w3id.org/include/assay/DataFile",
- "annotations": [
- {
- "tag": "required",
- "value": "True",
- "@type": "Annotation"
- },
- {
- "tag": "requires_component",
- "value": "Study,Participant,Biospecimen",
- "@type": "Annotation"
- }
- ],
- "description": "A DataFile Associated with a Participant or Study or Biospecimen",
- "title": "Data File",
- "from_schema": "https://w3id.org/include/assay",
- "is_a": "Thing",
- "slots": [
- "hasStudy",
- "hasParticipant",
- "hasBiospecimen",
- "fileId",
- "fileName",
- "fileHash",
- "dataAccess",
- "dataCategory",
- "dataType",
- "experimentalStrategy",
- "experimentalPlatform",
- "fileFormat",
- "fileSize",
- "fileSizeUnit",
- "accessUrl",
- "publicationDoi"
- ],
- "slot_usage": {},
- "class_uri": "https://w3id.org/include/assay/DataFile",
- "@type": "ClassDefinition"
- },
- {
- "name": "Participant",
- "definition_uri": "https://w3id.org/include/participant/Participant",
- "annotations": [
- {
- "tag": "required",
- "value": "True",
- "@type": "Annotation"
- },
- {
- "tag": "requires_component",
- "value": "Study,DataFile",
- "@type": "Annotation"
- }
- ],
- "description": "Demographic and clinical information about the participant",
- "title": "Participant",
- "from_schema": "https://w3id.org/include/participant",
- "is_a": "Thing",
- "slots": [
- "hasStudy",
- "participantId",
- "participantExternalId",
- "familyId",
- "familyType",
- "fatherId",
- "motherId",
- "siblingId",
- "otherFamilyMemberId",
- "familyRelationship",
- "sex",
- "race",
- "ethnicity",
- "downSyndromeStatus",
- "ageAtFirstPatientEngagement",
- "firstPatientEngagementEvent",
- "outcomesVitalStatus",
- "ageAtLastVitalStatus"
- ],
- "slot_usage": {},
- "class_uri": "https://w3id.org/include/participant/Participant",
- "@type": "ClassDefinition"
- },
- {
- "name": "Condition",
- "definition_uri": "https://w3id.org/include/participant/Condition",
- "annotations": [
- {
- "tag": "required",
- "value": "False",
- "@type": "Annotation"
- }
- ],
- "description": "Co-occurring conditions and other observations for the participant",
- "title": "Condition",
- "from_schema": "https://w3id.org/include/participant",
- "is_a": "Thing",
- "slots": [
- "hasStudy",
- "hasParticipant",
- "eventId",
- "eventType",
- "conditionSourceText",
- "ageAtConditionObservation",
- "conditionInterpretation",
- "conditionStatus",
- "conditionDataSource",
- "hpoLabel",
- "hpoCode",
- "mondoLabel",
- "mondoCode",
- "maxoLabel",
- "maxoCode",
- "otherLabel",
- "otherCode",
- "measureType",
- "measureValue",
- "measureUnit",
- "ageAtMeasurement"
- ],
- "slot_usage": {},
- "class_uri": "https://w3id.org/include/participant/Condition",
- "@type": "ClassDefinition"
- },
- {
- "name": "Study",
- "definition_uri": "https://w3id.org/include/study/Study",
- "annotations": [
- {
- "tag": "required",
- "value": "True",
- "@type": "Annotation"
- }
- ],
- "description": "General information about the study",
- "title": "Study",
- "from_schema": "https://w3id.org/include/study",
- "is_a": "Thing",
- "slots": [
- "studyCode",
- "studyName",
- "program",
- "dbgap"
- ],
- "slot_usage": {},
- "class_uri": "https://w3id.org/include/study/Study",
- "@type": "ClassDefinition"
- }
- ],
- "metamodel_version": "1.7.0",
- "source_file": "include_schema.yaml",
- "source_file_date": "2022-11-29T13:33:41",
- "source_file_size": 433,
- "generation_date": "2023-03-03T10:38:27",
- "@type": "SchemaDefinition",
- "@context": [
- "project/jsonld/include_schema.context.jsonld",
- "https://w3id.org/linkml/types.context.jsonld",
- "include_core.context.jsonld",
- "include_assay.context.jsonld",
- "include_participant.context.jsonld",
- "include_study.context.jsonld",
- {
- "@base": "https://w3id.org/include/"
- }
- ]
-}
diff --git a/project/jsonschema/include_schema.schema.json b/project/jsonschema/include_schema.schema.json
deleted file mode 100644
index 9b1d1214..00000000
--- a/project/jsonschema/include_schema.schema.json
+++ /dev/null
@@ -1,551 +0,0 @@
-{
- "$defs": {
- "Biospecimen": {
- "additionalProperties": false,
- "description": "A Biospecimen Collected from A Participant",
- "properties": {
- "ageAtBiospecimenCollection": {
- "description": "Age in days of participant at time of biospecimen collection",
- "type": "integer"
- },
- "biospecimenStorage": {
- "description": "Method by which Container is stored (e.g. Minus 80 degrees Celsius, Liquid nitrogen storage)",
- "type": "string"
- },
- "collectionId": {
- "description": "Identifier for the eldest sample in a lineage of processed, pooled, or aliquoted samples - typically the material actually collected from the Participant. This may be the same as Parent Sample ID or Sample ID (if no processing was performed).",
- "type": "string"
- },
- "collectionSampleType": {
- "description": "Type of biological material comprising the Collected Sample (e.g. Whole blood, Not reported, Saliva, Derived cell line)",
- "type": "string"
- },
- "containerId": {
- "description": "Identifier for specific container/aliquot of sample, if applicable. For example, distinct aliquots of a sample will have the same Sample ID but different Container IDs.",
- "type": "string"
- },
- "hasParticipant": {
- "$ref": "#/$defs/Participant",
- "description": "Link to a Participant"
- },
- "hasStudy": {
- "$ref": "#/$defs/Study",
- "description": "Link to a Study"
- },
- "laboratoryProcedure": {
- "description": "Procedure by which Sample was derived from Parent Sample (e.g. Centrifugation, RBC lysis, Lyse/fix buffer, FACS, PAXgene DNA, PAXgene RNA, Qiagen Allprep, Ficoll)",
- "type": "string"
- },
- "parentSampleId": {
- "description": "Identifier for the direct parent from which Sample was derived, processed, pooled, etc. (if applicable)",
- "type": "string"
- },
- "parentSampleType": {
- "description": "Type of biological material comprising the Parent Sample (e.g. Peripheral Whole Blood, Derived Cell Line, Saliva, Whole blood, WBCs)",
- "type": "string"
- },
- "sampleAvailability": {
- "$ref": "#/$defs/EnumSampleAvailability",
- "description": "Whether or not the sample is potentially available for sharing through the Virtual Biorepository"
- },
- "sampleId": {
- "description": "Identifier for sample. A sample is a unique biological material; two samples with two different IDs are biologically distinct.",
- "type": "string"
- },
- "sampleType": {
- "description": "Type of biological material comprising the Sample (e.g. Plasma, White blood cells, Red blood cells, DNA, RNA, Peripheral blood mononuclear cells, CD4+ Tconv cells, NK cells, Monocytes, CD8+ T cells, B cells, Granulocytes, Treg cells)",
- "type": "string"
- },
- "volume": {
- "description": "Amount of sample in container",
- "type": "number"
- },
- "volumeUnit": {
- "description": "Unit of sample volume",
- "type": "string"
- }
- },
- "required": [
- "sampleId",
- "sampleType"
- ],
- "title": "Biospecimen",
- "type": "object"
- },
- "Condition": {
- "additionalProperties": false,
- "description": "Co-occurring conditions and other observations for the participant",
- "properties": {
- "ageAtConditionObservation": {
- "description": "Age in days at which condition was observed, recorded, or diagnosed",
- "type": "integer"
- },
- "ageAtMeasurement": {
- "description": "Age in days at which measurement was performed",
- "type": "integer"
- },
- "conditionDataSource": {
- "$ref": "#/$defs/EnumConditionDataSource",
- "description": "Whether condition information was obtained from medical records or reported by participant/family member"
- },
- "conditionInterpretation": {
- "$ref": "#/$defs/EnumConditionInterpretation",
- "description": "Whether condition was observed or not"
- },
- "conditionSourceText": {
- "description": "Phenotype or diagnosis, as described by data contributor. The Down Syndrome Genetic Diagnosis will be rolled into this field.",
- "type": "string"
- },
- "conditionStatus": {
- "$ref": "#/$defs/EnumConditionStatus",
- "description": "Whether the Condition is ongoing, has been resolved, or this is a general history of the condition without known dates"
- },
- "eventId": {
- "description": "Identifier for event (Visit, Survey completion, Sample collection, etc.) to which the Condition data are linked, if applicable. There may be multiple events linked to a Participant.",
- "type": "string"
- },
- "eventType": {
- "description": "Type of event for which Event ID is given (Visit, Survey completion, Sample collection, etc.)",
- "type": "string"
- },
- "hasParticipant": {
- "$ref": "#/$defs/Participant",
- "description": "Link to a Participant"
- },
- "hasStudy": {
- "$ref": "#/$defs/Study",
- "description": "Link to a Study"
- },
- "hpoCode": {
- "description": "Code for condition in the Human Phenotype Ontology (HPO)",
- "type": "string"
- },
- "hpoLabel": {
- "description": "Label for condition in the Human Phenotype Ontology (HPO)",
- "type": "string"
- },
- "maxoCode": {
- "description": "Code for condition in the Medical Action Ontology (MAXO)",
- "type": "string"
- },
- "maxoLabel": {
- "description": "Label for condition in the Medical Action Ontology (MAXO)",
- "type": "string"
- },
- "measureType": {
- "description": "Type of measure. A Measure is an observation with a numeric value, e.g. Weight, Height, BMI, Blood glucose, Bone density, Blast percentage, etc.",
- "type": "string"
- },
- "measureUnit": {
- "description": "Unit that is associated with Measure Value (e.g. kg, cm, %, x10^9/L, etc.)",
- "type": "string"
- },
- "measureValue": {
- "description": "Numeric value of Measure",
- "type": "integer"
- },
- "mondoCode": {
- "description": "Code for condition in the Mondo Disease Ontology (Mondo)",
- "type": "string"
- },
- "mondoLabel": {
- "description": "Label for condition in the Mondo Disease Ontology (MONDO)",
- "type": "string"
- },
- "otherCode": {
- "description": "Code for condition in another ontology (if no match in HPO, MONDO, or MAXO)",
- "type": "string"
- },
- "otherLabel": {
- "description": "Label for condition in another ontology (if no match in HPO, MONDO, or MAXO)",
- "type": "string"
- }
- },
- "title": "Condition",
- "type": "object"
- },
- "DataFile": {
- "additionalProperties": false,
- "description": "A DataFile Associated with a Participant or Study or Biospecimen",
- "properties": {
- "accessUrl": {
- "description": "URL/URI to file repository location",
- "type": "string"
- },
- "dataAccess": {
- "$ref": "#/$defs/EnumDataAccess",
- "description": "Type of access control on this file, determined by DCC"
- },
- "dataCategory": {
- "description": "General category of data in file (e.g. Clinical, Genomics, Proteomics, Metabolomics, Immune profiling, Transcriptomics)",
- "type": "string"
- },
- "dataType": {
- "description": "Specific type of data contained in file (e.g. Preprocessed metabolite relative abundance, Absolute protein concentration, Aligned reads, Simple nucleotide variations, GVCF, Gene expression quantifications, Gene fusions, Somatic copy number variations, Somatic structural variations)",
- "type": "string"
- },
- "experimentalPlatform": {
- "description": "Specific platform used to perform experiment (e.g. SOMAscan, MSD, Luminex, Illumina)",
- "type": "string"
- },
- "experimentalStrategy": {
- "description": "Experimental method used to obtain data in file (e.g. Whole genome sequencing, RNAseq, Multiplex immunoassay, Mass spec metabolomics)",
- "type": "string"
- },
- "fileFormat": {
- "description": "Format of file (e.g. tsv, cram, gvcf, vcf, maf, txt, pdf, html, png)",
- "type": "string"
- },
- "fileHash": {
- "description": "md5 hash of this file for validation (if known)",
- "type": "string"
- },
- "fileId": {
- "description": "File identifier, assigned by DCC",
- "type": "string"
- },
- "fileName": {
- "description": "Name of file, assigned by data contributor",
- "type": "string"
- },
- "fileSize": {
- "description": "Size of file, if known (mainly important if large)",
- "type": "integer"
- },
- "fileSizeUnit": {
- "description": "Unit of file size",
- "type": "string"
- },
- "hasBiospecimen": {
- "$ref": "#/$defs/Biospecimen",
- "description": "Link to a Biospecimen"
- },
- "hasParticipant": {
- "$ref": "#/$defs/Participant",
- "description": "Link to a Participant"
- },
- "hasStudy": {
- "$ref": "#/$defs/Study",
- "description": "Link to a Study"
- },
- "publicationDoi": {
- "description": "DOI of publication associated with this file, if published",
- "type": "string"
- }
- },
- "required": [
- "fileName",
- "dataCategory",
- "fileFormat"
- ],
- "title": "DataFile",
- "type": "object"
- },
- "EnumConditionDataSource": {
- "description": "",
- "enum": [
- "clinical",
- "self_reported"
- ],
- "title": "EnumConditionDataSource",
- "type": "string"
- },
- "EnumConditionInterpretation": {
- "description": "",
- "enum": [
- "observed",
- "not_observed"
- ],
- "title": "EnumConditionInterpretation",
- "type": "string"
- },
- "EnumConditionStatus": {
- "description": "",
- "enum": [
- "current",
- "resolved",
- "history_of"
- ],
- "title": "EnumConditionStatus",
- "type": "string"
- },
- "EnumDataAccess": {
- "description": "",
- "enum": [
- "controlled",
- "open",
- "registered"
- ],
- "title": "EnumDataAccess",
- "type": "string"
- },
- "EnumDownSyndromeStatus": {
- "description": "",
- "enum": [
- "d21",
- "t21"
- ],
- "title": "EnumDownSyndromeStatus",
- "type": "string"
- },
- "EnumEthnicity": {
- "description": "",
- "enum": [
- "hispanic_or_latino",
- "not_hispanic_or_latino",
- "prefer_not_to_answer",
- "unknown"
- ],
- "title": "EnumEthnicity",
- "type": "string"
- },
- "EnumFamilyRelationship": {
- "description": "",
- "enum": [
- "proband",
- "father",
- "mother",
- "sibling",
- "other_relative",
- "unrelated_control"
- ],
- "title": "EnumFamilyRelationship",
- "type": "string"
- },
- "EnumFamilyType": {
- "description": "",
- "enum": [
- "control_only",
- "duo",
- "other",
- "proband_only",
- "trio",
- "trio_plus"
- ],
- "title": "EnumFamilyType",
- "type": "string"
- },
- "EnumProgram": {
- "description": "",
- "enum": [
- "include",
- "kf"
- ],
- "title": "EnumProgram",
- "type": "string"
- },
- "EnumRace": {
- "description": "",
- "enum": [
- "american_indian_or_alaskan_native",
- "asian",
- "black_or_african_american",
- "more_than_one_race",
- "native_hawaiian_or_other_pacific_islander",
- "other",
- "white",
- "prefer_not_to_answer",
- "unknown",
- "east_asian",
- "latin_american",
- "middle_eastern_or_north_african",
- "south_asian"
- ],
- "title": "EnumRace",
- "type": "string"
- },
- "EnumSampleAvailability": {
- "description": "",
- "enum": [
- "available",
- "unavailable"
- ],
- "title": "EnumSampleAvailability",
- "type": "string"
- },
- "EnumSex": {
- "description": "",
- "enum": [
- "female",
- "male",
- "other",
- "unknown"
- ],
- "title": "EnumSex",
- "type": "string"
- },
- "EnumStudyCode": {
- "description": "",
- "enum": [
- "abcds",
- "ads",
- "aecom_ds",
- "brainpower",
- "bri_dsr",
- "charge_ds",
- "ds_brain",
- "ds_cog_all",
- "ds_cog_aml",
- "ds_determined",
- "ds_hsat",
- "ds_isp",
- "ds_nexus",
- "ds_pals",
- "ds_pcgc",
- "ds_sleep",
- "ds360_chd",
- "dsc",
- "ecods",
- "exceeds",
- "htp",
- "trc_ds",
- "x01_desmith",
- "x01_hakon"
- ],
- "title": "EnumStudyCode",
- "type": "string"
- },
- "EnumVitalStatus": {
- "description": "",
- "enum": [
- "dead",
- "alive",
- "unknown_or_not_available"
- ],
- "title": "EnumVitalStatus",
- "type": "string"
- },
- "Participant": {
- "additionalProperties": false,
- "description": "Demographic and clinical information about the participant",
- "properties": {
- "ageAtFirstPatientEngagement": {
- "description": "Age in days of Participant at first recorded study event (registration/enrollment, visit, observation, sample collection, survey completion, etc.). Age at registration/enrollment is preferred, if available.",
- "type": "integer"
- },
- "ageAtLastVitalStatus": {
- "description": "Age in days when participant's vital status was last recorded",
- "type": "integer"
- },
- "downSyndromeStatus": {
- "$ref": "#/$defs/EnumDownSyndromeStatus",
- "description": "Down Syndrome status of participant"
- },
- "ethnicity": {
- "$ref": "#/$defs/EnumEthnicity",
- "description": "Ethnicity of Participant"
- },
- "familyId": {
- "description": "Unique identifer for family to which Participant belongs, assigned by data contributor",
- "type": "string"
- },
- "familyRelationship": {
- "$ref": "#/$defs/EnumFamilyRelationship",
- "description": "Relationship of Participant to proband"
- },
- "familyType": {
- "$ref": "#/$defs/EnumFamilyType",
- "description": "Structure of family members participating in the study"
- },
- "fatherId": {
- "description": "Participant External ID for Participant's father (NA if Participant is not the proband)",
- "type": "string"
- },
- "firstPatientEngagementEvent": {
- "description": "Event for which Age at First Patient Engagement is given (registration/enrollment, visit, observation, sample collection, survey completion, etc.). Age at registration/enrollment is preferred, if available.",
- "type": "string"
- },
- "hasStudy": {
- "$ref": "#/$defs/Study",
- "description": "Link to a Study"
- },
- "motherId": {
- "description": "Participant External ID for Participant's mother (NA if Participant is not the proband)",
- "type": "string"
- },
- "otherFamilyMemberId": {
- "description": "Participant External ID for Participant's other family members (NA if Participant is not the proband)",
- "type": "string"
- },
- "outcomesVitalStatus": {
- "$ref": "#/$defs/EnumVitalStatus",
- "description": "Whether participant is alive or dead"
- },
- "participantExternalId": {
- "description": "Unique, de-identified identifier for the participant, assigned by data contributor. External IDs must be two steps removed from personal information in the study records.",
- "type": "string"
- },
- "participantId": {
- "description": "Unique identifier for the participant, assigned by DCC",
- "type": "string"
- },
- "race": {
- "$ref": "#/$defs/EnumRace",
- "description": "Race of Participant"
- },
- "sex": {
- "$ref": "#/$defs/EnumSex",
- "description": "Sex of Participant"
- },
- "siblingId": {
- "description": "Participant External ID for Participant's sibling(s) (NA if Participant is not the proband)",
- "type": "string"
- }
- },
- "required": [
- "participantExternalId",
- "familyType",
- "sex",
- "race",
- "ethnicity",
- "downSyndromeStatus",
- "ageAtFirstPatientEngagement",
- "firstPatientEngagementEvent"
- ],
- "title": "Participant",
- "type": "object"
- },
- "Study": {
- "additionalProperties": false,
- "description": "General information about the study",
- "properties": {
- "dbgap": {
- "description": "dbGaP study accession code",
- "type": "string"
- },
- "program": {
- "$ref": "#/$defs/EnumProgram",
- "description": "Funding source for the study"
- },
- "studyCode": {
- "$ref": "#/$defs/EnumStudyCode",
- "description": "Unique identifer for the study, assigned by DCC"
- },
- "studyName": {
- "description": "Full name of the study, chosen by data contributor",
- "type": "string"
- }
- },
- "required": [
- "studyCode",
- "studyName",
- "program"
- ],
- "title": "Study",
- "type": "object"
- },
- "Thing": {
- "additionalProperties": false,
- "description": "Highest Level Class",
- "title": "Thing",
- "type": "object"
- }
- },
- "$id": "https://w3id.org/include",
- "$schema": "http://json-schema.org/draft-07/schema#",
- "additionalProperties": true,
- "metamodel_version": "1.7.0",
- "title": "include-schema",
- "type": "object",
- "version": null
-}
\ No newline at end of file
diff --git a/project/owl/include_schema.owl.ttl b/project/owl/include_schema.owl.ttl
deleted file mode 100644
index 723c4d2f..00000000
--- a/project/owl/include_schema.owl.ttl
+++ /dev/null
@@ -1,1373 +0,0 @@
-@prefix IAO: .
-@prefix dcterms: .
-@prefix include: .
-@prefix linkml: .
-@prefix owl: .
-@prefix rdf: .
-@prefix rdfs: .
-@prefix skos: .
-@prefix xsd: .
-
- a owl:Ontology ;
- rdfs:label "include-schema" ;
- IAO:0000700 ;
- dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
- linkml:generation_date "2023-03-03T10:38:32" ;
- linkml:metamodel_version "1.7.0" ;
- linkml:source_file "include_schema.yaml" ;
- linkml:source_file_date "2022-11-29T13:33:41" ;
- linkml:source_file_size 433 .
-
- a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "DataFile" ;
- dcterms:title "Data File" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:onClass linkml:String ;
- owl:onProperty ;
- owl:qualifiedCardinality 1 ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:Integer ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:onClass linkml:String ;
- owl:onProperty ;
- owl:qualifiedCardinality 1 ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:Uriorcurie ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:onClass linkml:String ;
- owl:onProperty ;
- owl:qualifiedCardinality 1 ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- ;
- skos:definition "A DataFile Associated with a Participant or Study or Biospecimen" ;
- include:required "True" ;
- include:requires_component "Study,Participant,Biospecimen" .
-
- a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "Condition" ;
- dcterms:title "Condition" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:Integer ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:Integer ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:Integer ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- ;
- skos:definition "Co-occurring conditions and other observations for the participant" ;
- include:required "False" .
-
-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" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "accessUrl" ;
- dcterms:title "Access URL" ;
- rdfs:range linkml:Uriorcurie ;
- skos:definition "URL/URI to file repository location" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "ageAtBiospecimenCollection" ;
- dcterms:title "Age At Biospecimen Collection" ;
- rdfs:range linkml:Integer ;
- skos:definition "Age in days of participant at time of biospecimen collection" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "biospecimenStorage" ;
- dcterms:title "Biospecimen Storage" ;
- rdfs:range linkml:String ;
- skos:definition "Method by which Container is stored (e.g. Minus 80 degrees Celsius, Liquid nitrogen storage)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "collectionId" ;
- dcterms:title "Collection ID" ;
- rdfs:range linkml:String ;
- skos:definition "Identifier for the eldest sample in a lineage of processed, pooled, or aliquoted samples - typically the material actually collected from the Participant. This may be the same as Parent Sample ID or Sample ID (if no processing was performed)." .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "collectionSampleType" ;
- dcterms:title "Collection Sample Type" ;
- rdfs:range linkml:String ;
- skos:definition "Type of biological material comprising the Collected Sample (e.g. Whole blood, Not reported, Saliva, Derived cell line)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "containerId" ;
- dcterms:title "Container ID" ;
- rdfs:range linkml:String ;
- skos:definition "Identifier for specific container/aliquot of sample, if applicable. For example, distinct aliquots of a sample will have the same Sample ID but different Container IDs." .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "dataAccess" ;
- dcterms:title "Data Access" ;
- rdfs:range ;
- skos:definition "Type of access control on this file, determined by DCC" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "dataCategory" ;
- dcterms:title "Data Category" ;
- rdfs:range linkml:String ;
- skos:definition "General category of data in file (e.g. Clinical, Genomics, Proteomics, Metabolomics, Immune profiling, Transcriptomics)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "dataType" ;
- dcterms:title "Data Type" ;
- rdfs:range linkml:String ;
- skos:definition "Specific type of data contained in file (e.g. Preprocessed metabolite relative abundance, Absolute protein concentration, Aligned reads, Simple nucleotide variations, GVCF, Gene expression quantifications, Gene fusions, Somatic copy number variations, Somatic structural variations)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "experimentalPlatform" ;
- dcterms:title "Experimental Platform" ;
- rdfs:range linkml:String ;
- skos:definition "Specific platform used to perform experiment (e.g. SOMAscan, MSD, Luminex, Illumina)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "experimentalStrategy" ;
- dcterms:title "Experimental Strategy" ;
- rdfs:range linkml:String ;
- skos:definition "Experimental method used to obtain data in file (e.g. Whole genome sequencing, RNAseq, Multiplex immunoassay, Mass spec metabolomics)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "fileFormat" ;
- dcterms:title "File Format" ;
- rdfs:range linkml:String ;
- skos:definition "Format of file (e.g. tsv, cram, gvcf, vcf, maf, txt, pdf, html, png)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "fileHash" ;
- dcterms:title "File Hash" ;
- rdfs:range linkml:String ;
- skos:definition "md5 hash of this file for validation (if known)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "fileId" ;
- dcterms:title "File ID" ;
- rdfs:range linkml:String ;
- skos:definition "File identifier, assigned by DCC" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "fileName" ;
- dcterms:title "File Name" ;
- rdfs:range linkml:String ;
- skos:definition "Name of file, assigned by data contributor" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "fileSize" ;
- dcterms:title "File Size" ;
- rdfs:range linkml:Integer ;
- skos:definition "Size of file, if known (mainly important if large)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "fileSizeUnit" ;
- dcterms:title "File Size Unit" ;
- rdfs:range linkml:String ;
- skos:definition "Unit of file size" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "hasBiospecimen" ;
- dcterms:title "Has Biospecimen" ;
- rdfs:range ;
- skos:definition "Link to a Biospecimen" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "laboratoryProcedure" ;
- dcterms:title "Laboratory Procedure" ;
- rdfs:range linkml:String ;
- skos:definition "Procedure by which Sample was derived from Parent Sample (e.g. Centrifugation, RBC lysis, Lyse/fix buffer, FACS, PAXgene DNA, PAXgene RNA, Qiagen Allprep, Ficoll)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "parentSampleId" ;
- dcterms:title "Parent Sample Id" ;
- rdfs:range linkml:String ;
- skos:definition "Identifier for the direct parent from which Sample was derived, processed, pooled, etc. (if applicable)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "parentSampleType" ;
- dcterms:title "Parent Sample Type" ;
- rdfs:range linkml:String ;
- skos:definition "Type of biological material comprising the Parent Sample (e.g. Peripheral Whole Blood, Derived Cell Line, Saliva, Whole blood, WBCs)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "publicationDoi" ;
- dcterms:title "Publication DOI" ;
- rdfs:range linkml:String ;
- skos:definition "DOI of publication associated with this file, if published" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "sampleAvailability" ;
- dcterms:title "Sample Availability" ;
- rdfs:range ;
- skos:definition "Whether or not the sample is potentially available for sharing through the Virtual Biorepository" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "sampleId" ;
- dcterms:title "Sample ID" ;
- rdfs:range linkml:String ;
- skos:definition "Identifier for sample. A sample is a unique biological material; two samples with two different IDs are biologically distinct." .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "sampleType" ;
- dcterms:title "Sample Type" ;
- rdfs:range linkml:String ;
- skos:definition "Type of biological material comprising the Sample (e.g. Plasma, White blood cells, Red blood cells, DNA, RNA, Peripheral blood mononuclear cells, CD4+ Tconv cells, NK cells, Monocytes, CD8+ T cells, B cells, Granulocytes, Treg cells)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "volume" ;
- dcterms:title "Volume" ;
- rdfs:range linkml:Float ;
- skos:definition "Amount of sample in container" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "volumeUnit" ;
- dcterms:title "Volume Unit" ;
- rdfs:range linkml:String ;
- skos:definition "Unit of sample volume" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "ageAtConditionObservation" ;
- dcterms:title "Age At Condition Observation" ;
- rdfs:range linkml:Integer ;
- skos:definition "Age in days at which condition was observed, recorded, or diagnosed" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "ageAtFirstPatientEngagement" ;
- dcterms:title "Age at First Patient Engagement" ;
- rdfs:range linkml:Integer ;
- skos:definition "Age in days of Participant at first recorded study event (registration/enrollment, visit, observation, sample collection, survey completion, etc.). Age at registration/enrollment is preferred, if available." .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "ageAtLastVitalStatus" ;
- dcterms:title "Age at Last Vital Status" ;
- rdfs:range linkml:Integer ;
- skos:definition "Age in days when participant's vital status was last recorded" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "ageAtMeasurement" ;
- dcterms:title "Age At Measurement" ;
- rdfs:range linkml:Integer ;
- skos:definition "Age in days at which measurement was performed" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "conditionDataSource" ;
- dcterms:title "Condition Data Source" ;
- rdfs:range ;
- skos:definition "Whether condition information was obtained from medical records or reported by participant/family member" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "conditionInterpretation" ;
- dcterms:title "Condition Interpretation" ;
- rdfs:range ;
- skos:definition "Whether condition was observed or not" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "conditionSourceText" ;
- dcterms:title "Condition Source Text" ;
- rdfs:range linkml:String ;
- skos:definition "Phenotype or diagnosis, as described by data contributor. The Down Syndrome Genetic Diagnosis will be rolled into this field." .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "conditionStatus" ;
- dcterms:title "Condition Status" ;
- rdfs:range ;
- skos:definition "Whether the Condition is ongoing, has been resolved, or this is a general history of the condition without known dates" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "downSyndromeStatus" ;
- dcterms:title "Down Syndrome Status" ;
- rdfs:range ;
- skos:definition "Down Syndrome status of participant" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "ethnicity" ;
- dcterms:title "Ethnicity" ;
- rdfs:range ;
- skos:definition "Ethnicity of Participant" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "eventId" ;
- dcterms:title "Event Id" ;
- rdfs:range linkml:String ;
- skos:definition "Identifier for event (Visit, Survey completion, Sample collection, etc.) to which the Condition data are linked, if applicable. There may be multiple events linked to a Participant." .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "eventType" ;
- dcterms:title "Event Type" ;
- rdfs:range linkml:String ;
- skos:definition "Type of event for which Event ID is given (Visit, Survey completion, Sample collection, etc.)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "familyId" ;
- dcterms:title "Family ID" ;
- rdfs:range linkml:String ;
- skos:definition "Unique identifer for family to which Participant belongs, assigned by data contributor" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "familyRelationship" ;
- dcterms:title "Family Relationship" ;
- rdfs:range ;
- skos:definition "Relationship of Participant to proband" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "familyType" ;
- dcterms:title "Family Type" ;
- rdfs:range ;
- skos:definition "Structure of family members participating in the study" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "fatherId" ;
- dcterms:title "Father ID" ;
- rdfs:range linkml:String ;
- skos:definition "Participant External ID for Participant's father (NA if Participant is not the proband)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "firstPatientEngagementEvent" ;
- dcterms:title "First Patient Engagement Event" ;
- rdfs:range linkml:String ;
- skos:definition "Event for which Age at First Patient Engagement is given (registration/enrollment, visit, observation, sample collection, survey completion, etc.). Age at registration/enrollment is preferred, if available." .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "hpoCode" ;
- dcterms:title "Hpo Code" ;
- rdfs:range linkml:String ;
- skos:definition "Code for condition in the Human Phenotype Ontology (HPO)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "hpoLabel" ;
- dcterms:title "Hpo Label" ;
- rdfs:range linkml:String ;
- skos:definition "Label for condition in the Human Phenotype Ontology (HPO)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "maxoCode" ;
- dcterms:title "Maxo Code" ;
- rdfs:range linkml:String ;
- skos:definition "Code for condition in the Medical Action Ontology (MAXO)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "maxoLabel" ;
- dcterms:title "Maxo Label" ;
- rdfs:range linkml:String ;
- skos:definition "Label for condition in the Medical Action Ontology (MAXO)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "measureType" ;
- dcterms:title "Measure Type" ;
- rdfs:range linkml:String ;
- skos:definition "Type of measure. A Measure is an observation with a numeric value, e.g. Weight, Height, BMI, Blood glucose, Bone density, Blast percentage, etc." .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "measureUnit" ;
- dcterms:title "Measure Unit" ;
- rdfs:range linkml:String ;
- skos:definition "Unit that is associated with Measure Value (e.g. kg, cm, %, x10^9/L, etc.)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "measureValue" ;
- dcterms:title "Measure Value" ;
- rdfs:range linkml:Integer ;
- skos:definition "Numeric value of Measure" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "mondoCode" ;
- dcterms:title "Mondo Code" ;
- rdfs:range linkml:String ;
- skos:definition "Code for condition in the Mondo Disease Ontology (Mondo)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "mondoLabel" ;
- dcterms:title "Mondo Label" ;
- rdfs:range linkml:String ;
- skos:definition "Label for condition in the Mondo Disease Ontology (MONDO)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "motherId" ;
- dcterms:title "Mother ID" ;
- rdfs:range linkml:String ;
- skos:definition "Participant External ID for Participant's mother (NA if Participant is not the proband)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "otherCode" ;
- dcterms:title "Other Code" ;
- rdfs:range linkml:String ;
- skos:definition "Code for condition in another ontology (if no match in HPO, MONDO, or MAXO)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "otherFamilyMemberId" ;
- dcterms:title "Other Family Member ID" ;
- rdfs:range linkml:String ;
- skos:definition "Participant External ID for Participant's other family members (NA if Participant is not the proband)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "otherLabel" ;
- dcterms:title "Other Label" ;
- rdfs:range linkml:String ;
- skos:definition "Label for condition in another ontology (if no match in HPO, MONDO, or MAXO)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "outcomesVitalStatus" ;
- dcterms:title "Outcomes Vital Status" ;
- rdfs:range ;
- skos:definition "Whether participant is alive or dead" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "participantExternalId" ;
- dcterms:title "Participant External ID" ;
- rdfs:range linkml:String ;
- skos:definition "Unique, de-identified identifier for the participant, assigned by data contributor. External IDs must be two steps removed from personal information in the study records." .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "participantId" ;
- dcterms:title "Participant ID" ;
- rdfs:range linkml:String ;
- skos:definition "Unique identifier for the participant, assigned by DCC" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "race" ;
- dcterms:title "Race" ;
- rdfs:range ;
- skos:definition "Race of Participant" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "sex" ;
- dcterms:title "sex" ;
- rdfs:range ;
- skos:definition "Sex of Participant" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "siblingId" ;
- dcterms:title "Sibling ID" ;
- rdfs:range linkml:String ;
- skos:definition "Participant External ID for Participant's sibling(s) (NA if Participant is not the proband)" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "dbgap" ;
- dcterms:title "dbGaP" ;
- rdfs:range linkml:String ;
- skos:definition "dbGaP study accession code" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "program" ;
- dcterms:title "Program" ;
- rdfs:range ;
- skos:definition "Funding source for the study" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "studyCode" ;
- dcterms:title "Study Code" ;
- rdfs:range ;
- skos:definition "Unique identifer for the study, assigned by DCC" .
-
- a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "studyName" ;
- dcterms:title "Study Name" ;
- rdfs:range linkml:String ;
- skos:definition "Full name of the study, chosen by data contributor" .
-
- a owl:Class,
- ;
- rdfs:label "t21" ;
- dcterms:title "T21" .
-
- a owl:Class,
- ;
- rdfs:label "latin_american" ;
- dcterms:title "Latin American" .
-
- a owl:Class,
- ;
- rdfs:label "east_asian" ;
- dcterms:title "East Asian" .
-
- a owl:Class,
- ;
- rdfs:label "black_or_african_american" ;
- dcterms:title "Black or African American" .
-
- a owl:Class,
- ;
- rdfs:label "female" ;
- dcterms:title "Female" .
-
- a owl:Class,
- ;
- rdfs:label "hispanic_or_latino" ;
- dcterms:title "Hispanic or Latino" .
-
- a owl:Class,
- ;
- rdfs:label "male" ;
- dcterms:title "Male" .
-
- a owl:Class,
- ;
- rdfs:label "other_relative" ;
- dcterms:title "Other relative" .
-
- a owl:Class,
- ;
- rdfs:label "father" ;
- dcterms:title "Father" .
-
- a owl:Class,
- ;
- rdfs:label "mother" ;
- dcterms:title "Mother" .
-
- a owl:Class,
- ;
- rdfs:label "sibling" ;
- dcterms:title "Sibling" .
-
- a owl:Class,
- ;
- rdfs:label "unrelated_control" ;
- dcterms:title "Unrelated control" .
-
- a owl:Class,
- ;
- rdfs:label "dead" ;
- dcterms:title "Dead" .
-
- a owl:Class,
- ;
- rdfs:label "alive" ;
- dcterms:title "Alive" .
-
- a owl:Class,
- ;
- rdfs:label "native_hawaiian_or_other_pacific_islander" ;
- dcterms:title "Native Hawaiian or Other Pacific Islander" .
-
- a owl:Class,
- ;
- rdfs:label "not_hispanic_or_latino" ;
- dcterms:title "Not Hispanic or Latino" .
-
- a owl:Class,
- ;
- rdfs:label "american_indian_or_alaskan_native" ;
- dcterms:title "American Indian or Alaska Native" .
-
- a owl:Class,
- ;
- rdfs:label "asian" ;
- dcterms:title "Asian" .
-
- a owl:Class,
- ;
- rdfs:label "white" ;
- dcterms:title "White" .
-
- a owl:Class,
- ;
- rdfs:label "south_asian" ;
- dcterms:title "South Asian" .
-
- a owl:Class,
- ;
- rdfs:label "middle_eastern_or_north_african" ;
- dcterms:title "Middle Eastern or North African" .
-
- a owl:Class,
- ;
- rdfs:label "proband" ;
- dcterms:title "Proband" .
-
- a owl:Class,
- ;
- rdfs:label "more_than_one_race" ;
- dcterms:title "More than one race" .
-
- a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "Biospecimen" ;
- dcterms:title "Biospecimen" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:Integer ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:onClass linkml:String ;
- owl:onProperty ;
- owl:qualifiedCardinality 1 ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:onClass linkml:String ;
- owl:onProperty ;
- owl:qualifiedCardinality 1 ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:Float ;
- owl:onProperty ],
- [ a owl:Restriction ;
- owl:maxQualifiedCardinality 1 ;
- owl:onClass linkml:String ;
- owl:onProperty ],
- ;
- skos:definition "A Biospecimen Collected from A Participant" ;
- include:required "True" ;
- include:requires_component "Study,Participant,DataFile" .
-
- a owl:Class,
- ;
- rdfs:label "controlled" ;
- dcterms:title "Controlled" .
-
- a owl:Class,
- ;
- rdfs:label "open" ;
- dcterms:title "Open" .
-
- a owl:Class,
- ;
- rdfs:label "registered" ;
- dcterms:title "Registered" .
-
- a owl:Class,
- ;
- rdfs:label "available" ;
- dcterms:title "Available" .
-
- a owl:Class,
- ;
- rdfs:label "unavailable" ;
- dcterms:title "Unavailable" .
-
- a owl:Class,
- ;
- rdfs:label "clinical" ;
- dcterms:title "Clinical" .
-
- a owl:Class,
- ;
- rdfs:label "self_reported" ;
- dcterms:title "Self-reported" .
-
- a owl:Class,
- ;
- rdfs:label "not_observed" ;
- dcterms:title "Not Observed" .
-
- a owl:Class,
- ;
- rdfs:label "observed" ;
- dcterms:title "Observed" .
-
- a owl:Class,
- ;
- rdfs:label "current" ;
- dcterms:title "Current" .
-
- a owl:Class,
- ;
- rdfs:label "history_of" ;
- dcterms:title "History Of" .
-
- a owl:Class,
- ;
- rdfs:label "resolved" ;
- dcterms:title "Resolved" .
-
- a owl:Class,
- ;
- rdfs:label "d21" ;
- dcterms:title "D21" .
-
- a owl:Class,
- ;
- rdfs:label "control_only" ;
- dcterms:title "Control-only" .
-
- a owl:Class,
- ;
- rdfs:label "duo" ;
- dcterms:title "Duo" .
-
- a owl:Class,
- ;
- rdfs:label "other" ;
- dcterms:title "Other" .
-
- a owl:Class,
- ;
- rdfs:label "proband_only" ;
- dcterms:title "Proband-only" .
-
- a owl:Class,
- ;
- rdfs:label "trio" ;
- dcterms:title "Trio" .
-
- a owl:Class,
- ;
- rdfs:label "trio_plus" ;
- dcterms:title "Trio+" .
-
- a owl:Class,
- ;
- rdfs:label "include" ;
- dcterms:title "INCLUDE" .
-
- a owl:Class,
- ;
- rdfs:label "kf" ;
- dcterms:title "KF" .
-
- a owl:Class,
- ;
- rdfs:label "abcds" ;
- dcterms:title "ABC-DS" .
-
- a owl:Class,
- ;
- rdfs:label "ads" ;
- dcterms:title "ADS" .
-
-