Ontology starting point

.github/workflows/docbuild.yml

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+name: Build and deploy docs
+
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Pages
+        id: pages
+        uses: actions/configure-pages@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Build
+        run: |
+          export "SITEDIR=./build/upload/$(git branch --show-current)"
+          export "SITEURL=https://concepts.datalad.org/$(git branch --show-current)"
+          make mkdocs-site
+          mkdir -p $SITEDIR
+          mv ./build/mkdocs-site $SITEDIR
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v2
+        with:
+          # Upload the directory created by mkdocs
+          path: ./build/upload
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.gitignore

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+# Generated
+build/
+*-stamp
+.*.swp

Makefile

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+all: mkdocs-site
+
+linkml-docs: linkml-docs-stamp
+linkml-docs-stamp:
+	gen-doc \
+		--mergeimports \
+		--hierarchical-class-view \
+		--use-slot-uris \
+		--include-top-level-diagram \
+		--diagram-type er_diagram \
+		--metadata \
+		--format markdown \
+		-d build/linkml-docs \
+		src/linkml/root.yaml
+	touch $@
+
+extra-docs: extra-docs-stamp
+extra-docs-stamp:
+	mkdir -p build/linkml-docs
+	cp -r src/extra-docs/* build/linkml-docs
+
+mkdocs-site: mkdocs-site-stamp
+mkdocs-site-stamp: linkml-docs extra-docs
+	mkdocs build
+	touch $@
+
+clean:
+	rm -rf build
+	rm -f *-stamp
+
+.PHONY: clean linkml-docs extra-docs  mkdocs-site

README.md

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+# The DataLad data model
+
+_WORK IN PROGRESS_
+
+## How to...
+
+Install (in a virtualenv)
+
+```
+pip install -r requirements.txt
+```
+
+Build docs:
+
+```
+gen-doc -d docs src/abcdj_schema.yaml
+```
+
+Serve docs locally
+
+```
+mkdocs serve
+```

mkdocs.yml

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+copyright:
+docs_dir: build/linkml-docs
+nav:
+  - Home: index.md
+  - About: about.md
+plugins:
+  - mermaid2
+repo_url: https://github.com/psychoinformatics-de/datalad-concepts
+site_author:
+site_description:
+site_dir: build/mkdocs-site
+site_name: DataLad Concepts Ontology (DLCO)
+site_url: !ENV [SITEURL, 'https://concepts.datalad.org']
+strict: true
+theme:
+  name: gitbook
+  locale: en

requirements.txt

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+linkml
+mkdocs
+mkdocs-gitbook
+mkdocs-mermaid2-plugin

src/linkml/classes/author.yaml

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+id: https://w3id.org/abcdj/author
+name: abcdj-author
+title: abcdj-author
+description: |-
+  A schema to describe an ABCD-J author
+license: MIT
+
+prefixes:
+  abcdj: https://w3id.org/abcdj/
+  linkml: https://w3id.org/linkml/
+  obo: https://purl.obolibrary.org/obo/
+  schema: http://schema.org/
+default_prefix: abcdj
+default_range: string
+
+imports:
+  - linkml:types
+
+classes:
+  Author:
+    class_uri: schema:Person
+    description: >-
+      An author of the Dataset or of a Publication linked to the
+      Dataset.
+    attributes:
+      affiliation:
+        slot_uri: schema:affiliation
+        required: false
+        description: >-
+          The author's affiliation to a group, institution, or
+          employer.
+      email:
+        slot_uri: schema:email
+        required: false
+        description: >-
+          The author's email address.
+      name:
+        slot_uri: schema:name
+        required: true
+        description: >-
+          The author's name in the format <givenName> <familyName>.
+      orcid:
+        slot_uri: obo:IAO_0000708
+        required: false
+        description: >-
+          The path of the file relative to the root of the Dataset,
+          provided in the POSIX format.

src/linkml/root.yaml

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+id: https://concepts.datalad.org
+name: datalad-concepts-ontology
+description: |-
+  [DataLad Concepts Ontology](https://concepts.datalad.org) (DLCO)
+
+imports:
+  - classes/author