Resource Ingest Guide Schema

A LinkML schema for describing Reference Ingest Guides (RIGs) - structured documents that capture the scope, rationale, and modeling approach for ingesting content from external sources into Biolink Model-compliant data repositories.

Overview

This repository provides:

• LinkML Schema: Formal specification for Reference Ingest Guides in src/resource_ingest_guide_schema/schema/
• Documentation Generator: Automated conversion of RIG YAML files to human-readable markdown
• Validation Tools: Schema validation for RIG files using LinkML
• Template System: Standardized templates and creation tools for new RIGs
• Example RIGs: Real-world examples from CTD, DISEASES, and Clinical Trials KP

What are Reference Ingest Guides (RIGs)?

RIGs are structured documents that describe:

• Source Information: Details about data sources (access, formats, licensing)
• Ingest Information: What content is included/excluded and filtering rationale
• Target Information: How data is modeled in the output knowledge graph
• Provenance Information: Contributors and related artifacts

RIGs help ensure reproducible, well-documented data ingestion processes for biomedical knowledge graphs.

Website

https://biolink.github.io/resource-ingest-guide-schema

Repository Structure

├── src/
│   ├── resource_ingest_guide_schema/
│   │   └── schema/                    # LinkML schema definition
│   ├── docs/
│   │   ├── files/                     # Static documentation files
│   │   ├── rigs/                      # Example RIG YAML files
│   │   └── doc-templates/             # Jinja2 templates for docs
│   └── scripts/                       # Python utilities for RIG processing
├── docs/                              # Generated documentation
├── tests/                             # Test suite
└── project/                           # Generated LinkML artifacts

Developer Documentation

Prerequisites

This project uses uv for dependency management. Install it with:

# On macOS and Linux
curl -LsSf https://astral.sh/uv/install.sh | sh

# On Windows
powershell -c "irm https://astral.sh/uv/install.ps1 | iex"

# Or with pip
pip install uv

Getting Started

Note that the following commands assume you are in the project root directory, and the equivalent just commands may be substituted for make (namely just test instead of make test)

1. Install dependencies:

   uv sync --extra dev

2. Run tests:

   make test

3. Generate documentation:

   make gendoc

4. Create a new RIG:

   make new-rig INFORES=infores:example NAME="Example Data Source"

Working with RIGs

Creating a New RIG

# Create a new RIG from the template
make new-rig INFORES=infores:mydatasource NAME="My Data Source RIG"

# This creates src/docs/rigs/mydatasource_rig.yaml
# Edit the file to fill in your specific information

Validating RIGs

# Validate all RIG files against the schema
make validate-rigs

# Validate a specific RIG
uv run linkml-validate --schema src/resource_ingest_guide_schema/schema/resource_ingest_guide_schema.yaml src/docs/rigs/my_rig.yaml

Building Documentation

# Generate all documentation including RIG index and markdown versions
make gendoc

# Test documentation locally
make testdoc  # Builds docs and starts local server

Development Workflow

1. Schema Development

The LinkML schema is defined in src/resource_ingest_guide_schema/schema/resource_ingest_guide_schema.yaml. After making changes:

# Regenerate Python datamodel and other artifacts
make gen-project

# Test the schema
make test-schema

# Lint the schema
make lint

2. Script Development

Python utilities are in src/scripts/:

• create_rig.py: Generate new RIG from template
• rig_to_markdown.py: Convert RIG YAML to markdown
• generate_rig_index.py: Create RIG index table

To test script changes:

# Run scripts directly
uv run python src/scripts/create_rig.py --help
uv run python src/scripts/rig_to_markdown.py --input-dir src/docs/rigs --output-dir docs

3. Documentation Development

Templates are in src/docs/doc-templates/ and static files in src/docs/files/:

# Regenerate docs after template changes
make gendoc

# View changes locally
make serve  # or make testdoc

Available Commands

Command	Description
make help	Show all available commands
make install	Install dependencies with uv
make test	Run full test suite
make test-schema	Test schema generation
make test-python	Run Python tests
make lint	Lint the LinkML schema
make gen-project	Generate LinkML artifacts (Python, JSON Schema, etc.)
make gendoc	Generate documentation including RIG processing
make serve	Start local documentation server
make testdoc	Build docs and start server
make new-rig	Create new RIG (requires INFORES and NAME)
make validate-rigs	Validate all RIG files
make clean	Clean generated files
make deploy	Deploy documentation

Project Structure Details

Key Directories

• src/resource_ingest_guide_schema/schema/: LinkML schema definition
• src/docs/rigs/: Example RIG YAML files (CTD, DISEASES, Clinical Trials KP)
• src/docs/files/: Static documentation files copied to output
• src/docs/doc-templates/: Jinja2 templates for documentation generation
• src/scripts/: Python utilities for RIG creation and processing
• docs/: Generated documentation output (do not edit directly)
• project/: Generated LinkML artifacts (Python models, JSON Schema, etc.)

Generated Artifacts

The make gen-project command generates:

• Python datamodel: src/resource_ingest_guide_schema/datamodel/
• JSON Schema: project/jsonschema/
• OWL ontology: project/owl/
• GraphQL schema: project/graphql/
• SQL DDL: project/sqlschema/
• And more: See project/ directory

Contributing

1. Fork the repository
2. Create a feature branch
3. Make changes following the existing patterns
4. Ensure tests pass: make test
5. Update documentation if needed: make gendoc
6. Submit a pull request

Adding New RIG Examples

1. Create YAML file in src/docs/rigs/
2. Follow the schema structure (see existing examples)
3. Validate: make validate-rigs
4. Regenerate docs: make gendoc
5. The RIG will automatically appear in the documentation index

Schema Changes

1. Modify src/resource_ingest_guide_schema/schema/resource_ingest_guide_schema.yaml
2. Regenerate artifacts: make gen-project
3. Update any affected RIG files
4. Test: make test
5. Update documentation as needed