Merge pull request #191 from include-dcc/doc_update

Doc and readme updates

Makefile

@@ -16,7 +16,6 @@ PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
 DOCDIR = docs
 
 TEMPLATEDIR = doc_templates
-VERSION ?= v2.2.0  # Default version if not specified
 
 
 # basename of a YAML file in model/
@@ -86,13 +85,6 @@ $(DOCDIR):
 #	cp $(SRC)/docs/*md $(DOCDIR) ; \
 #	$(RUN) gen-doc -d $(DOCDIR) --template-directory $(SRC)/$(TEMPLATEDIR) $(SOURCE_SCHEMA_PATH)
 
-#gendoc: $(DOCDIR)
-#	@for version in $$(git tag | grep -v "rc"); do \
-#		git checkout $$version ; \
-#		$(RUN) gen-doc -d $(DOCDIR)/$$version --template-directory $(SRC)/$(TEMPLATEDIR) $(SOURCE_SCHEMA_PATH) ; \
-#		cp $(SRC)/docs/*md $(DOCDIR)/$$version ; \
-#	done
-
 gendoc: $(DOCDIR)
 	@initial_branch=$$(git branch --show-current); \
 	latest_version=$$(git tag | sort -V | tail -n 1); \
@@ -113,8 +105,6 @@ gendoc: $(DOCDIR)
 	done; \
 	git checkout $$initial_branch
 
-
-
 testdoc: gendoc serve
 
 MKDOCS = $(RUN) mkdocs

README.md

@@ -1,31 +1,47 @@
-# INCLUDE v2 LinkML Data Model
+[![INCLUDE DCC Logo](src/docs/images/include-dcc_logo.png)](https://includedcc.org/)
 
-This repository includes the LinkML model and tooling for the v2 Data Model
+# INCLUDE LinkML Data Model
 
-# Where to find the data model:
+## Overview
 
-* The YAML files are in `src > linkml`
-* The JSON-LD schema is in `src > data > schematic`
+This repository hosts the INCLUDE LinkML Model, a specialized data model crafted to empower collaboration and streamline data integration within Down syndrome research. By harnessing advanced [LinkML](https://linkml.io/) features, it provides a versatile framework for harmonizing data representation, articulating metadata, and delineating intricate relationships between entities. This structured approach not only promotes seamless data exchange but also facilitates interoperability and scalability across diverse research initiatives.
 
+## Getting Started
 
+To work with the INCLUDE Model, follow these steps:
 
-# Poetry Environment
-This repo requires poetry as a system dependency
+1. **Clone the Repository**: Clone this repository to your local machine.
 
-https://python-poetry.org/docs/#installation
+2. **Install Poetry**: If not already installed, install Poetry as a system dependency. Refer to [Poetry Documentation](https://python-poetry.org/docs/#installation) for installation instructions.
 
-When poetry is installed run:
-`poetry install`
+3. **Install Dependencies**: Run the following command to install project dependencies using Poetry:
 
+```bash
+poetry install
+```
 
+After running `poetry install`, you can proceed with further setup or usage instructions specific to your project.
 
+## Repository Structure
 
-# Workflow to update the model from:
-## [INCLUDE Schemasheets Google Sheets Project](https://docs.google.com/spreadsheets/d/1w6zDfz3_yrCjjrqfpXBGNmd0LZL4B03gr1KfzJtk5Cs/edit?usp=sharing)
-1. Run the Schematic JSON-LD transformer to generate the JSON-LD that Schematic will use to generate Manifests
+The repository structure is organized as follows:
 
-` poetry run python src/main.py schematic_transform   `
+- `src/linkml`: Contains the YAML files defining the INCLUDE Model.
 
-4. Run Schematic configured to point at the generated json-ld at src/schematic/include_schematic_linkml.jsonld
+## Updates Since Previous Release (v2.2.0)
+
+### Model Enhancements:
+
+- Updated Assay component to include latest Virtual Biorepository model.
+- Updated Study component and added new Dataset and DatasetManifest components to support new Study/Dataset pages in Data Hub.
+- Inclusion of over 25 new slots.
+- 5 new enumerations: EnumClinicalDataSourceType, EnumDataCategory, EnumGuidType, EnumParticipantLifespanStage, EnumResearchDomain.
+
+### CLI Enhancements:
+
+- **Validation**: Streamlines data cleaning and validation via the command line (CLI), allowing users to specify the data type and file path. The CLI reads, cleans, and validates data using LinkML-defined models for robust validation. For more details, use:
+
+```bash
+validate-data --help
+```
 
-`schematic manifest --config */schematic/config.yml get -s`

mkdocs.yml

@@ -27,7 +27,7 @@ nav:
   - Index: index.md
   - About: about.md
   - Previous Releases:
-      - Version 2.2.0: https://include-dcc.github.io/include-linkml/v2.2.0/index.html
-      - Version 2.1.0: https://include-dcc.github.io/include-linkml/v2.1.0/index.html
+      - Version 2.2.0: v2.2.0/index.md
+      - Version 2.1.0: v2.1.0/index.md
 site_url: https://include-dcc.github.io/include-linkml/
 repo_url: https://github.com/include-dcc/include-linkml/

src/docs/about.md

@@ -1,3 +1,43 @@
-# About my-project
+## INCLUDE LinkML Model
 
-...
+The INCLUDE LinkML Model is designed to streamline collaboration and data integration focusing on Down syndrome research and healthcare advancement. It provides a standardized framework for defining metadata related to Down syndrome research, promoting seamless data sharing and collaboration.
+
+### About INCLUDE
+The INCLUDE (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE) Project, launched in June 2018, supports critical health and quality-of-life needs for individuals with Down syndrome by investigating co-occurring conditions such as Alzheimer’s disease/dementia, autism, cataracts, celiac disease, congenital heart disease, and diabetes.
+
+### About LinkML
+LinkML is a flexible modeling language that allows you to author schemas (“models”) in YAML, describing the structure of your data. Designed for both simple and complex use cases, LinkML facilitates the creation of interoperable and standard-compliant data models.
+
+### Key Features
+- **Standardized Metadata:** Ensures clarity, consistency, and interoperability across diverse datasets and research endeavors.
+
+- **Facilitated Collaboration:** Promotes collaboration among researchers, clinicians, and stakeholders, accelerating research progress.
+
+- **Accessible Data Hub:** Provides easy access to valuable resources, datasets, and insights through the Data Hub.
+
+- **Targeted Basic Science Studies:** Focuses on high-risk, high-reward research on chromosome 21 to better understand Down syndrome biology and develop new treatments.
+
+- **Large Cohort Assembly:** Connects existing cohorts and enrolls new participants to study the full range of conditions experienced by individuals with Down syndrome across their lifespan.
+
+- **Inclusive Clinical Trials:** Identifies and supports clinical trials addressing conditions common in the Down syndrome population, establishing measures specific to Down syndrome for evaluating clinical success.
+
+### How LinkML Enhances the Model
+- **Flexible Data Modeling:** LinkML supports a range of data structures, from simple spreadsheets to complex interlinked schemas, enabling comprehensive and adaptable metadata descriptions.
+
+- **Interoperability:** Designed to work with semantic frameworks like RDF and familiar developer frameworks like JSON, ensuring that data models are widely accessible and usable across different platforms and applications.
+
+- **Human-Readable Syntax:** Utilizing YAML for schema definitions, LinkML offers an approachable syntax for both technical and non-technical users, promoting broader participation in schema development.
+
+- **Integration Capabilities:** LinkML's compatibility with various data standards and technologies facilitates seamless integration with existing systems and data sources, enhancing data utility and research outcomes.
+
+### How to Get Involved
+- **Explore the Model:** Gain a deeper understanding of essential metadata elements for Down syndrome research.
+
+- **Collaborate:** Join forces to leverage the INCLUDE LinkML Model and accelerate progress.
+
+- **Contribute:** Share expertise, insights, and data to enrich the model and shape the future of Down syndrome research.
+
+### Start Exploring
+Visit [INCLUDE Data Coordinating Center (DCC)](https://includedcc.org/) to access the INCLUDE LinkML Model and join the collaborative effort toward transforming Down syndrome research and healthcare.
+
+For more information about LinkML, visit [LinkML](https://linkml.io/).