add in doc and PDF of tutorial slides

README.md

@@ -1,31 +1,65 @@
-# linkml-tutorial-2024
+## linkml-tutorial-2024
 
-A repostitory that walks through schema generation.
+This repository contains the source code for the LinkML tutorial for the 2024 Intelligent Systems for Molecular Biology
+Conference ([ISMB 2024](https://ismb.landing.showcare.io/2024-conference/?utm_source=google-ad-grant&utm_medium=showcare&gad_source=1&gclid=Cj0KCQjwv7O0BhDwARIsAC0sjWPB_OFEy4AkvGpiiHw10O9iSNap3JZ-8p9EsPFRL1RFobgt9YZAxE4aAgohEALw_wcB))
 
-## Website
+In this tutorial, we discuss best practices for data modeling; introduce LinkML as a modeling framework 
+and tool suite; work together to set up a LinkML project from scratch; develop a model and validate it with 
+test data; and auto-generate model documentation.
 
-[https://linkml.github.io/linkml-tutorial-2024](https://linkml.github.io/linkml-tutorial-2024)
+The slides that accompany this repository can be viewed at [https://linkml.io/linkml-tutorial-2024/LinkML_tutorial_for_ISMB 2024_ slides.pdf](https://linkml.io/linkml-tutorial-2024/LinkML_tutorial_for_ISMB 2024_ slides.pdf).
+
+To follow along, please use the slides and the tags in this repo to see how we build up a linkml project from scratch using
+the LinkML Project Cookiecutter (https://gituhub.com/linkml/linkml-project-cookiecutter).
+
+### Step 0: Executing the LinkML Project Cookiecutter
+
+At the end of Step 0, you will have a new LinkML project that is ready to be developed.  Check out the tag
+`step_0_basic_project_creation` to see the project at this stage.
+
+This step begins at slide 29.
+
+### Step 1: Explore some LinkML modeling elements.  
+The example schema generated here follows the use case introduced in the slides.
+
+At the end of Step 1, you will have a LinkML schema that models the use case introduced in the slides.  Check out the tag
+`step_1_modeling` to see the project at this stage.
+
+This step begins at slide 48.
+
+### Step 2: Lint the schema
 
-## Repository Structure
+Understand how the LinkML linter works, how to customize it to ignore or enforce linting rules
+and fix the sample schema appropriately.
 
-* [examples/](examples/) - example data
-* [project/](project/) - project files (do not edit these)
-* [src/](src/) - source files (edit these)
-  * [linkml_tutorial_2024](src/linkml_tutorial_2024)
-    * [schema](src/linkml_tutorial_2024/schema) -- LinkML schema
-      (edit this)
-    * [datamodel](src/linkml_tutorial_2024/datamodel) -- generated
-      Python datamodel
-* [tests/](tests/) - Python tests
+At the end of Step 2, you will have a LinkML schema that passes linting.  Check out the tag
+`step_2_linting` to see the project at this stage.
 
-## Developer Documentation
+This step begins at slide 70.
 
-<details>
-Use the `make` command to generate project artefacts:
+### Step 3: Generate Documentation from the schema and deploy it to GitHub Pages.
 
-* `make all`: make everything
-* `make deploy`: deploys site
-</details>
+At the end of Step 3, you will have a LinkML schema that has been documented and deployed to GitHub Pages.  
+Check out the tag `step_3_documentation` to see the project at this stage.
+
+This step begins at slide 92.
+
+### Step 4: Generate a Python data model from the schema
+
+At the end of Step 4, you will have a Python data model that has been tested. 
+Check out the tag `step_4_code_generation` to see the project at this stage.
+
+This step begins at slide 105.
+
+### Step 5: Validate example data
+
+At the end of Step 5, you will have validated example data with the LinkML Validator.
+Check out the tag `step_5_validation` to see the project at this stage.
+
+This step begins at slide 115.
+
+The resulting datamodel, tutorial schema documentation, and schema diagrams can be viewed at:
+[https://linkml.github.io/linkml-tutorial-2024](https://linkml.github.io/linkml-tutorial-2024)
 
 ## Credits
 

src/docs/about.md

@@ -1,3 +1,62 @@
 # linkml-tutorial-2024
 
-A repostitory that walks through schema generation.
+This repository contains the source code for the LinkML tutorial for the 2024 Intelligent Systems for Molecular Biology
+Conference ([ISMB 2024](https://ismb.landing.showcare.io/2024-conference/?utm_source=google-ad-grant&utm_medium=showcare&gad_source=1&gclid=Cj0KCQjwv7O0BhDwARIsAC0sjWPB_OFEy4AkvGpiiHw10O9iSNap3JZ-8p9EsPFRL1RFobgt9YZAxE4aAgohEALw_wcB))
+
+In this tutorial, we discuss best practices for data modeling; introduce LinkML as a modeling framework 
+and tool suite; work together to set up a LinkML project from scratch; develop a model and validate it with 
+test data; and auto-generate model documentation.
+
+The slides that accompany this repository can be viewed at [https://linkml.io/linkml-tutorial-2024/LinkML_tutorial_for_ISMB 2024_ slides.pdf](https://linkml.io/linkml-tutorial-2024/LinkML_tutorial_for_ISMB 2024_ slides.pdf).
+
+To follow along, please use the slides and the tags in this repo to see how we build up a linkml project from scratch using
+the LinkML Project Cookiecutter (https://gituhub.com/linkml/linkml-project-cookiecutter).
+
+### Step 0: Executing the LinkML Project Cookiecutter
+
+At the end of Step 0, you will have a new LinkML project that is ready to be developed.  Check out the tag
+`step_0_basic_project_creation` to see the project at this stage.
+
+This step begins at slide 29.
+
+### Step 1: Explore some LinkML modeling elements.  
+The example schema generated here follows the use case introduced in the slides.
+
+At the end of Step 1, you will have a LinkML schema that models the use case introduced in the slides.  Check out the tag
+`step_1_modeling` to see the project at this stage.
+
+This step begins at slide 48.
+
+### Step 2: Lint the schema
+
+Understand how the LinkML linter works, how to customize it to ignore or enforce linting rules
+and fix the sample schema appropriately.
+
+At the end of Step 2, you will have a LinkML schema that passes linting.  Check out the tag
+`step_2_linting` to see the project at this stage.
+
+This step begins at slide 70.
+
+### Step 3: Generate Documentation from the schema and deploy it to GitHub Pages.
+
+At the end of Step 3, you will have a LinkML schema that has been documented and deployed to GitHub Pages.  
+Check out the tag `step_3_documentation` to see the project at this stage.
+
+This step begins at slide 92.
+
+### Step 4: Generate a Python data model from the schema
+
+At the end of Step 4, you will have a Python data model that has been tested. 
+Check out the tag `step_4_code_generation` to see the project at this stage.
+
+This step begins at slide 105.
+
+### Step 5: Validate example data
+
+At the end of Step 5, you will have validated example data with the LinkML Validator.
+Check out the tag `step_5_validation` to see the project at this stage.
+
+This step begins at slide 115.
+
+The resulting datamodel, tutorial schema documentation, and schema diagrams can be viewed at:
+[https://linkml.github.io/linkml-tutorial-2024](https://linkml.github.io/linkml-tutorial-2024)