update doc

docs/20_project_structure.md

@@ -5,27 +5,37 @@ main ones are the following.
 
 - [reproschema](https://github.com/ReproNim/reproschema)
 - [reproschema-library](https://github.com/ReproNim/reproschema-library)
-- [reproschema-ui](https://github.com/ReproNim/reproschema-ui)
 - [reproschema-py](https://github.com/ReproNim/reproschema-py)
+- [reproschema-ui](https://github.com/ReproNim/reproschema-ui)
+- [reproschema-protocol-cookiecutter](https://github.com/ReproNim/reproschema-protocol-cookiecutter)
 
 A brief description of how they all interact could be along the following lines:
 
->If you are about to start a new study that needs you to use some standardized assessments, you can create new **ReproSchema** `protocol` either by reusing some of the ones that we have already created and are listed in the `activities` of the **reproschema-library**, or by using the tools of **reproschema-py** to create the `activities` describing new questionnaires you might want to use. You can also use the **reproschema-py** to make sure that the these `activities` conform to the specifications described in the **reproschema**. Once you have added all the `activities` to your study `protocol`, you can use the **reproschema-ui** to visualize the `protocol` and collect data.
+> If you're gearing up to launch a research project that requires standardized questionnaires, starting with **reproschema-protocol-cookiecutter** is your best first step. This tool sets you up with a custom protocol for your study, integrating handy features for a smooth setup right from the get-go. You'll have two main paths for adding questionnaires, or activities, to your study:
+
+> Option 1: Dive into **reproschema-library** where we've got a stash of ready-made questionnaires. Pick what fits your study, and you're good to go.
+
+> Option 2: Feeling creative? Craft your own activities with **reproschema-py**. This tool not only lets you design new activities but also checks that they meet all the ReproSchema standards.
+
+> Once your protocol is packed with all the activities you need, **reproschema-ui** automatically steps in. This part of the toolkit lets you see your study in action before you even start, making sure everything's set up just right for gathering data.
 
 ## [reproschema](https://github.com/ReproNim/reproschema)
 
-This repository contains the actual ReproSchema with the [`contexts`](https://github.com/ReproNim/reproschema/tree/master/contexts)
-of the schema and the [`terms`](https://github.com/ReproNim/reproschema/tree/master/terms)
-that define its different elements and how they relate to each other and to other
-external entities.
+GPT
 
-This repository also contains SHACL-based validation information in [`validation`](https://github.com/ReproNim/reproschema/tree/master/validation),
-which allows you to ensure that any new `protocol`, `activity` or `item` you create
-conforms to the specifications of the schema.
+The ReproSchema is like a blueprint for research projects, ensuring everyone collects data in a consistent way, which makes it easier to compare results from different studies. Here’s a simpler breakdown of what’s inside:
+
+- **Key Terms:** These are the building blocks, like common types of answers and data formats, that help everyone understand and use data the same way.
+- **How Data is Organized:** ReproSchema sorts information into three main layers to keep things neat:
+- - **Item Level:** This is where individual questions or parts of a survey are detailed, allowing for close examination of each element.
+- - **Activity Level:** At this stage, an entire survey or tool, made up of many items, is grouped together as an "Activity." It gives a complete overview of what the survey involves.
+- - **Protocols Level:** The highest level, a "Protocol," bundles together all the activities a participant will do in a study, providing a comprehensive plan.
+- **[Validation](https://github.com/ReproNim/reproschema/tree/master/validation):** The schema uses special standards (like SHACL files) to make sure the data and forms are up to standard and consistent.
+- **Context Files:** These files ([`contexts`](https://github.com/ReproNim/reproschema/tree/master/contexts)and [`terms`](https://github.com/ReproNim/reproschema/tree/master/terms)) specify user-interface details and enhance schema flexibility. They define elements like input types, visibility conditions, and response options, supporting a tailored user experience. Additionally, they enable internationalization and multiple language support for broad applicability.
 
 There is also an [`example`](https://github.com/ReproNim/reproschema/tree/master/examples)
 schema that can help give you a quick overview of what the protocol and activity
-for a study might look like. For more details see the [schema section](../30_schema).
+for a study might look like. For more details see the [schema section](../docs/30_schema.md).
 
 ## [reproschema-library](https://github.com/ReproNim/reproschema-library)
 
@@ -42,21 +52,29 @@ All assessments are listed in [the `activity` folder](https://github.com/ReproNi
 and are served [here](https://schema.repronim.org/rl/) if you want to visualize
 them.
 
+- **Standard Alignment:** Each element in the library aligns with the ReproSchema framework, ensuring uniformity in terms and structure and upholding validation protocols for consistency across the ecosystem.
+- **Research Protocol Integration:** Researchers can utilize these assessments in various combinations to align with specific protocol needs, customizing their application per study objectives. This process can be integrated using the reproschema-protocol-cookiecutter for constructing user interfaces.
+- **Collaborative Expansion:** The library supports expansion through researcher contributions, allowing adding new, relevant assessments. These contributions are automatically validated using reproschema-py, maintaining the library’s standardization and relevance to evolving research demands.
+
+## [reproschema-py](https://github.com/ReproNim/reproschema-py)
+
+This is the ReproSchema python library. This is a python Command Line Interface (CLI)
+that allows you to help create and validate the schemas of new assessments.
+
+- **Schema Development and Validation:** This tool streamlines the creation and validation of new assessment schemas, verifying their alignment with ReproSchema's standards. It rigorously tests protocols, activities, and items to meet predefined specifications.
+- **Consistency Assurance:** Integrated with the ReproSchema-library and ReproSchema-Protocol-Cookiecutter, reproschema-py validates library assessments for quality and uniformity. It also automatically ensures the consistency of research protocols generated through the ReproSchema-Protocol-Cookiecutter.
+- **Interoperability with REDCap:** Its capability to convert between REDCap and ReproSchema formats exemplifies its role in harmonizing diverse data collection methods in complex, multi-faceted research environments.
+
 ## [reproschema-ui](https://github.com/ReproNim/reproschema-ui)
 
 This repository contains the code for the user-interface for the ReproSchema to
 visualize questionnaires and collect data.
 
 You can see it in action [here](https://www.repronim.org/reproschema-ui/)
 
-## [reproschema-py](https://github.com/ReproNim/reproschema-py)
+## [reproschema-protocol-cookiecutter](https://github.com/ReproNim/reproschema-protocol-cookiecutter)
 
-This is the ReproSchema python library. This is a python Command Line Interface (CLI)
-that allows you to help create and validate the schemas of new assessments.
-
-- test that a schema for a `protocol`, `activity` or `item` is valid and matches
-the specification of the ReproSchema
-- convert a csv file of a questionnaire into its equivalent ReproSchema
+The reproschema-protocol-cookiecutter is a straightforward tool that helps you quickly set up a research study. It offers a ready-to-use template for organizing your study's structure and surveys, ensuring everything meets standard guidelines. Think of it as a quick-start guide to get your research project up and running smoothly. A step-by-step guide see [here](../docs/41_create_new_protocol.md).
 
 ## Other repositories
 
@@ -68,9 +86,3 @@ This repository contain a full fledge protocol that can be used as demonstration
 
 This contains some additional information on how the activities are served on
 [https://schema.repronim.org/rl/](https://schema.repronim.org/rl/).
-
-### [reproschema-builder](https://github.com/ReproNim/reproschema-builder)
-
-This repository contains a javascript conversion tool that have been used to
-create some of our activities, and can be used to convert RedCap data
-dictionaries to ReproSchema.