Strategy, Code of conduct & Contribution Guide

ATLAS_Strategy.md

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+# ATLAS/WebAPI Strategy
+
+The following strategy for ATLAS/WebAPI follows the format as described in [Red Hat's "Developing a strategy for your open source project"](https://www.redhat.com/en/resources/developing-strategy-open-source-project). 
+
+## 1. What is the project?
+
+ATLAS/WebAPI is a web-based tool for desiging observational studies using [HADES Standardized Analytics](https://ohdsi.github.io/Hades/) for patient-level health data converted to the OMOP Common Data Model. 
+
+## 2. Who are the project's users?
+
+ATLAS/WebAPI's users are researchers (individuals and teams) who want to design cohort definitions. They will then use these cohort definitions to run analytics to perform characterization, and population-level effect estimation and patient-level prediction for these populations of patients.
+
+## 3. How do you engage with your user base today?
+
+Users of ATLAS are encouraged to participate in the [ATLAS/WebAPI Working group](https://www.ohdsi.org/workgroups/).
+
+## 4. What alternatives to your project already exist?
+
+[i2b2](https://www.i2b2.org/software/index.html) provides an open-source cohort definition solution that is now compatible with the OMOP CDM.
+
+## 5. Are you already associated with adjacent projects?
+
+ATLAS/WebAPI is adjacent to a number of projects in the OHDSI open-source ecosystem. ATLAS/WebAPI provides a designer for [HADES Standardized Analytics](https://ohdsi.github.io/Hades/). [Athena](https://athena.ohdsi.org) provides capabilities to search the OMOP Vocabularies to download these vocabularies. [ARES](https://ohdsi.github.io/Ares/) provides database level characterization and data quality assessments. [Arachne](https://github.com/OHDSI/Arachne) provides the capabilities to execute studies designed in ATLAS.
+
+## 6. What are your goals for the project?
+
+We have the following goals and priorities for the ATLAS/WebAPI project:
+
+- **ATLAS for phenotype development and evaluation**: ATLAS will provide a cohesive set of features for phenotype development and storage.
+- **ATLAS for study design and execution via Arachne & Strategus**: currently cohorts are the only reusable element of design that is produced by ATLAS for consumption in Strategus. We should aim to make all of the Strategus HADES modules available for design in ATLAS. We should also have a documented solution for running Strategus via Arachne integrated with ATLAS. 
+- **Modernize the application stack**: ATLAS/WebAPI has fallen behind on some core libraries which require prioritization to fix.
+
+## 7. Who are your key stakeholders?
+
+Researchers who want to design observational studies using the OMOP CDM.

CODE_OF_CONDUCT.md

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+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[OHDSI ATLAS/WebAPI Working Group](https://ohdsi.org/workgroups/).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

CONTRIBUTING.md

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+# Contributing to OHDSI Atlas
+
+Thank you for considering contributing to OHDSI Atlas! By contributing, you help improve the tool and contribute to the collaborative effort in advancing observational health data sciences.
+
+## Table of Contents
+
+1. [Code of Conduct](#code-of-conduct)
+2. [How Can I Contribute?](#how-can-i-contribute)
+    - [Reporting Bugs](#reporting-bugs)
+    - [Requesting Features](#requesting-features)
+    - [Contributing Code](#contributing-code)
+3. [Development Setup](#development-setup)
+4. [Coding Guidelines](#coding-guidelines)
+5. [Pull Request Process](#pull-request-process)
+6. [Community](#community)
+7. [Maintainers](#maintainers)
+
+## Code of Conduct
+
+This project and its community adhere to the [Code of Conduct](CODE_OF_CONDUCT.md). Please familiarize yourself with this code before contributing.
+
+**NOTE:** Can we add to the Code of Conduct a section on behaviors to avoid. The focus of discussions should be on the work.
+
+## How Can I Contribute?
+
+### Reporting Bugs
+
+If you come across a bug or unexpected behavior, please ensure it hasn't already been reported by checking the [issue tracker](https://github.com/OHDSI/Atlas/issues). If not, please [open a new issue](https://github.com/OHDSI/Atlas/issues/new) with detailed information about the problem and steps to reproduce it.
+
+### Requesting Features
+
+We welcome suggestions for new features or enhancements. If you have an idea, check if it's already in the [feature requests](link-to-feature-requests) or [open a new one](link-to-new-feature-request). Describe the feature, its use case, and any relevant details.
+
+### Contributing Code
+
+If you're interested in contributing code, follow these steps:
+
+1. Fork the repository.
+2. Clone the forked repository to your local machine.
+3. Create a new branch for your feature or bug fix: `git checkout -b feature-name`.
+4. Implement your changes and ensure tests pass.
+5. Commit your changes: `git commit -m "Your descriptive commit message"`.
+6. Push the changes to your fork: `git push origin feature-name`.
+7. [Open a pull request](link-to-pull-request) with a detailed description of your changes.
+
+## Development Setup
+
+To set up the development environment for OHDSI Atlas, follow the instructions in the [development setup guide](link-to-development-setup).
+
+NOTES: Potentially use Docker for a development environment. Additionally, we should describe setup of a local system for development.
+
+## Coding Guidelines
+
+Please adhere to the [coding guidelines](link-to-coding-guidelines) when contributing code. These guidelines help maintain a consistent codebase and ensure readability.
+
+## Pull Request Process
+
+Before submitting a pull request:
+
+1. Ensure your code follows the coding guidelines.
+2. Update or add tests to cover your changes.
+3. Verify that the build passes and tests are successful.
+4. Make sure your commit messages are clear and descriptive.
+
+## Community
+
+Join the OHDSI community to connect with other contributors, ask questions, and participate in discussions:
+
+- Community Forum: [link-to-community-forum]
+- Chat: [link-to-chat]
+
+## Maintainers
+
+The OHDSI Atlas project is maintained by:
+
+- Maintainer 1 ([@maintainer1](link-to-maintainer1-profile))
+- Maintainer 2 ([@maintainer2](link-to-maintainer2-profile))
+
+If you have any questions or need assistance, feel free to reach out to the maintainers.
+
+---
+
+Replace the placeholder links (`link-to-...`) with the actual URLs, and customize the sections to match the specific processes and guidelines of the OHDSI Atlas project.

README.md

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 <a href="http://www.ohdsi.org/web/atlas"><img src="http://www.ohdsi.org/web/wiki/lib/exe/fetch.php?cache=&media=documentation:software:logo_without_text.png" align="left" hspace="10" vspace="6" width="164" height="200"></a>
 
-**ATLAS** is an open source software tool for researchers to conduct scientific analyses on standardized observational data converted to the [OMOP Common Data Model V5](https://github.com/OHDSI/CommonDataModel/wiki "OMOP Common Data Model V5"). Researchers can create cohorts by defining groups of people based on an exposure to a drug or diagnosis of a particular condition using healthcare claims data. ATLAS has vocabulary searching of medical concepts to identify people with specific conditions, drug exposures etc. Patient profiles can be viewed within a specific cohort allowing visualization of a particular subject's health care records. Population effect level estimation analyses allows for comparison of two different cohorts and leverages R packages.
+**ATLAS** is an open source software tool for researchers to conduct scientific analyses on patient-level healthcare data standardized to the [OMOP Common Data Model V5](https://ohdsi.github.io/CommonDataModel/ "OMOP Common Data Model V5"). Researchers can create cohorts by defining groups of people based on an exposure to a drug or diagnosis of a particular condition using healthcare claims data. ATLAS has vocabulary searching of medical concepts to identify people with specific conditions, drug exposures etc. More information on ATLAS is found in [Chapter 8 in the Book of OHDSI](https://ohdsi.github.io/TheBookOfOhdsi/OhdsiAnalyticsTools.html).
+
+The vision for ATLAS is to provide a common set of study design tools that are capable of running one or more [HADES](https://ohdsi.github.io/Hades/) analytical R packages.
 
 ## Resources