change readme file

Author: walid-sbr

README.md

@@ -1,92 +1,47 @@
-# scfair
+# scFAIR: Single-Cell Genomics Data Standardization Initiative
 
+## Overview
 
+scFAIR is an initiative to standardize single-cell genomics data and promote findable, accessible, interoperable, and reusable (FAIR) single-cell data. Our goal is to build a collaborative platform that supports and disseminates open research data (ORD) practices within the single-cell genomics community. This platform will enable researchers to upload, annotate, and access single-cell data and associated metadata, ensuring that these data are useful to an increasing community of specialists and non-specialists.
 
-## Getting started
+## Background
 
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+Single-cell genomics has emerged as a transformative field within molecular biology, revolutionizing our understanding of cellular heterogeneity and paving the way for unprecedented insights into complex biological systems. As the quantity and diversity of single-cell data rapidly increase, the lack of clear reporting standards has led to multiple non-compatible datasets, limiting reusability. This presents challenges in making these data useful to the broader scientific community.
 
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+## Need for Standardization
 
-## Add your files
+To address these challenges, there is a critical need for:
+- A centralized, standardized repository where researchers can collaboratively upload, annotate, and access single-cell data and associated metadata.
+- Standardized methods for storing and annotating single-cell data, particularly regarding essential metadata. This includes:
+  - Protocols
+  - Normalization and pipeline characteristics
+  - Cell type classifications and the methods used to classify them
+  - Association between barcodes and annotations
 
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
+Adopting systematic data-sharing practices and standards is integral to fostering transparency, reproducibility, and effective utilization of single-cell genomics data.
 
-```
-cd existing_repo
-git remote add origin https://pccig4007.unil.ch/fabrice/scfair.git
-git branch -M main
-git push -uf origin main
-```
+## Objectives
 
-## Integrate with your tools
+- Build a collaborative platform for sharing datasets and their metadata.
+- Standardize the way data are shared across datasets.
+- Promote communication and outreach to increase the relevance and implementation of these standards within the single-cell genomics community.
 
-- [ ] [Set up project integrations](https://pccig4007.unil.ch/fabrice/scfair/-/settings/integrations)
+## Getting Started
 
-## Collaborate with your team
+To set up the project, follow these steps:
 
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
+1. Create a `/data` folder in the root directory of the project.
+2. Download the composite metazoan ontology file from the following link: [http://purl.obolibrary.org/obo/uberon/composite-metazoan.obo](http://purl.obolibrary.org/obo/uberon/composite-metazoan.obo).
+3. Place the downloaded file in the `/data` folder.
 
-## Test and Deploy
+After setting up the /data folder and placing the ontology file, run the following Rake commands in sequence:
 
-Use the built-in continuous integration in GitLab.
+    rake obo:parse[/data/composite-metazoan.obo]
+    rake obo:update_adjacency_lists
+    rake api_updates
 
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
+These commands will parse the ontology file, update the adjacency lists, and finally, update the API.
 
-***
+---
 
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-
-## License
-For open source projects, say how it is licensed.
-
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+Thank you for being part of the scFAIR initiative! Together, we can make single-cell genomics data more findable, accessible, interoperable, and reusable.