Skip to content

GenomicsStandardsConsortium/mixs6.2_release_candidate

 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Harmonized MIxS 6.2 Release Candidate

Documentation and data validator: http://w3id.org/mixs-6-2-rc/

  • This validator does not submit data to any repository
Repo | Report Bug | Releases



Table of Contents
  1. About The Project
  2. Getting Started
  3. Usage
  4. Roadmap
  5. Contributing
  6. License
  7. Contact


About The Project

The Minimal Information about any (x) Sequence (MIxS) standard is a product of the Genomic Standards Consortium (GSC). The GSC has a mission of enabling genomic data integration, discovery, and comparison through international community-driven standards.

This code repository was developed in collaboration between the National Microbiome Data Collaborative (NMDC) and the GSC. It transitions a spreadsheet version of the MIxS standard into a machine-actionable, self-documenting schema adhering to the Linked Data Modelling Language (LinkML).

  • Term attributes are harmonized
  • Previously informal data constraints are formalized
  • Implicit classes are made explicit
  • Example data is provided
  • Validation tools are provided

This work is provided for consideration as MIxS 6.2 and will be presented at the 23rd Genomic Standards Consortium Meeting in August 2023 in Bangkok, Thailand.

See also Social and Technical Aspects of Implementing MIxS in LinkML

(back to top)

Getting Started

This is a standard Python project that runs on the CLI. No installation is required for

Prerequisites for Rebuilding Locally

  • software build tools like GNU Make that are often present on many Linux and MacOS systems
    • or Windows systems using interoperability layers like WSL
  • python >= 3.9
  • poetry >= 1.2

First Time Setup

  1. Install Poetry if necessary
  2. Install dependencies > poetry install
  3. Run with > make all

(back to top)

See the open issues for a full list of proposed features (and known issues).

(back to top)

Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!

  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request

(back to top)

License

Distributed under the MIT License. See LICENSE.md for more information.

(back to top)

Contact

Mark Andrew Miller, National Microbiome Data Collaborative, Lawrence Berkeley National Laboratory

(back to top)

Releases

No releases published

Packages

No packages published

Languages

  • Python 71.2%
  • Makefile 18.8%
  • Jinja 7.8%
  • Other 2.2%