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

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.

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Getting Started

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

• viewing the schema file
• accessing the schema in other formats
• accessing examples of valid and invalid data in various formats
• accessing reports about modifications applied
• visiting the documentation and ephemeral validator

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

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

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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

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License

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

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Contact

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

• MAM@lbl.gov

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