Schema resources for the National Microbiome Data Collaborative (NMDC)

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  • License: MIT License (MIT)
  • Author: Bill Duncan
  • Tags NMDC, schema, metadata, microbiome
  • Requires: Python >=3.9, <4.0
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Project description

National Microbiome Data Collaborative Schema

PyPI - License PyPI version

The NMDC is a multi-organizational effort to integrate microbiome data across diverse areas in medicine, agriculture, bioenergy, and the environment. This integrated platform facilitates comprehensive discovery of and access to multidisciplinary microbiome data in order to unlock new possibilities with microbiome data science.

This repository mainly defines a LinkML schema for managing metadata from the National Microbiome Data Collaborative (NMDC).

Repository Contents Overview

Some products that are maintained, and tasks orchestrated within this repository are:

  • Maintenance of LinkML YAML that specifies the NMDC Schema
  • Makefile targets for converting the schema from it's native LinkML YAML format to other artifact like JSON Schema
  • Build, deployment and distribution of the schema as a PyPI package
  • Automatic publishing of refreshed documentation upon change to the schema, accessible here

Background

The NMDC Introduction to metadata and ontologies primer provides some the context for this project.

Maintaining the Schema

New system requirement: Mike Farah's GO-based yq

See MAINTAINERS.md for instructions on maintaining and updating the schema.

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