Skip to main content

Schema resources for the National Microbiome Data Collaborative (NMDC)

Project description

National Microbiome Data Collaborative Schema

PyPI - License PyPI version

The mission of the NMDC is to build a FAIR microbiome data sharing network, through infrastructure, data standards, and community building, that addresses pressing challenges in environmental sciences. The NMDC platform is built on top of a unified data model (schema) that weaves together existing standards and ontologies to provide a systematic representation of all aspects of the microbiome data life cycle.

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

Documentation

The documentation for the NMDC schema can be found at https://microbiomedata.github.io/nmdc-schema/. This documentation is aimed at consumers of NMDC data and metadata, it describes the different data elements used to describe studies, samples, sample processing, data generation, workflows, and downstream data objects.

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

The remainder of this page is primary for the internal maintainers and contributors to the NMDC schema

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

Maintaining the Schema

See DEVELOPMENT.md for instructions on setting up a development environment.

See MAINTAINERS.md for instructions on using that development environment to maintain the schema.

Makefiles

Makefiles are text files people can use to tell make (a computer program) how it can make things (or—in general—do things). In the world of Makefiles, those things are called targets.

This repo contains 2 Makefiles:

  • Makefile, based on the generic Makefile from the LinkML cookiecutter
  • project.Makefile, which contains targets that are specific to this project

Here's an example of using make in this repo:

# Deletes all files in `examples/output`.
make examples-clean

The examples-clean target is defined in the project.Makefile. In this repo, the Makefile includes the project.Makefile. As a result, make has access to the targets defined in both files.

Data downloads

The NMDC's metadata about biosamples, studies, bioinformatics workflows, etc. can be obtained from our nmdc-runtime API. Try entering "biosample_set" or "study_set" into the collection_name box at https://api.microbiomedata.org/docs#/metadata/list_from_collection_nmdcschema__collection_name__get

Or use the API programmatically! Note that some collections are large, so the responses are paged.

You can learn about the other available collections at https://microbiomedata.github.io/nmdc-schema/Database/

Project details


Release history Release notifications | RSS feed

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

nmdc_schema-10.1.3.tar.gz (673.7 kB view details)

Uploaded Source

Built Distribution

nmdc_schema-10.1.3-py3-none-any.whl (697.0 kB view details)

Uploaded Python 3

File details

Details for the file nmdc_schema-10.1.3.tar.gz.

File metadata

  • Download URL: nmdc_schema-10.1.3.tar.gz
  • Upload date:
  • Size: 673.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.0.0 CPython/3.8.18

File hashes

Hashes for nmdc_schema-10.1.3.tar.gz
Algorithm Hash digest
SHA256 1959a18cb40dfe60f2af8b1cf1f20a730a1df0b6d7ec00670f63ccb464640712
MD5 2cb3ce4faefd8ce6c9e00854b852db15
BLAKE2b-256 6c36d351fbf063bc10f63163ef4696ebf6213a9c297c7044121b053af33cda9c

See more details on using hashes here.

Provenance

File details

Details for the file nmdc_schema-10.1.3-py3-none-any.whl.

File metadata

  • Download URL: nmdc_schema-10.1.3-py3-none-any.whl
  • Upload date:
  • Size: 697.0 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.0.0 CPython/3.8.18

File hashes

Hashes for nmdc_schema-10.1.3-py3-none-any.whl
Algorithm Hash digest
SHA256 ce25cdc6fd71d3a1d11b2e69347f6c597b52556cfcfc216963a44127ba23ddf6
MD5 2a2f59d89633bae44db4b57c4e12dc2b
BLAKE2b-256 b8f5d6735ddf06213ace501445521255a5c83ba6a68a5ad6cfb3cc977d6db812

See more details on using hashes here.

Provenance

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page