NMDC Documentation

NMDC Overview:

• NMDC Overview
• About our documentation

Tutorials:

• Submitting to NMDC
• Running the Workflows
  • NMDC EDGE QuickStart
  • Metagenomics
  • Metatranscriptomics
  • Answers to Tutorial Questions
• Navigating the Data Portal
  • Answers to Tutorial Questions

How-To Guides:

• Creating a Data Mgt. Plan
  • What is a Data Management Plan?
  • What to include in your DMP?
  • For more information
  • Contact us
• Submitting to NMDC
  • Introduction
  • Portal Functionality
• Running the Workflows
  • NMDC EDGE Quick Start User Guide
  • Metagenomics Workflows
  • Metatranscriptomics Workflow
  • Natural Organic Matter Workflow
• Navigating the Data Portal
  • Introduction
  • User-Centered Design Process
  • Available Studies & Data
  • Studies
  • Standards
  • Omics Data
  • Portal Functionality
  • Interactive visualizations
  • References

Reference:

• NMDC Metadata
  • NMDC Schema
  • NMDC
  • The NMDC Metadata Standards Documentation
  • Validating json objects against the NMDC schema
  • Identifiers in NMDC
  • MIxS Soil Package
  • Credits
• NMDC Workflows
  • Overview
  • Reads QC Workflow (v1.0.2)
  • The Read-based Taxonomy Classification (v1.0.1)
  • Metagenome Assembly Workflow (v1.0.2)
  • Metagenome Annotation Workflow (v1.0.0)
  • Metagenome Assembled Genomes Workflow (v1.0.4)
  • Metatranscriptome Workflow (v0.0.2)
  • Metaproteomic Workflow (v1.0.0)
  • Metabolomics Workflow
  • Natural Organic Matter Workflow
• NMDC Data Portal
  • Software versions
  • General architecture
  • API Documentation
  • Development documentation
  • Data Ingest

Explanation:

• FAIR Data
  • Making microbiome data Findable, Accessible, Interoperable, and Reusable (FAIR).
• IDEA
• Community Conversations
  • 7. How High are Your Standards? The Importance of Metadata Standards for FAIR Data
  • 6. The True Potential of Citing Data
  • 5. Enabling Shared Ownership of Science Gateways with User-Centered Design
  • 4. Flowing into Shared Data: Advantages and Disadvantages of Easily Distributable Containerized Open Source Bioinformatics Workflows
  • 3. Developing Data Science resources in Partnership with Scientific Communities
  • 2. Making Ontologies Work for Microbiome Research
  • 1. Setting Up for Success: The Importance of a Data Management Plan
• Publications
  • NMDC Team Publications
  • Related Publications