Format for new Compiled Documentation Read the Docs

[mslarae13]

NMDC Documentation Read the Docs Chapters

Chapters

1. Home: Describe NMDC
2. Standards
3. Workflows
4. Portal User Guide (NAR Paper)

Chapter Subsections

Standards @mslarae13

1. Schema
2. Schema Validation
3. Identifiers
4. Metadata Standards
5. Soil MIxS (EXCLUDE IN 1ST DRAFT. Updates needed)
6. Data Harmonizer (EXCLUDE IN 1ST DRAFT. Needs created)

Workflows @kwdavenport

1. Metagenomics
2. Metatranscriptomics
3. Metaproteomics
4. Metabolomics
5. Natural Organic Matter

Portal User Guide (NAR Paper) - Sections TBD @kwdavenport

[mslarae13]

This is how Karen and I brainstormed formatting the Compiled read the docs. Each component will be pulled from its respective repo that generated the individual documentation

Standards: https://microbiomedata.github.io/nmdc-schema/Metadata_Documentation_Overview/ https://github.com/microbiomedata/metadata_documentation

Workflows: https://nmdc-workflow-documentation.readthedocs.io/en/latest/chapters/overview.html https://github.com/microbiomedata/workflow_documentation

Portal: https://the-nmdc-portal-user-guide.readthedocs.io/en/latest/ https://github.com/microbiomedata/portal_user_guide

[mslarae13]

Bill updated the figures, and noted that the "Schema" section is accurate.

MIxS soil package is inaccurate and v5. This needs updated to v6. @cmungall i know you mentioned this was done manually, but I think I remember discussion that there is possibly some way to do this computationally. Is that accurate?

[mslarae13]

Michal has completed the compiled documentation. Follow up tasks need captured

• Re-format using diataxis framework
• Update schema definitions and pull directly
• Update MIxS to use v6
• generate data harmonizer read the docs.

@ssarrafan , tasks to be made into github tickets and discussed where they land in priorities and who will be responsible.