Overall Documentation Layout

[carolyncaron]

This issue is to open a discussion regarding the layout and structure of the docs. During the monthly writer retreats over the summer, @laceysanderson and I hashed out a layout for the sidebar (ie. table of contents). The thought is to divide the docs into 3 major sections: User Documentation, Curation, File Upload and Management , and Administration Documentation. We chose to do this instead of sectioning by module, as this allows more intuitive navigation depending on who is using the module and their role in either administrating, curating or using the functionality. It is highly likely that a user does not need to know how to import data or install the module, and an administrator can just focus on what they need to know to configure the module.

NOTE: This is currently biased towards curation and the genotypes module specifically as those were the sections I was actively developing on at the time 🙈 So please make suggestions to fill in the blanks 😄

Tripal Cultivate: Documentation

• User Documentation

• Curation, File Upload and Management

  • Germplasm Data
    • Germplasm Accessions
      • File format
    • Germplasm Crosses
      • File format
    • Germplasm Collections
  • Phenotypic Data
    • Phenotypic Traits
      • File Format
    • Phenomic Data Collection
      • File Format (format not set yet: TripalCultivate/TripalCultivate-Phenotypes#63)
    • Open Science Phenotypic Data
      • See https://analyzedphenotypes.readthedocs.io/en/latest/user_guide/loading.html
      • File Format (format not set yet: TripalCultivate/TripalCultivate-Phenotypes#63)
    • Data Storage Model
      • https://analyzedphenotypes.readthedocs.io/en/latest/admin_guide/data_storage.html
  • Genotypic Data
    • Step 1) Metadata Preparation
      • Organism
      • Genome
      • Project
    • Step 2) File preparation
      • File Formats
        • VCF
        • Matrix
        • Flat-file (legacy format)
      • Mapping samples between database and files
    • Step 3) Data Import
      • Tripal Importer
      • Drush command method
      • File Distribution
  • Genetic Maps

• Administration Documentation

  • Installation
    • Germplasm
    • Phenotypes (optional)
    • Genetics (optional)
  • Setup and Configuration
  • Ongoing Site Management
    • File Management
    • Publishing Content
    • Updating Materialized Views