COPO: Guidelines

Welcome to the guidelines for submission, updates and retrieval for the Collaborative OPen Omics project. Please use the links to find instructions specific to your needs.

Getting Started

• Getting Started
  • Accessing COPO Website
• Projects Brokered through COPO
  • Primary Projects
  • Secondary Projects
• New User
  • First time login
• Sample Managers
  • Accessing the Accept or Reject Samples web page
  • Guidelines for Sample Managers Assigned to More than one Manifest Group
  • Accepting or Rejecting Samples
    • Accepting samples
    • Accepting ASG or DTOL samples
    • Accepting ERGA samples as a BGE checker
    • Accepting ERGA samples as a Sample Manager
    • Rejecting samples
  • Download Submitted Permits
  • View Submitted Images
  • Upload Manifest or Update Submitted Manifest on behalf of Manifest Submitters

COPO Profile

• Stand-alone Profile
  • Steps to Create a Stand-alone Profile
  • Stand-alone Profile Components
• Tree of Life Profile
  • Steps to Create a Tree of Life Profile
    • Provide Profile Title & Description
    • Choose Profile Type
    • Choose Associated Profile Type(s) (if required)
    • Choose Sequencing Centre (if required)
    • Profile created
  • Tree of Life Profile Components
• Sharing Profiles
  • Sharer
  • Sharee
• Sorting Profiles
• Profile Types Legend

COPO Data Submission

• General Tree of Life Visual Submission Documentation
• Assembly Submission
  • How to Submit Assemblies
    • Accessing the Assembly Web Page
      • Use Components’ Button to Navigate to Assembly Web Page
      • Use Actions’ Button to Navigate to Assembly Web Page
    • Submit Assembly
  • How to Delete Assemblies
• Barcoding Manifest Submission
  • How to Submit Barcoding Manifests
    • Accessing the Barcoding Manifest Web Page
      • Use Components’ Button to Navigate to Barcoding Manifest Web Page
      • Use Actions’ Button to Navigate to Barcoding Manifest Web Page
    • Upload Barcoding Manifest
    • Submit Barcoding Manifests
  • How to Delete Barcoding Manifests
• Files Submission
  • How to Submit Files
    • Accessing the Files’ Web Page
      • Use Components’ Button to Navigate to Files’ Web Page
      • Use Actions’ Button to Navigate to Files’ Web Page
    • Submit Files from your Local (Computer) System
    • Submit Files via the Terminal
  • How to Delete Files
• Images Submission
  • How to Submit Images
  • View Submitted Images
    • On Samples web page
    • On Accept or Reject Samples web page
• Permits Submission
  • How to Submit Permits
  • Download Submitted Permits
    • On Samples web page
    • On Accept or Reject Samples web page
• Reads Submission
  • How to Submit Reads
    • Accessing the Reads’ Web Page
      • Use Components’ Button to Navigate to Reads’ Web Page
      • Use Actions’ Button to Navigate to Reads’ Web Page
    • Upload Reads
    • Submit Reads
• Samples Submission
  • How to Download Submitted Sample Manifest
• Sequence Annotations Submission
  • How to Submit Sequence Annotations
    • Accessing the Sequence Annotations’ Web Page
      • Use Components’ Button to Navigate to Sequence Annotations’ Web Page
      • Use Actions’ Button to Navigate to Sequence Annotations’ Web Page
    • Submit Sequence Annotations
  • How to Delete Sequence Annotations

COPO Data Updates

• Updating Profiles
  • Deleting Profiles
• Updating Samples
• Updating Sequence Annotations
• Updating Reads
• Adding Children Projects to Parent Projects
  • In COPO
  • In Public Repositories

COPO Data Discovery & Retrieval

• Downloading Manifest Templates & Standard Operating Procedures (SOPs)
  • Downloading Manifest Templates
  • Recording Data in Manifests
    • ASG SOP
    • DToL SOP
    • DToL_ENV SOP
    • ERGA SOP
    • POP_GENOMICS SOP
• Using COPO API
  • API End-points
    • Audit Endpoints
      • Fetch Sample Updates Between Dates
      • Fetch Sample Updates by Manifest ID
      • Fetch Sample Updates by COPO ID
      • Fetch Sample Updates by Update Type
      • Fetch Sample Updates by Field and Field Value
      • Fetch Sample Updates by ASG Sample Type
      • Fetch Sample Updates by DTOL Sample Type
      • Fetch Sample Updates by ERGA Sample Type
    • Manifest Endpoints
      • Fetch Manifests
      • Fetch Current Manifest Versions
      • Fetch Sample Records by Manifest ID
      • Fetch Manifests between Dates
      • Fetch Manifests between Dates for a Project
      • Fetch Sample Record Status in a Manifest
      • Validate Manifest by Profile ID
      • Validate Manifest by Report ID
      • Validate Manifest
    • Sample Endpoints
      • Fetch Sample Records by Project
      • Fetch Sample Records by Associated Project Type
      • Fetch Sample Records between Dates
      • Fetch Sample Records between Dates
      • Fetch Updatable Fields by Project
      • Fetch Sample Records by COPO ID
      • Fetch Sample Records by Biosample ID
      • Fetch Sample Records by Field and Values
      • Fetch Study Records by Sample ID
      • Fetch Sample Records by Study ID
    • Profile Endpoints
      • Create Profile Record
      • Fetch Profile Records
    • Statistics’ Endpoints
      • Fetch Number of COPO Users
      • Fetch Number of Sample Records by Sample Type
      • Fetch Tree of Life (ToL) Projects Brokered by COPO
      • Fetch Associated Tree of Life (ToL) Projects Brokered by COPO
• Exploring Manifest Wizard
  • Prefill Manifests
• Tree of Life Dashboard
  • Tree of Life Inspection
  • Tree of Life Inspection by Genome Acquisition Lab
• Retrieving Accessions
• COPO Statistics
  • Statistics over Time
  • Statistics by Variable
• Manifest Checklist
  • Barcoding Manifest Checklists
  • Sample Manifest Checklists

Advanced

• Setting Up COPO Project Locally with Docker
  • Install Docker
  • Initialise Docker Swarm
    • Add Docker Node Labels
      • Adding One Docker Node Label
      • Adding More than Docker One Node Labels
      • Create Docker Volumes
      • Create Networks on Docker Swarm Manager
      • Create Secrets on Docker Swarm Manager
      • Build COPO Project Docker Image
      • Deploy Docker Image on Docker Swarm Manager
      • Set up PostgreSQL database
    • Updating COPO Website Service
    • Launch COPO Website
    • Tips
• Setting Up COPO Project Locally without Docker
  • Set Up COPO Project on Linux
    • Install Python
    • Install Python Development Tools
    • Install Required Packages
    • Install Integrated Development Environment (IDE)
    • Configure IDE
      • PyCharm
      • VSCode
    • Declare Environment Variables
    • Set up Python virtual environment
    • Set Up Mongo Database in COPO Project
      • Set up MongoDB in Studio3T
    • Set Up PostgreSQL Database in COPO Project
    • Launch COPO Website
  • Set Up COPO Project on Windows
    • Option 1: Using Ubuntu Terminal
    • Option 2: Using Windows Terminal

Policies

• Brokering Data in COPO with FAIR Data Principles
  • Findable
    • Using DataTables’ search engine
    • Using COPO API
  • Accessible
  • Interoperable
  • Reusable
  • FAIR Webinars
• Licence
• Contributor Covenant Code of Conduct
  • Our Pledge
  • Our Standards
  • Enforcement Responsibilities
  • Scope
  • Enforcement
  • Enforcement Guidelines
    • 1. Correction
    • 2. Warning
    • 3. Temporary Ban
    • 4. Permanent Ban
  • Attribution
• Privacy Notice
  • Consent
    • Data Collected
      • Information collected:
      • Usage of information collected:
  • Data Access
  • Data Retention
  • Cookies
  • Questions
• Terms of Use

Help

• Contact COPO
• Frequently Asked Questions
  • Dashboard
  • Manifest Update
  • Permits
  • Profiles
  • Samples
  • Sample Managers
• Glossary