Data import: checklist (draft)

Introduction

This checklist is intended to help formalize the decision-making process for importing new data into Pathway Commons. The aim is to help structure and update information about providers along with useful considerations about the data and the actual status of import.

General

• Homepage
• Downloads
• Publications

Contact

• Primary
  • Name
  • Email
  • Position
• Technical
  • Name
  • Email
  • Position
• Helpdesk

Value

• Uniqueness
• Size (No. interactions)
• Curated
• Database identifiers
• Publications associated
• Biological areas
  • Immunity
  • Metabolism
  • Drugs
  • Signalling
  • Gene regulatory network
  • Genetic interactions
  • Interactions (PPI, DNA, RNA)
• Species
  • human

Format

• Available as standard
  • BioPAX
  • PSI-MI
  • Does validate
    • Has gene identifiers
    • Has publication references
    • Estimated coverage
  • Usability
    • Is immediately usable
    • Not immediately usable
      • Provider can do all required work
      • Pathway Commons must do required work
        • Estimated time, effort
        • Tasks required
          • Critical errors
          • Converter
            • New
            • Update existing
• Not available as standard
  • Provider can do all required work
  • Pathway Commons will do required work
    • Estimated time, effort
    • Tasks required
      • Create mapping document

Data (post-conversion)

• Can load in partial data
• Compatibility
  • SIF
  • Visualization

Maintenance

• Hosting
  • Provider will host
  • Pathway Commons will host
• Updates
  • Data will not be updated
  • Data will be updated

Licensing

• Use
  • Free for academic and commercial use
  • Restrictions on commercial use
  • Restrictions on academic and commercial use
• Redistribution
  • Explicit permission required
  • Restriction on data modification
  • Must provide data access logs