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Modularity Survey Project

This is a literature survey database tracking academic papers on modularity in biology. The database is stored as a CSV file and can be queried via DataSette.

Project Structure

  • db/modularity_survey.csv — Main literature database with detailed paper metadata
  • README.md — Project overview and basic query examples

Database Schema

The CSV contains these key columns (see header rows for full documentation):

  • Metadata: AddedBy, AIAgentAndModel, LastNameOf1stAuthor, All authors, Paper title, Year, Paper type, DOI URL
  • Technical: Modeling framework, Definition of module, Algorithmic aspect, Data
  • Biological Context: Context of system, Purpose of module, Level of organization, Organism
  • Impact: Impact of paper, Citations, Summary, Primary theme
  • Review Status: Read by, Notes (multiple columns for different reviewers)

Common Workflows

Adding New Papers

When adding entries to modularity_survey.csv:

  1. Maintain consistent formatting with existing entries
  2. Include all required metadata fields (especially: authors, title, year, DOI)
  3. Use standardized keywords for: Paper type (research/review/perspective), Modeling framework (Boolean network/ODE/graph based/stochastic), Level of organization (cell/tissue/organism)
  4. Provide concise 1-2 sentence summary for the Summary column
  5. Always credit AddedBy and AIAgentAndModel used

Expanding the Bibliography

Use the @literature-search-agent to find related papers:

  • Find papers that cite influential works already in the database
  • Expand specific subdisciplines (e.g., Boolean networks, evolutionary modularity)
  • Identify follow-up work on key papers

Example: "@literature-search-agent find papers that cite the Newman 2006 modularity matrix paper and filter by >50 citations"

Querying the Database

The README shows basic SQL examples. More complex queries via DataSette:

  • Filter by year range, organism, modeling framework
  • Aggregate by primary theme or level of organization
  • Search summaries for specific concepts

Conventions

  • Citation format: Standard academic format with all authors listed
  • DOI URLs: Always use https://doi.org/ format
  • Keywords: Use controlled vocabulary from existing entries when possible
  • AI attribution: When AI agents help curate entries, note the agent and model version in AIAgentAndModel column

License

MIT License — see LICENSE file