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Case Studies

Real-world examples of querying across JGI and KBase genomics databases.

Available Case Studies

mll BGC in Methylorubrum extorquens AM1

A detailed walkthrough of querying the methylolanthanin biosynthetic gene cluster across multiple databases:

  • Databases queried: KBase Pangenome, JGI GOLD, JGI IMG, MIBiG, NCBI
  • Key findings: KBase pangenome missing megaplasmid genes; MIBiG has different BGC
  • Join points identified: Assembly accession, BioSample, NCBI taxonomy ID
  • Lessons learned: Data gaps, locus tag format variations, query strategies

Microbial Isolates Across Lakehouses

Survey of microbial isolate data availability across JGI, KBase, and NMDC:

  • Databases surveyed: JGI GOLD, JGI IMG, KBase, NMDC
  • Key findings: 518K cultured organisms in GOLD; 196K isolate genomes in IMG; NMDC focuses on metagenomes
  • Join points identified: NCBI taxonomy ID, GOLD IDs, biosample identifiers
  • Practical queries: Finding isolates by domain, culture type, and genome completeness

Purpose

These case studies demonstrate:

  1. Practical query patterns - Real SQL queries with actual results
  2. Join point identification - How to link data across databases
  3. Data gap discovery - What's missing and where to find alternatives
  4. Best practices - Recommended strategies for cross-database analysis

Contributing

To add a new case study:

  1. Create a new .md file in docs/case-studies/
  2. Follow the template structure:
  3. Background (organism, genes, biological context)
  4. Database queries (with actual SQL and results)
  5. Join points summary (diagram showing linkages)
  6. Data availability matrix
  7. Lessons learned
  8. Update this index and mkdocs.yml