jgi-lakehouselisted

# JGI Lakehouse Skill ## Quick Start **What is it?** JGI's unified data warehouse (651 tables) + filesystem access to genome files. **Two data access methods:** 1. **Lakehouse (Dremio)** → Metadata, annotations, taxonomy (no sequences) 2. **JGI Filesystem** → Actual genome files (FNA, FAA, GFF) via taxon OID **SQL Dialect:** ANSI SQL (not PostgreSQL) - Use `CAST(x AS type)` not `::` - Use `REGEXP_LIKE()` not `~` - Identifiers with dashes need double quotes: `"gold-db-2 postgresql"` ```sql -- Quick test SELECT gold_id, project_name FROM "gold-db-2 postgresql".gold.project WHERE is_public = 'Yes' LIMIT 5; ``` --- ## When to Use - Query JGI genomics metadata (GOLD, IMG, Mycocosm, Phytozome) - Find genomes and/or metagenomes by taxonomy, ecosystem, or phenotype. - Download microbial genomes with IMG taxon OIDs - Cross-reference GOLD projects with IMG annotations ## Instructions 1. Decide whether the task needs metadata, files, or read recovery. 2. Use Lakehouse SQL for metadata/annotations and the JGI filesystem or JAMO for sequence files. 3. Inspect schemas with a small `LIMIT`; remove `LIMIT` for comprehensive results. 4. Record source, table, fields, filters, and access route in every result summary. ## Quick Reference | Task | Action | |---|---| | Test Lakehouse | Query `"gold-db-2 postgresql".gold.project` | | Query IMG metadata | Use `"img-db-2 postgresql".img_core_v400.*` tables | | Query NUMG proteins | Join `faa` and `gene2pfam` on both `oid` and `gene_oid`