Kbase All The Bacteria

Why This Collection Matters

kbase_all_the_bacteria is a live BERDL database in the KBase tenant. This scaffold page makes the collection visible to humans and agents even before a domain-specific curator has written a richer interpretation.

What It Contains

The live Spark inventory records 3 tables. Key tables include: assembly_file_index, bakta_file_index, file_index

Best Uses

Use this page as an entry point for deciding whether the database should be promoted into a curated collection, linked to a data-type page, or used as a source for a derived product.

High-Value Joins

Start by inspecting stable identifiers in the table schemas, then connect through the linked data-type page. For user, staging, or imported namespaces, write a join recipe before using the collection as evidence for a claim.

Reuse And Gaps

High-value reuse would turn this raw collection into a documented mapping table, benchmark, feature matrix, annotation layer, or caveat label. Missing complementary data should be recorded as a data_gap page once the blocker is clear.

Caveats

• The live Phase 1 refresh used Spark SQL table inventory and intentionally skipped per-table schemas to avoid long-running DESCRIBE calls across user and staging namespaces.