{"entity":{"id":"duckdb-catalog","kind":"term","name":"Analytical databases as a data catalogue (DuckDB, PostgreSQL)","aka":["DuckDB","PostgreSQL","Postgres","metadata catalogue","data catalogue","queryable metadata spine","Patient to Specimen to Assay hierarchy"],"tldr":"DuckDB is an in-process analytical database that queries Parquet files with SQL; PostgreSQL is the standard client-server database; either can hold the metadata spine that joins patients, specimens and assays.","summary":"DuckDB is an open-source column-oriented relational database designed for high performance on analytical queries in embedded configurations (Wikipedia); PostgreSQL is a free relational database emphasising extensibility and SQL compliance (Wikipedia). A research data layer typically keeps the large arrays in HDF5, Zarr or Parquet and a small catalogue in one of these, modelling the hierarchy patient to specimen to assay with provenance on every row so that a query can say which files went into a result.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/DuckDB","links":[{"label":"Wikipedia: PostgreSQL","url":"https://en.wikipedia.org/wiki/PostgreSQL"},{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/DuckDB"}],"tags":["cansim-terms"],"related":["cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":[],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["hdf5-zarr-parquet","provenance-fields","tcga-barcode"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":["Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/duckdb."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme"},"category":"Methods and models"},"route":"/terms/duckdb-catalog/","neighbours":{"term":[{"id":"hdf5-zarr-parquet","kind":"term","name":"Array and table formats: HDF5, Zarr, OME-Zarr, Parquet","route":"/terms/hdf5-zarr-parquet/"},{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"provenance-fields","kind":"term","name":"Provenance fields for research data","route":"/terms/provenance-fields/"},{"id":"tcga-barcode","kind":"term","name":"TCGA barcode","route":"/terms/tcga-barcode/"}]}}