JUMP production metadata

The JUMP production augmented metadata database is the source for the compound target and mechanism-of-action (MoA) annotations used in the JUMP production analysis. These are annotations of compounds, not annotations of the corresponding genetic perturbations.

Database contents

The DuckDB database combines:

• core JUMP metadata for compounds, ORF and CRISPR perturbations, plates, wells, controls, and microscope configurations;
• Drug Repurposing Hub compound names, targets, MoAs, clinical phases, diseases, and indications;
• ChEMBL, Chemical Probes, and MOTIVE compound-target annotations;
• ToxCast, toxicity, pharmacokinetic, MitoTox, chemical-property, and cell-count annotations.

The compound_metadata view provides one row per JUMP compound and joins the fields most commonly needed for analysis, including the JUMP ID, InChIKey, chemical structure, targets, and MoAs.

Attach the database with DuckDB

Open the DuckDB Web Shell or start a local DuckDB CLI session, then run:

INSTALL httpfs;
LOAD httpfs;

ATTACH 'https://imaging-platform.s3.amazonaws.com/projects/cpg0042-chandrasekaran-jump/workspace/publication_data/2025_Chandrasekaran/jump_production_datastore/interim/jump_metadata_augmented.duckdb'
    AS meta (READ_ONLY);

DESCRIBE meta.compound_metadata;

The database remains remote and is attached read-only as the meta catalog. Tables and views can then be queried with names such as meta.compound_metadata, meta.compound, and meta.repurposing_hub_annotations.

Query compound annotations

Drug Repurposing Hub MoA annotations are available in Metadata_repurposing_moa. This example retrieves compounds annotated as HSP inhibitors:

SELECT "Metadata_JCP2022" AS jump_id,
       "Metadata_InChIKey" AS inchikey,
       "Metadata_repurposing_name" AS compound_name
FROM meta.compound_metadata
WHERE 'HSP inhibitor' IN (
    SELECT trim(x)
    FROM UNNEST(string_split("Metadata_repurposing_moa", '|')) AS t(x)
);

Chemical Probes target genes are available in Metadata_chmprb_target_genes. This example retrieves the compounds associated with HSP90AA1, together with their Drug Repurposing Hub MoA when available:

SELECT "Metadata_JCP2022" AS jump_id,
       "Metadata_InChIKey" AS inchikey,
       "Metadata_repurposing_name" AS compound_name,
       "Metadata_repurposing_moa" AS mechanism_of_action
FROM meta.compound_metadata
WHERE 'HSP90AA1' IN (
    SELECT trim(x)
    FROM UNNEST(string_split("Metadata_chmprb_target_genes", '|')) AS t(x)
);

Replace HSP inhibitor or HSP90AA1 with the exact MoA or target label of interest. The annotations can contain pipe-delimited lists; splitting those lists and testing exact membership avoids false matches between similarly named targets.