Reactome identifiers enrichment

Purpose

Run a lightweight Reactome pathway over-representation query from a small list of identifiers and summarize the top enriched pathways.

When to use

• You have a short list of genes or other supported identifiers and need quick pathway context.
• You want a compact Reactome enrichment snapshot before a larger systems-biology workflow.

When not to use

• You need a complete enrichment pipeline with custom background models.
• You need offline execution.
• You need unsupported identifier conversion or pathway visualization.

Inputs

• Identifier list via --identifiers or --input-file
• Optional page size, page number, and output path

Outputs

• JSON payload with query metadata, top pathway summaries, species coverage, resource coverage, and not-found identifiers

Requirements

• Python 3.10+
• Network access to reactome.org

Procedure

1. Run python3 skills/systems-biology/reactome-identifiers-enrichment/scripts/analyze_reactome_identifiers.py --identifiers BRCA1,TP53 --page-size 5 --out skills/systems-biology/reactome-identifiers-enrichment/assets/brca1_tp53_enrichment.json.
2. Inspect pathways for stable_id, name, species, entities_fdr, entities_p_value, and reactions_found.
3. Review identifiers_not_found before using the results downstream.

Validation

• Command exits successfully.
• pathways contains at least one Reactome stable ID for a known human gene list.
• The first pathway has non-empty stable_id, name, and numeric enrichment statistics.

Failure modes and fixes

• No pathways returned: check the identifiers and reduce the list to supported gene symbols or IDs.
• Many missing identifiers: provide one symbol or accession per line or comma-separated item.
• HTTP errors: retry later and keep the identifier list small for smoke validation.

Safety and limits

• Knowledge lookup only.
• This skill does not justify biological claims on its own and does not replace statistical study design.

Example

• python3 skills/systems-biology/reactome-identifiers-enrichment/scripts/analyze_reactome_identifiers.py --identifiers BRCA1,TP53 --page-size 3

Provenance

• Reactome Analysis Service docs: https://reactome.org/dev/analysis
• Reactome platform: https://reactome.org/

Related skills

• reactome-event-summary
• ncbi-gene-search