Finding a Report

BF4 ships with a growing set of reports — entity lookups, neighborhood summaries, variant annotations, ETL status, and more. Three ways to find the one that fits your need.

1. Browse the catalog

The Report Catalog is the canonical index. It groups reports by purpose (ETL monitoring, entity exploration, variant analysis, modeling) and gives you, for each one:

  • A one-line description of what it does.

  • A link to its Explain Guide (parameters, output columns, examples).

  • A link to a Notebook tutorial that runs end-to-end.

Use the catalog when you want to scan everything available.

2. Ask the GPT assistant

For natural-language questions like “I have a list of genes from a GWAS — which report should I run to see what pathways they touch?”, BF4 ships with a GPT assistant kit in the assistent/ folder of the repository. It contains:

  • A system prompt tuned for BF4 terminology.

  • A FAQ.

  • A manifest of all reports with their inputs, outputs, and use cases.

Link to GPT BF4 Assistent: BF4 Assistent

3. Use the CLI to introspect

If you already have BF4 installed and just want a quick list:

biofilter report list

For details on a specific report:

biofilter report explain --report-name entity_filter

This prints the full Explain Guide directly in your terminal, including parameters and example invocations.

Common starting points

If you’re new and not sure where to start, these reports are good entry points:

Report

Use it when

etl_status

You want to see what data is loaded in the database

entity_filter

You have a list of names and want to check which exist in BF4

entity_neighborhood_summary

You have an entity and want to see everything connected to it (1-hop)

annotation_master_gene

You want to browse the full gene catalog

Next step

Picked one? Run your first report.