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AI agent for bioinformaticians

Research Dataset Documentation Agent

Dataset documentation that describes exactly what happened to the data.

Research Dataset Documentation Agent: what goes in, what the agent does and what you get

What it does

Dataset documentation often leaves out processing steps that were actually applied, so other researchers cannot understand or trust the data. This agent runs when a dataset is prepared for sharing. It traces provenance through the transformation logs and scripts, step by step, from raw input to final file. It checks whether every change in the data, such as rows removed or values recoded, matches a logged step. When a change has no log, it records an explicit documentation gap for the data steward instead of inventing a method description. It then drafts documentation from what was observed, compares the draft with the logs once more, and the data steward approves publication. Edge case: a manual edit in a spreadsheet with no log is listed as an undocumented step, even if someone remembers doing it.

How it works

Follow the arrows from top to bottom. The orange dashed arrow is the loop: when a check fails, the agent goes back and tries again.

Start and resultWhat it doesA check on its own workWaits for your OKGoes back and retries
Yes, continueYes, continueApprovedNoNo 1 STARTS WHEN Dataset prepared 2 USES A TOOL Trace provenance through the logs 3 USES A TOOL Compare data changes with logged steps 4 CHECKS THE RESULT Is every transformation logged? If not: record a documentation gap. Back to step 3. 5 DOES Draft the documentation 6 CHECKS THE RESULT Does the draft match the logs exactly? If not: correct the description. Back to step 5. 7 YOU APPROVE Data steward approves publication 8 RESULT Source-linked dataset documentation
Read the steps as a list
  1. Dataset prepared
  2. Trace provenance through the logs
  3. Compare data changes with logged steps
  4. Is every transformation logged?If not: record a documentation gap. Back to step 3.
  5. Draft the documentation
  6. Does the draft match the logs exactly?If not: correct the description. Back to step 5.
  7. Data steward approves publicationThe agent waits here for your OK.
  8. Source-linked dataset documentation

How it decides

It documents observed transformations only.

  • Undocumented steps become gaps, never invented methods.
  • Row count changes must be explained by logged steps.
  • The draft describes only what the logs show.
  • The data steward approves publication.

Make it yours

Every agent is a starting point. You choose these settings for your own situation.

  • Log and script locations to trace
  • Documentation template (default: README with provenance table)
  • Who resolves gaps (default: data steward)
  • Whether to compare row counts at every step (default yes)
  • Publication repository

What keeps you in control

It always asks you first

  • Dataset publication
  • Licensing

Hard limits

  • No invented methods.

It stops when

  • Done: documentation drafted.

Set it up

We guide you through the set-up, step by step

Members get the full set-up guide for this agent. No technical skills needed: you copy, paste and upload.

10 minto set it up in your AI
5 AIsChatGPT, Claude, Copilot, Gemini, Grok
  • One set of instructions to paste into your AI, with the clicks for ChatGPT, Claude, Microsoft 365 Copilot, Gemini and Grok
  • The agent then walks you through connecting your own data, one source at a time
  • A downloadable copy with the flow chart, the rules and the full guide
Get access to this agent

An example run

What happensFor the 2026 survey dataset, the agent traces 12 logged steps. Row counts drop from 4,120 to 3,986, but the logs explain only 96 removals. The check fails, so it records a gap for 38 rows. It also finds a filter removing values above 3 SD that the draft did not mention and adds it. The steward explains the 38 rows as test entries, and approves publication.

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