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AI agent for neuroscientists

Open Data Deposit Preparation Agent

Submit a dataset that passes the repository checks the first time

Quality controlComplianceScience and research
See how it worksGet access
Open Data Deposit Preparation Agent: what goes in, what the agent does and what you get

What it does

A paper is accepted and the journal requires data deposit in a public repository. The submission is rejected for missing sample metadata, wrong file formats or a failed checker, and the paper waits. This agent prepares the deposit. It checks the dataset against the repository's required metadata, flags gaps, requests details from authors with the exact fields needed, validates the file formats and then runs the repository's own checker. It repeats until the checker passes clean. It also prepares the descriptions and links needed for the paper's data availability statement. The PI approves the submission. Edge case: a sample record contains personal information. The agent flags it and holds the file.

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 Deposit required 2 USES A TOOL Load the repository's metadata and file requirements 3 DOES Compare the dataset and sample sheet with therequirements 4 DOES List missing or invalid fields and files 5 CHECKS THE RESULT Does any record hold personal or sensitive data? If not: Hold those files and ask the PI how to handlethem. Back to step 3. 6 USES A TOOL Ask authors for the missing details with exact fieldnames 7 DOES Validate file formats and convert where allowed 8 USES A TOOL Run the repository's checker on the package 9 CHECKS THE RESULT Does the checker pass with no errors? If not: Fix each listed error and rerun the checker.Back to step 5. 10 YOU APPROVE PI approves the submission 11 RESULT Accepted deposit with accession number and statementtext
Read the steps as a list
  1. Deposit required
  2. Load the repository's metadata and file requirements
  3. Compare the dataset and sample sheet with the requirements
  4. List missing or invalid fields and files
  5. Does any record hold personal or sensitive data?If not: Hold those files and ask the PI how to handle them. Back to step 3.
  6. Ask authors for the missing details with exact field names
  7. Validate file formats and convert where allowed
  8. Run the repository's checker on the package
  9. Does the checker pass with no errors?If not: Fix each listed error and rerun the checker. Back to step 5.
  10. PI approves the submissionThe agent waits here for your OK.
  11. Accepted deposit with accession number and statement text

How it decides

A deposit is ready only when all required fields are filled, formats are accepted and the checker returns no errors. Sensitive data is held for review.

  • All required metadata fields must be filled
  • Only accepted file formats may be deposited
  • Personal data is held until the PI decides
  • The checker must pass before submission

Make it yours

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

  • Target repository
  • Required fields
  • Author contacts
  • Data availability statement template
  • Checker settings

What keeps you in control

It always asks you first

  • PI approves the submission and the data availability statement

Hard limits

  • Never uploads data itself
  • Does not guess missing metadata

It stops when

  • Done: deposit accepted and accession numbers recorded
  • Stop: required data cannot be shared, ask the PI and journal about exceptions

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 happensA sequencing dataset has 48 samples. The agent finds that 12 lack tissue and collection date, and 3 files are in a format the repository rejects. It asks the authors and converts the files. The checker first reports a missing platform field on 6 samples, which the agent fills. The second run passes. The PI approves submission.

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