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Do not paste research data into ChatGPT or another AI service until you have confirmed that the dataset, the proposed task, the service and your institution all permit it. A dataset can be de-identified and still be subject to consent limits, an institutional review-board determination, a repository data-use agreement, controlled-access rules or other law. A public prompt can also be an external disclosure because the provider may retain, review, share or otherwise use inputs and outputs under its current terms.

The safe approach is a documented, risk-based workflow: identify every data restriction, obtain the required approvals, use an environment approved for that classification and task, minimize what leaves the research system, and have a qualified person verify every consequential output. The guidance below is primarily U.S.-focused and does not replace project-specific advice from your IRB or research-compliance, privacy, information-security, data-steward and funder offices.

Start with a permission decision, not a prompt

Whether you may use AI is determined by the data and the proposed operation, not by the fact that an AI tool is popular or that a prompt contains only a few lines. Treat summarization, coding help, image analysis, model training, question answering and data cleaning as separate uses. Each can create a different disclosure, retention and derivative-data risk.

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Before any upload, write down the exact inputs, the expected outputs, the people who will see them, and whether the AI system will store logs, backups or model artifacts. Include material that is easy to overlook: free-text fields, images, audio, codebooks, linkage keys, derived tables, rare-case examples and training data. A small excerpt can still reveal a participant when combined with public information.

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Map the dataset’s provenance

For every input, record where it came from and which document governs it. Possible sources include direct participant collection, an institutional repository, a controlled-access genomic database, a collaborator, a clinical system or another research project. Link each source to its consent language, IRB or ethics determination, repository terms, data-use agreement (DUA), funder conditions and institutional classification.

NIH’s NICHD Office of Data Science and Sharing explains that several obligations can apply at the same time, including HIPAA, the Common Rule, IRB decisions, participant consent, repository rules and institutional policy. De-identification does not automatically cancel those obligations. If a DUA limits cloud processing, re-identification, recontact, redistribution or model development, those limits remain part of the decision.

Ask what the consent and approvals allow

Check whether participants were told about secondary analysis, automated processing, commercial services, international transfers, model development, future sharing and downstream users. If the consent language is silent or restrictive, ask the IRB or privacy office for a determination instead of assuming that a new AI task is compatible.

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Record the approval number, data steward, permitted purpose, user population, geographic limits and expiry or review date. Pass relevant restrictions to collaborators and downstream analysts. NIH supplemental privacy guidance recommends proactively assessing protections, clearly communicating future use and sharing in consent processes, justifying limitations, and having institutions review sharing conditions. It is supplemental guidance rather than a standalone compliance manual, so other laws and repository rules may impose additional requirements.

Classify the proposed operation

Distinguish between an operation that keeps data inside an approved environment and one that sends data to an external service. Also distinguish between asking for a transformation and creating a reusable model. A model, embedding index, prompt log or fine-tuning checkpoint may contain information derived from the original dataset and may be regulated as a derivative.

Define the minimum output you need. If the goal is to draft code documentation, use synthetic examples or a schema without records. If the goal is to summarize participant narratives, determine whether a human-approved secure system can perform that task without exposing direct or indirect identifiers. Data minimization is a design decision, not a last-minute redaction exercise.

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Why a public AI prompt can count as disclosure

Public AI services generally operate outside your institution’s security boundary. The current terms for a service may allow the provider to host, copy, retain, review, use, disclose or otherwise process prompts and outputs for service delivery, safety, product improvement, legal or operational purposes. Terms differ by provider and product and can change, so read the exact service agreement and privacy documentation that apply to your account and date of use.

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Turning off model training is not a complete answer. You still need to know who can access prompts and outputs, how long logs and backups persist, whether humans may review content, what deletion means, where processing occurs, and whether the provider can disclose data to subcontractors or authorities. An enterprise label or a paid subscription does not by itself prove that a service is approved for your data classification.

NSF gives a clear, process-specific example. In its December 14, 2023 notice to the research community, the agency states: "NSF reviewers are prohibited from uploading any content from proposals, review information and related records to non-approved generative AI tools." NSF further says that proposal information sent through the open internet violates confidentiality and integrity principles and that information uploaded to tools outside the NSF firewall is considered to enter the public domain for its merit-review process. That statement governs NSF review; it should not be presented as a universal legal definition for every AI service or jurisdiction.

De-identification lowers exposure but does not grant permission

Remove direct identifiers to the greatest extent compatible with the scientific purpose, and document what you removed, generalized or masked. Then assess residual risk. Dates, rare diagnoses, geographic detail, occupations, genomic variants, free text, images and combinations of innocuous fields can support re-identification or sensitive inferences.

NIH advises proactive privacy assessment even for de-identified data because information can be combined to produce new inferences. Controlled-access requirements may continue to apply. A DUA can prohibit re-identification or recontact, limit who may use the data, require security controls or restrict redistribution and model development. Those restrictions should travel with derived datasets and outputs.

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Use controlled access when residual risk warrants it

NIH privacy guidance says researchers and institutions should proactively assess protections for participant data, including whether sharing should be restricted through controlled access. Controlled access is not a sign that de-identification failed; it is a governance choice for data whose residual risk, consent terms or scientific sensitivity calls for additional accountability.

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Do not treat a de-identification script as proof of compliance. Keep the method, reviewer, date, assumptions and known failure modes with the project record. Have the data steward decide whether the transformed data can leave the approved environment and whether each downstream user must sign an agreement.

Special rules for NIH controlled-access human genomic data

NIH Notice NOT-OD-25-081, issued March 28, 2025, addresses generative AI models built by Approved Users of NIH controlled-access data. NIH states: "Additionally, NIH considers generative AI models, including model parameters, developed by Approved Users of controlled-access data to constitute Data Derivatives as defined in the DUC provision 14. Definitions."

Until NIH issues further guidance, the notice sets three practical conditions:

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  • Use of controlled-access data to develop a generative AI model must be approved under the applicable NIH process.
  • The model and its parameters may be shared only with collaborators who are also Approved Users.
  • The model may not be retained after project closeout as instructed by the Data Use Certification (DUC).

These are interim conditions. Check the notice, the project’s current DUC, repository instructions and any newer NIH direction before training, transferring, deploying or retaining a model. Do not assume that a model is outside the DUC merely because it no longer contains the original files or because the provider calls it an output.

Choose an environment that is approved for the data and task

No deployment model is automatically secure or compliant. Compare the options against the actual dataset, purpose, institutional policy and service terms.

Workflow What must be established Residual risks to manage
Public AI service Consent, IRB, DUA and institutional approval permit external processing; current terms define access, retention, training, disclosure and deletion. External disclosure, provider or subcontractor access, persistent logs or backups, changing terms and outputs that expose sensitive content.
Institution-approved secure platform The institution has approved the platform for the data classification and purpose; administrators define inputs, outputs, users, logging, retention and deletion. Misconfigured permissions, excessive retention, administrator or vendor access, and unverified or misleading outputs.
Local or otherwise isolated processing Security staff confirm the system, model, dependencies, updates, endpoint controls and storage meet project requirements; derivative-data rules are addressed. Compromised hosts, copied checkpoints, weak access controls, model leakage and the mistaken belief that isolation alone satisfies consent or DUA terms.

Use these questions when reviewing any platform:

  • Does the source consent and DUA permit this specific AI use and location?
  • Is the environment approved by the institution for this classification and purpose?
  • Who can access prompts, uploads, outputs, logs and backups?
  • How long is each item retained, and what does deletion actually remove?
  • May the provider train on inputs or outputs, and can it disclose them?
  • Could a model, embedding, index or checkpoint become a regulated derivative?
  • Can a qualified human verify the output, and can the team document that review?

Apply layered controls before processing

Limit people and privileges

Use named accounts, least-privilege access and role separation appropriate to the dataset. Restrict administrative access, review membership periodically and remove access when a person leaves the project. Keep sensitive data out of shared prompt libraries, public workspaces and personal accounts.

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Separate identities from analysis data

Store linkage keys separately from analytic files. Do not send a key, a near-identifier and a detailed narrative in the same request. If a task requires joining records, perform the join inside the approved research environment and send only the minimum result needed for the AI operation.

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Define retention and deletion

Set retention for prompts, outputs, logs, temporary files, backups and model artifacts before use. Obtain written confirmation of provider deletion where the service contract requires it, and record closeout actions. For controlled-access genomic projects, follow the DUC’s model-retention instruction rather than relying on a generic account-deletion feature.

Protect confidentiality, integrity and availability

NIST frames AI security around confidentiality, integrity and availability of systems, training data and outputs, as well as the underlying software and hardware. Use your organization’s established information-security controls as the baseline and involve security staff for sensitive workloads. NIST also describes AI security as an active, rapidly changing area whose existing guidance does not comprehensively cover every AI-specific attack class; a current approval is not a reason to stop monitoring the system.

Verify every consequential output

Require a person with subject-matter expertise to check citations, calculations, code, classifications, extracted fields and summaries. Compare generated results with source records or an independent method. Record the model or service version, date, prompt or instruction set, relevant settings, input transformation and reviewer decision when the task affects participants, publications, clinical interpretation, funding, compliance or public release.

A practical approval workflow

  1. Inventory the inputs. List files, fields, images, text, code, derived data and any model-training material that would enter the workflow.
  2. Identify governing documents. Collect consent language, IRB determinations, HIPAA or Common Rule analysis where applicable, repository terms, DUA, DUC, funder rules and institutional policy.
  3. Describe the task. State whether the AI will summarize, classify, generate code, search, transform, fine-tune or produce a reusable model. Define the required output.
  4. Minimize. Remove direct identifiers and unnecessary detail. Use synthetic or public examples for prompt design and testing.
  5. Obtain a written determination. Ask the IRB or research-compliance, privacy office, data steward and security team whether the use and environment are permitted.
  6. Review the actual service terms. Check retention, human review, training, disclosure, location, subcontractors, deletion, backups and derivative-model provisions for the exact product and account.
  7. Configure controls. Set approved users, access roles, logging, retention, export and deletion rules. Prevent automatic sharing and personal-account use.
  8. Run a low-risk pilot. Test with synthetic or fully public data, then confirm that prompts, outputs and logs behave as expected before introducing approved research data.
  9. Process the minimum data. Keep identifiers, linkage keys and unnecessary raw records inside the controlled system. Transfer only the fields needed for the approved task.
  10. Review and document outputs. Have an accountable researcher verify results and record corrections, uncertainty and the AI’s role.
  11. Close out. Remove temporary files, revoke access, complete required deletion and handle models, checkpoints and derivatives according to the DUA, DUC and institutional records policy.
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Agency-specific limits you must keep separate

NIH scientific peer review

NIH prohibits its scientific peer reviewers from using generative AI to analyze or formulate peer-review critiques for grant applications and research-and-development contract proposals. That is a confidentiality rule for NIH review work, not a blanket ban on every AI use in research.

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NSF merit review and proposal preparation

NSF prohibits reviewers from uploading proposal content, review information or related records to non-approved generative AI tools. NSF also encourages proposers to describe whether and how they used generative AI to develop proposals; proposers remain responsible for the accuracy and authenticity of submissions. Follow any later NSF guidance for the specific process.

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What to do when something goes wrong

You already uploaded identifiable or restricted data to a public tool

Stop further use, preserve the prompt, account, timestamps and service terms, and contact your institution’s privacy, security, research-compliance and data-steward offices immediately. They can determine whether the event is an incident, whether the provider can delete or restrict access, whether participants or a repository must be notified, and what corrective action is required. Do not quietly delete local evidence before the responsible offices advise you.

The data are de-identified but the DUA forbids external processing

Do not proceed. De-identification does not override a contractual restriction. Move the task to an approved environment or request a formal amendment from the data steward and repository.

The service says it does not train on prompts

Ask about retention, logs, backups, human review, subcontractors, geographic processing, legal disclosure and deletion. Training is only one of the possible uses of uploaded information.

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The model produces a plausible but wrong result

Quarantine the output, compare it with authoritative records and document the error. Adjust the task or discontinue AI use if a qualified reviewer cannot reliably detect and correct mistakes. Never treat fluent text as evidence that an analysis, citation, calculation or classification is valid.

A project is closing while a model still exists

Check the governing agreement before archiving or transferring the model. For NIH controlled-access genomic data, the interim NOT-OD-25-081 conditions require following the DUC instruction on model retention and limit sharing to Approved Users.

NIH secure-tool examples are not universal approvals

The NIH Library’s November 2025 staff toolkit tells NIH users not to enter personally identifiable information, protected health information or sensitive data into public tools and to use NIH-secure platforms for sensitive information. It notes that individual NIH Institutes and Centers may impose stricter requirements. The toolkit lists resources such as CHIRP, an NIH ChatGPT Enterprise license, GENESIS and STRIDES as examples for NIH staff. Those examples are staff guidance, not endorsements, availability promises or approvals for another university, funder or dataset. Your institution must make its own determination.

Scope and currentness

The main sources behind this guidance are U.S. federal materials: NIH notices and privacy guidance, NSF’s merit-review notice and NIST’s AI-security work. They do not resolve obligations under non-U.S. law, every funder’s policy or every commercial service’s contract. Service terms and agency guidance can change, and NIST identifies AI security as an evolving field. Recheck the current documents and obtain a project-specific determination before a new dataset, model, provider or purpose is introduced.

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Decision checklist

  • The dataset’s provenance, consent, IRB status and DUA or DUC are documented.
  • The proposed AI task and output are defined, minimized and approved.
  • The chosen environment is institutionally approved for this classification and purpose.
  • Prompt, output, log, backup and model access and retention are understood.
  • Provider terms on training, review, disclosure, deletion and derivatives have been checked.
  • Residual re-identification and inference risks have been assessed.
  • Human verification, incident reporting and closeout procedures are assigned.
  • Agency-specific peer-review restrictions have been checked separately.

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