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Health data anonymisation

A framework of categories, verifiable thresholds and decision trees that puts formal bounds on re-identification risk

What it is

We design the methodological framework for anonymising health data extracts consistently and verifiably. Each request is classified by use and granularity, and each class has its own techniques and thresholds, prescribed through decision trees.

The framework rests on formal privacy models: k-anonymity, l-diversity and differential privacy. It uses per-instance pseudonymisation and is compatible with both a dimensional model and OMOP CDM.

Objectives

  • Design an anonymisation protocol with category-based classification and deterministic decision trees.
  • Define verifiable thresholds for each class of request (k, l, minimum cell size for aggregates).
  • Set up a pre-delivery validation checklist that blocks anything that does not meet the thresholds.
  • Apply per-instance pseudonymisation, which prevents different extracts of the same individual from being linked.
Key points

Request classification and decision trees

  • Each request is classified by requester, intended use and data granularity.
  • The decision tree for each class prescribes techniques and thresholds deterministically.
  • Treatment techniques to suit the case: hierarchical generalisation, suppression, microaggregation, date shifting.

Formal privacy models

  • k-anonymity and l-diversity on microdata, with the threshold that applies to each class.
  • Differential privacy for publishable aggregates, where it provides a formal bound without destroying utility.
  • The model is chosen by output type; no single model is applied to everything.

Per-instance pseudonymisation

  • A pseudonym that stays the same across deliveries makes it possible to reconstruct an individual's trajectory by cross-referencing extracts.
  • We generate a different pseudonym for each instance to neutralise that linkage.
  • Implemented reproducibly through HMAC-based derivation.

Verification before delivery

  • Every output passes a threshold check before it is released.
  • A validation checklist records what has been verified.
  • Anything that falls short of the threshold is not delivered: verification is a gate, not an after-the-fact report.

What it is for

  • Release or share health microdata and aggregates for research or management without exposing people to re-identification.
  • Publish indicators on open data portals with formal bounds on the risk accepted.
  • Give anonymisation a reproducible, verifiable framework that applies the same treatment to the same class of request.
Why choose this service

Anonymisation is not just deleting the name. Re-identification comes from combining quasi-identifiers, not from the direct identifier.

Removing names and national ID numbers leaves age, postcode, an admission date or a rare diagnosis untouched, and that combination is enough to single out a person. The framework we design starts from the three re-identification attacks (singling out, linkage and inference) and prescribes, for each type of request, what has to be treated and to what threshold.

Consistency across extracts

The same class of request receives the same treatment, reproducibly. The criterion is fixed in a verifiable protocol, not in a decision that is remade with every delivery.

Defence against combined quasi-identifiers

The protocol is designed against the real re-identification vector: the combination of apparently harmless variables. The k-anonymity and l-diversity thresholds bound that risk measurably.

Safe publication of aggregates

For the indicators you publish, differential privacy puts a formal bound on what a third party could infer, without draining the published table of its utility.

A reproducible, verifiable process

The categories, decision trees and checklist mean that the treatment applied to each delivery is documented and can be reviewed, maintained and re-run without ambiguity.

Our process

What working with us looks like

We apply our D²I (Data to Insights) methodology to every service. A structured, iterative and transparent process that turns complex data into actionable knowledge.

01

Kick-off and problem definition

We meet with you to understand the clinical problem, the data available and the objectives of the project. We agree on deliverables, timelines and communication channels, and we sign whatever confidentiality agreements you need to protect your data.

02

Data review and preparation

We assess the quality of your data, identify inconsistencies and limitations, and structure the data for analysis. If critical information is missing, we tell you before going any further. We document every cleaning decision so that the process is traceable and reproducible. We classify the request by requester, use and granularity, and identify the quasi-identifiers and sensitive variables in the extract to place it in the right category.

03

Analysis and modelling

We apply the statistical methodology that fits your questions. We work iteratively: we share preliminary results with you, discuss the findings and adjust the approach where needed. We do not work in the dark until the final delivery. We apply the techniques and thresholds prescribed by that category's decision tree, and check the result against the pre-delivery checklist before accepting the output as valid.

04

Communicating results

We turn the findings into the format you need: a technical report, tables and figures for publication, an interactive dashboard or an executive presentation. We always include the clinical interpretation, not just the figures.

05

Impact review session

30 days after delivery we meet with you again for a 60-minute strategy session. By then you have had time to present the results internally, the real implementation questions have come up and you can assess the impact of the work with some perspective. We answer your questions, adjust interpretations where necessary and agree together on the way forward.

This is our general process. If you want to understand how we apply it technically to each type of analysis, see our full D²I methodology.

Have a data project on your hands?

Tell us about your case and we will work out together how to approach it.

Book a session
FAQs

Frequently asked questions

If I remove names and national ID numbers from my data, aren't they already anonymised?

No. Removing direct identifiers, such as names or national ID numbers, does not anonymise the data, because re-identification comes mainly from combining quasi-identifiers. This applies to any health data extract you want to release or share, where apparently harmless variables, such as age, postcode, an admission date or a rare diagnosis, are enough in combination to single out a person. The anonymisation framework starts from the three re-identification attacks (singling out, linkage and inference) and prescribes, for each type of request, which variables have to be treated and to what threshold. Removing the direct identifier is only the first step. The combination of quasi-identifiers is the real vector, and it is the one a formal framework bounds measurably. Anonymisation is a matter of combinations, not of deleting a column.

What is k-anonymity, and how much protection does it really give against re-identification?

k-anonymity is a formal property that requires every combination of quasi-identifiers to appear in at least k individuals, so that no one is unique on that combination. It applies to the treatment of health microdata, where the risk of singling out is high. On that basis, l-diversity adds a condition on the sensitive variables: within each group there must be enough variety that belonging to the group does not reveal the sensitive attribute. The specific values of k and l are not universal. They correspond to each class of request according to its use and granularity, and are set in the decision tree. One limit is worth stating: these models bound the risk measurably, they do not eliminate it, and the protection they offer depends on which variables are treated as quasi-identifiers. What they provide is a formal, verifiable bound on the risk accepted, not a promise that re-identification is absolutely impossible.

Doesn't anonymisation destroy the usefulness of the data for research?

Not necessarily: the framework aims to bound re-identification risk while preserving analytical utility, choosing the technique by output type instead of applying one technique to everything. This applies when you are concerned that anonymisation will leave the data unusable for the planned analysis. For microdata, the options are hierarchical generalisation, suppression, microaggregation or date shifting, with the appropriate k-anonymity and l-diversity thresholds. For publishable aggregates, differential privacy limits what a third party could infer, and the table stays useful when the noise level is compatible with the intended use. The key is that the model is chosen by output type and intended use, not imposed as a single model that ruins everything else. There is a real trade-off between privacy and utility, and the framework manages it explicitly and with documentation, not blindly. The aim is the treatment that protects people without destroying the research question.

I will release several extracts from the same registry at different times. Can they be cross-referenced to reconstruct an individual?

That cross-referencing is a real risk, and per-instance pseudonymisation reduces it: a different pseudonym in each extract prevents the outputs for the same individual from being linked across deliveries. This applies to any organisation that releases data recurrently from the same registry or system. A pseudonym that is stable across deliveries, the same code for the same person in every extract, would make it possible to reconstruct that person's full trajectory by cross-referencing outputs, even if each one looked safe on its own. Generating a different pseudonym for each instance breaks the direct identifier link between deliveries. It is implemented reproducibly through HMAC-based derivation, so that the process is consistent and can be re-run. The limit: this protects against linkage across extracts, and it does not replace the treatment of quasi-identifiers within each one. It is the piece that stops repeated releases from undoing the anonymisation of each delivery.

Can you assure me that the data will be anonymised in line with the GDPR?

No. The health data anonymisation service does not offer assurance of GDPR compliance or a legal validation of the anonymisation, because that is a legal assessment that belongs to another field. What we design is the methodological framework: the classification of requests, the formal privacy models, the verifiable thresholds and the pre-delivery checklist that put formal bounds on re-identification risk. This limit is worth stating because "anonymisation" has a legal reading as well as a technical one, and the two should not be confused. How robust the result is in practice also depends on how the client implements and maintains the process in its own environment: ADI designs the protocol and analyses the risk; the organisation owns the data, releases them and operates the framework. What you receive is a traceable, verifiable methodological assessment of the risk accepted, not an opinion on regulatory compliance.

Is the anonymisation you design irreversible? Can you rule out re-identification for good?

No. Absolute irreversibility cannot be promised, because no serious anonymisation framework can claim that re-identification will be impossible under every future circumstance. This applies to any release of health data, where risk is managed and bounded, not eliminated altogether. What the framework does is quantify and limit that risk measurably: k-anonymity and l-diversity thresholds bound singling out and linkage, differential privacy limits inference from aggregates, and the checklist blocks anything that falls short of the threshold before delivery. The residual risk also depends on the auxiliary data a third party may hold and on what information becomes available in the future. That is why we speak of formal bounds on the risk accepted, with their assumptions stated, not of re-identification being impossible. Anonymising well means bounding the risk at a known, justified level, not promising the impossible.

How does health data anonymisation differ from data traceability and forensic watermarking?

Health data anonymisation is used when the aim is to release or share data while reducing the risk that people are re-identified, by treating quasi-identifiers and sensitive variables. Data traceability and forensic watermarking fit when what you need is to identify the source of a leak or to show where an extract came from, by marking the data so that every copy can be attributed. They are sequential and complementary, since an organisation can anonymise data to release them and also watermark each delivery to trace its source. But they do not answer the same question: anonymisation protects people against re-identification; forensic watermarking protects the organisation against unauthorised dissemination. They can be commissioned separately or as a linked process, depending on what you need.

What exactly do you deliver, and who applies the anonymisation day to day?

The health data anonymisation service delivers the methodological framework: the classification of requests by use and granularity, the decision trees that prescribe techniques and thresholds for each class, the formal privacy models applied by output type and the pre-delivery validation checklist. ADI designs the protocol, defines the thresholds and analyses the risk; the organisation owns the data, releases them and operates the framework day to day. The protocol is designed to be reproducible and verifiable. The categories, trees and checklist are documented, so the treatment applied to each delivery can be reviewed, maintained and re-run without ambiguity. What you receive is not a one-off anonymised extract, but a reproducible framework for applying consistent treatment to the same class of request.

Shall we talk?

Tell us what you are working on and we will give you a straight answer on how we can help.