The digital clinical trial protocol
The Clinical Trial Protocol Model (CTPM)
The Clinical Trial Protocol Model (CTPM) is Concordare's machine-readable digital clinical trial protocol. Apta, the conversion engine, extracts it from the protocol PDF. The study team reviews and approves it. Structura and Porta then generate the site's source documents, EDC build and CTMS configuration from it, so the protocol is read once and every system is built from the same source of truth.
Last reviewed
What a CTPM is
A CTPM is a typed schema, not a free-form document. It captures every operationally relevant detail of a protocol once, in fields that match how clinical operations actually work. Fields are CDISC-aligned where a standard applies and extensible where one does not exist yet. The schema is versioned, so an amendment produces a record of what changed rather than a new document.
The model exists because a protocol PDF is written for people, and every system in a trial needs the same information from it in a different shape. Without a CTPM, the protocol is re-entered by hand into source documents, EDC, CTMS, IRT and payments before the first patient enrolls. With one, it is extracted once and generated everywhere.
What a CTPM contains
- Visit schedule with windows, dependencies and conditional branches
- Assessment matrix mapping each procedure to the visits where it occurs
- Eligibility criteria, inclusion and exclusion
- Endpoint definitions with derivation rules and data sources
- Dosing rules and administration attributes on each assessment
- Lab panels, procedures and the reference lists they depend on
- Adverse event grading scales and reporting thresholds
How a protocol becomes a CTPM
Upload the protocol
Apta, Concordare's conversion engine, reads the protocol PDF and parses every visit, procedure, eligibility criterion, lab and assessment into a structured draft CTPM. The conversion runs in minutes.
Review and validate
The study team checks the draft field by field, confirming visit windows and flagging ambiguous criteria. AI extracts. Humans approve. Nothing is generated until this step is complete.
Approve
The approved CTPM becomes the study's single source of truth. Editing an approved CTPM returns it to draft, so an output can never be generated from an unreviewed change.
Amend
When an amendment arrives, it is converted against the existing model. The CTPM is versioned, so the amendment produces a record of what changed, and every output regenerates from the new revision.
What is generated from it
Source documents
Structura generates protocol-aligned source documents and visit-by-visit worksheets in the templates a site already uses. Every value is pulled from the CTPM rather than retyped, and each document is version-locked to the CTPM revision it came from.
EDC builds
Porta pushes the CTPM into the electronic data capture system a study uses, starting with REDCap: visit schedules, eligibility, lab panels and procedures populate from the model instead of being built by hand from a protocol read.
CTMS configuration
Visit calendars, milestone trackers and study setup fields populate from the same fields, so the trial management system and the source documents agree by construction.
Billing grids and study documents
Coverage analysis grids, patient calendars and other study documents are generated from the same model, and regenerate when it changes.
The products are described on the solutions page, with separate pages for research sites and sponsors and CROs.
How accurate is the extraction
In June 2026 Concordare completed a third-party structured quality assessment of Apta against a real protocol. The clinical team built a reviewed ground truth of every discrete data element a complete extraction should capture, then scored Apta's output element by element.
The errors that remain are clustered and repeatable, and the assessment is repeated as protocol coverage grows. Every CTPM is still reviewed and approved by the study team before a single output is generated. The full method and results are in the published audit.
How a CTPM differs from a protocol PDF
| Aspect | Protocol PDF | CTPM |
|---|---|---|
| Written for | People. Prose, tables and footnotes that reference other footnotes. | Systems and people. Typed fields that match how operations work. |
| Getting it into a system | Re-entered by hand into each of source documents, EDC, CTMS, IRT and payments, in a different shape each time. | Generated into each output from one model. Zero fields transcribed. |
| Amendments | A new document. Every downstream artifact is re-read and rebuilt. | A versioned change to the model. Outputs regenerate; the diff is on record. |
| Review | Each transcription is checked separately, in each system. | One review of the model, then deterministic generation. |
| Consistency across sites | Each site interprets the same PDF on its own. | Every site works from the same structured trial data. |
Frequently asked questions
- What does CTPM stand for?
- Clinical Trial Protocol Model. It is Concordare's machine-readable representation of a clinical trial protocol. Some early coverage abbreviated it CPTM; CTPM is the correct name and the only one Concordare uses.
- Does a site have to write a CTPM?
- No. A site does not author a CTPM. Apta extracts it from the protocol PDF the sponsor already provides, and the study team reviews and approves the result.
- Does AI generate the source documents and EDC builds?
- No. AI is used only at extraction, when the protocol PDF is converted into a CTPM. Once the CTPM is approved, every document, build and configuration is generated by deterministic logic from the model, not by a model guessing at the answer.
- How accurate is the extraction?
- In a June 2026 third-party structured assessment of a real protocol, Apta produced 3,171 scored data elements at 99.62% precision and 97.47% recall. The remaining gaps were clustered and repeatable. Every CTPM is still reviewed and approved by the study team before any output is generated.
- What happens when the protocol is amended?
- The amendment is converted against the existing CTPM. Because the model is versioned, the change is recorded as a diff rather than a new document, and every generated output regenerates from the new revision.
- Which systems can a CTPM populate?
- Source documents and visit worksheets in the site's own templates through Structura, and the site's EDC and CTMS through Porta, starting with REDCap. Billing grids, patient calendars and other study documents are generated from the same model.
- Is the CTPM aligned with CDISC?
- Fields are CDISC-aligned where a standard applies, with alignment expanding as the schema develops. The schema is extensible where no standard exists yet.
Read more
- Introducing the Clinical Trial Protocol Model · the original announcement, with the workflow in detail
- Audit of the conversion engine: 99.6% precision · method, results and the remaining gaps
- Public comment to FDA on the Expedited IND Pilot Program · why parallel trial initiation needs a structured protocol
To see a protocol converted into a CTPM and the documents generated from it, request a demo.