Step 1 of 5

Protocol Extraction Engine

Upload a protocol PDF. Watch it become a structured study in seconds.

NEXION3_protocol_v2.0.pdf Parsed

248 pages · 3.2 MB · Phase III Oncology

47s elapsed

Visits

eCRF Forms

312

Fields

Arms

CDISC Domains

✓

21 CFR §11

clinly — extraction log

$ clinly parse NEXION3_protocol_v2.0.pdf --output=structured

Initializing extraction engine...

→ Reading document structure (248 pages)

→ Identifying trial design: Phase III, Open-label, 2-arm RCT

✓ Study title: NEXION3 — Investigational Agent + Chemotherapy vs. SoC

✓ Sponsor: [Confidential] · Phase III Oncology

✓ Primary endpoint: Progression-Free Survival (PFS)

Extracting visit schedule...

✓ Screening (C1D-14 to C1D-1): 4 forms mapped

✓ Baseline (C1D1): 8 forms mapped

✓ Cycles 1–6 (Day 1 each): VS, Labs, AE, CM forms

✓ EOT + Follow-up visits: 3 forms each

Mapping CDISC domains...

✓ DM (Demographics) → 12 fields

✓ AE (Adverse Events) → 18 fields, CTCAE v5.0 grading

✓ VS (Vital Signs) → 9 fields

✓ LB (Lab Results) → 47 fields, LOINC coded

✓ CM (Con. Meds) → 11 fields, WHO Drug dict.

✓ EX (Exposure) → 8 fields

✓ DS (Disposition) → 6 fields

⚑ 3 fields flagged for CDM review (ambiguous protocol language)

Configuring audit infrastructure...

✓ PostgreSQL triggers deployed (INSERT/UPDATE/DELETE)

✓ 21 CFR Part 11 architecture: aligned

━━━ Extraction complete in 47.3s ━━━

Status: Ready for CDM review. 3 items require attention before publish.

CDM Review Required (3 items)

Human-in-the-loop gate — study cannot publish until resolved

LB.LBCLSIG — Clinical Significance flag

Protocol section 8.3.2 references "clinically significant" without defining criteria. Recommend mapping to CDISC LBCLSIG with site-defined threshold.

AE.AECONTRT — Concomitant treatment for AE

Two conflicting guidance statements in protocol sections 9.1 and Appendix C. Recommend using Appendix C (more specific).

Visit window — Cycle 4 Day 1 (±3 vs ±5 days)

Schedule of Events table and section 7.2 have conflicting visit windows. Please confirm correct window before site activation.

Step 2 of 5

Study Dashboard — NEXION3

Real-time enrollment and data completion overview.

Study Title

NEXION3

Inv. Agent + Chemo vs. SoC Chemo

Phase / TA

Phase III

Oncology

Sites Active

6 / 8

2 sites in startup

Status

Enrolling

Enrolled Subjects

Target: 50

87%

Forms Complete

68 forms outstanding

Open Queries

3 overdue >7 days

SAEs Reported

All reported on time

Enrollment by Site

UK-SITE-01

DE-SITE-01

US-SITE-02

JP-SITE-01

FR-SITE-01

Step 3 of 5

Visit Matrix

Subject NEXION3-UK01-003 · Arm A: Inv. Agent + Chemo

Subject ID

UK01-003

Age / Sex

58F

Arm

A — Study Drug 80mg + Pemetrexed/Carbo

Screen Date

14 Jan 2026

Status

Active

✓ Complete ~ Partial … In Progress Not Started N/A

Form	Scr	BL	C1D1	C2D1	C3D1	C4D1	C5D1	EOT	FU1
Demographics	✓Completed 14 Jan 2026	—	—	—	—	—	—	—	—
Vital Signs	✓Completed 14 Jan	✓Completed 21 Jan	✓Completed 28 Jan	✓Completed 25 Feb	✓Completed 25 Mar	…In progress — 4 of 9 fields
Lab Results	✓Completed	✓Completed	✓Completed	~Partial — CBC complete, CMP pending	✓Completed
Adverse Events	—	—	✓2 AEs reported (Gr1 nausea, Gr1 fatigue)	✓1 AE updated	✓No new AEs
Con. Medications	✓Completed	✓Completed	✓No changes	✓1 new medication	✓No changes
Drug Exposure	—	—	✓C1: 80mg/day ×21d	✓C2: 80mg/day ×21d	✓C3: Dose reduced to 40mg	…C4 in progress

Step 4 of 5

Audit Trail

Immutable log of every data change — enforced at the database trigger level.

Append-only · Cannot be deleted

Timestamp (UTC)

Operation

User

Detail

2026-04-05 09:41:22.114

UPDATE

cdm.jones

subject_data.vs_weight · UK01-003 · C4D1 was 67.2 → 66.8 kg

2026-04-05 09:38:05.882

INSERT

cra.smith

subject_data.vs_pulse · UK01-003 · C4D1 · value: 72 bpm

2026-04-05 09:37:51.003

INSERT

cra.smith

subject_data.vs_sbp · UK01-003 · C4D1 · value: 124 mmHg

2026-04-04 16:12:30.447

UPDATE

cdm.jones

adverse_events.ae_grade · AE-003-02 · Grade 1 → Grade 2 (investigator assessment updated)

2026-04-04 14:55:18.221

INSERT

cra.smith

conc_medications · UK01-003 · Added: Ondansetron 8mg PO PRN (antiemetic, study-related)

2026-04-03 11:20:04.559

INSERT

sys.clinly

query_log · Auto-query raised: LB.LBRESULT null at C3D1 for ALAT — outstanding >5 days

2026-04-02 08:44:12.003

UPDATE

cdm.jones

drug_exposure.ex_dose · UK01-003 · C3D1 · study drug: 80mg → 40mg (dose modification per protocol section 9.4)

2026-03-25 13:02:44.771

INSERT

cra.smith

subjects · UK01-003 · Subject enrolled · Arm A · Screen date: 2026-01-14

Showing 8 of 2,847 audit records for NEXION3. Records are immutable and cannot be modified or deleted by any user, including system administrators.

Step 5 of 5

Regulatory Export Engine

Six export formats. One click. Every regulatory destination covered.

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CDISC ODM-XML 1.3.2

FDA & EMA regulatory submission

XML

Full study metadata, form definitions, and collected data in CDISC ODM-XML format. Includes audit trail records and SDTM annotations.

NEXION3_ODM_2026-04-05.xml

Export

Medidata Rave ALS

Annotated Layout Spreadsheet

XLSX

Rave-compatible ALS spreadsheet for import into Medidata Rave. Includes all field definitions, edit checks, and CDASH mappings.

NEXION3_Rave_ALS.xlsx

Export

REDCap Data Dictionary

Academic & institutional EDC

CSV

REDCap-compatible data dictionary CSV for direct import. Supports all REDCap field types including branching logic and validation.

NEXION3_REDCap_DD.csv

Export

SAS Transport (XPT)

SDTM-structured statistical package

XPT

SAS XPT transport files for each SDTM domain. Structured per CDISC SDTM Implementation Guide with DEFINE-XML metadata.

NEXION3_SDTM_XPT.zip

Export

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Subjects — NEXION3

24 enrolled subjects across 6 active sites. Demo data only.

Subject ID	Site	Arm	Screen Date	Status	Forms %
UK01-001	UK-SITE-01	A	2025-11-03	Active	94%
UK01-002	UK-SITE-01	B	2025-11-18	Active	91%
UK01-003	UK-SITE-01	A	2026-01-14	Active	78%
DE01-001	DE-SITE-01	B	2025-12-05	Active	89%
US02-001	US-SITE-02	A	2025-12-20	On Hold	62%
+ 19 more subjects	Click a subject to view their visit matrix →

CRF Library

Pre-built CDASH-compliant eCRF templates. Deploy as-is or customize for your study.

Demographics

CDISC CDASH DM domain

12 fields · Age, sex, race, ethnicity, informed consent date, eligibility criteria

Adverse Events

CDISC CDASH AE domain

18 fields · Term, start/end dates, severity, CTCAE grade, seriousness, outcome, relatedness

Vital Signs

CDISC CDASH VS domain

9 fields · SBP, DBP, pulse, temp, weight, height, BMI, ECOG PS, O₂ saturation

Lab Results

CDISC CDASH LB domain

47 fields · CBC, CMP, LFTs, urinalysis · LOINC coded · reference ranges

Con. Medications

CDISC CDASH CM domain

11 fields · Drug name, dose, route, frequency, indication, start/end dates · WHO Drug coded

Drug Exposure

CDISC CDASH EX domain

8 fields · Study drug, dose administered, dose modifications, route, administration dates

Reports

SQL-powered reporting dashboard. Run preset queries or write custom SQL. One-click CSV export.

Enrollment Summary

Total enrolled24

Arm A / Arm B12 / 12

Target enrollment50

Monthly accrual rate3.2 / month

Export CSV

AE Summary

Total AEs34

Grade 1–229

Grade 3+5

SAEs3

Export CSV

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Protocol Extraction Engine

CDM Review Required (3 items)

Study Dashboard — NEXION3

Enrollment by Site

Visit Matrix

Audit Trail

Regulatory Export Engine

Ready to See It With Your Protocol?

Subjects — NEXION3

CRF Library

Reports

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