ELN – Electronic Laboratory Notebook

This topic is part of the SG Systems Global regulatory & operations glossary.

Updated October 2025 • Lab Execution & Knowledge Capture • ELN, LIMS, QA, Data Integrity

Electronic Laboratory Notebook (ELN) software is the laboratory’s narrative and evidence hub. It captures the how—the protocol actually followed, the instrument status, the reagents and identities used, the raw files generated, and the calculations performed—under controls that satisfy 21 CFR Part 11, Annex 11, and ALCOA+. ELN is not an island: it ties each experiment to LIMS samples, eBMR in-process steps, and the quality system for Deviations/NCs and CAPA. The point is simple: ELN explains; LIMS decides; MES/WMS enforce.

“If it isn’t in the ELN, it didn’t happen—and if it lives only in the ELN, it can’t release product. Writing and gating are different responsibilities.”

1) What ELN Is—and Isn’t

ELN is a lab execution and knowledge system: think structured pages that combine narrative text with controlled fields, attachments, and validated calculations. Scientists design or select a template (often governed by Document Control), execute steps, attach raw files (HPLC/GC chromatograms, spectra, images), and sign with meaning (prepared, reviewed, approved). ELN pages link to sample IDs created by LIMS, batches from ERP and BMR, and equipment with IQ/OQ/PQ lineage and Calibration Status. It is not the authority for pass/fail vs specification—that belongs to LIMS. It also isn’t a dumping ground for uncontrolled spreadsheets; calculations inside ELN must be validated and versioned, just like in LIMS.

2) Template Discipline and Version Governance

Without template discipline, ELN devolves into pretty free text. Good ELNs use locked, versioned templates with required fields such as reagent ID and expiry, instrument ID and status, environmental conditions (EM), and analyst training. Templates are controlled via Document Control and changed through Change Control with validation impact assessment (CSV). Effective dating ensures new work cannot start on obsolete versions; the ELN should actively block initiation if a template is superseded, and present a reason-for-change path when historical templates are referenced during investigations or APR/PQR.

3) Identity, Materials, and Chain of Custody

Identity is non-negotiable. ELN pages reference LIMS sample IDs, goods receipt lots, and in-process samples from the eBMR. Material items and lots are verified by Barcode Validation and tied to shelf-life rules like FIFO/FEFO. When ELN documents pre-weigh or solution prep, it references gravimetric weighing entries and container/kit labels generated under controlled label verification. Chain of custody is visible end-to-end using Batch Genealogy models that tie ELN evidence to LIMS decisions and Finished Goods Release.

4) Raw Data, Attachments, and Reproducibility

Reproducibility demands access to originals. ELN entries include raw chromatograms, spectra, micro images, titration curves, and gravimetric logs. When a separate CDS or instrument system holds raw files, the ELN stores checksums and immutable links, ensuring Data Integrity remains testable. Attachments are tagged with method version, instrument firmware, lot IDs of standards/columns/media, and operator identity; reviewers see exactly what was done. All edits are recorded in a computer-generated audit trail with old/new values, timestamps, and reason-for-change; deletions are disallowed—only supersedures are permitted, per Part 11/Annex 11.

5) Calculations, Units, and Significant Figures

ELN calculations (assay %, impurity %, potency adjustments, content uniformity, moisture, recovery) must mirror LIMS math precisely. That means identical unit handling, rounding rules, and reportable precision to prevent “rounded passes.” Calculation objects are validated under CSV and locked to template versions. The ELN may show in-progress numbers; the authoritative comparison to spec occurs in LIMS against the currently effective specification governed by Document Control. This separation keeps ELN fast and expressive while maintaining a single truth for release.

6) Instrument & Environment Interlocks

Bad instruments make bad science look convincing. ELN must query Calibration Status and cleaning status before an experiment starts; out-of-status instruments block execution. Environmental conditions—temperature, humidity, pressure, vibration—are captured or linked to EM records, with SPC control limits for alert/action thresholds (e.g., incubator drifts in micro). For risky manipulations (e.g., potent API weighing), ELN can require dual verification inside the page and record PPE/gowning steps tied to cross-contamination control and cleaning validation programs.

7) From ELN to LIMS to Plant Control

Integration is where value materializes. Typical flow: a receiving event in WMS creates a sample in LIMS and applies QA Hold. ELN links to that sample, the analyst runs methods, attaches raw data, and signs. The ELN posts reportables to LIMS; LIMS compares to the effective specification, triggers Deviation/NC if needed, and—after review and QA approval—flips disposition to Released/Quarantine/Reject. That disposition then controls movement: WMS directed picking and dynamic lot allocation refuse quarantined lots; MES blocks eBMR progression when IPC results are pending or failed; label services won’t print if master data or disposition is wrong. ELN is the evidence; LIMS and MES are the brakes.

8) Micro, Chemistry, Stability, and EM—Different Clocks, Same Rules

ELN must serve chemistry, microbiology, stability, and EM with equal rigor. Chemistry pages emphasize method IDs, integration rules, standards traceability, and suitability tests. Micro pages emphasize incubation windows, media/reagent lots, and colony counts with acceptable ranges (including “TNTC” handling). Stability pages orchestrate timepoints and storage conditions; EM pages link to routes and rooms and trend counts under SPC. All inherit the same core controls—identity, version-correct method, instrument status, analyst authority, and audit trail—and all hand reportables to LIMS for disposition.

9) Investigations: OOS/OOT without Drama

When a result fails or trends off (CPV), the worst mistake is overwriting the past. ELN protects history: OOS Phase I examines lab error—prep steps, calibration, suitability, integration—using immutable entries and attachments; Phase II considers process causes. All results remain visible (including failed and repeat runs) to satisfy Data Integrity. Links to batch genealogy and batch-to-bin traceability let QA test hypotheses across products, suppliers, and instruments, converting anecdotes into trends and trends into CAPA.

10) Data Retention, Archival, and Cyber Hygiene

ELN records must survive time and turnover. Policies for data retention & archival define how long raw files, derived results, templates, and audit trails persist, and in what form. Backups and restores are validated exercises, not IT folklore. Access follows least privilege with periodic recertification; e-signature credentials are personal and revoked promptly at offboarding. Environments are separated (DEV/TEST/PROD) per GAMP 5; time sources are synchronized to a trusted server to maintain audit trail credibility. When ELN links feed CoA generation downstream, templates are versioned and IDs (lots, GTIN, batch numbers) come from authoritative systems to prevent drift.

11) Metrics that Prove the ELN Matters

Measure what proves control: percentage of experiments executed on the current template version; audit-trail change rate on critical fields; right-first-time entries (no rework, no re-entry); reviewer cycle time; percent of attachments with verified checksums; OOS/OOT per thousand results by method and instrument; and latency from QA approval in LIMS to status flips in WMS/MES. Tie ELN learnings to APR/PQR and supplier scorecards. If shipments leave before dispositions post, you have an integration failure—fix the gates, not the dashboard.

12) Common Failure Modes & Antidotes

Shadow spreadsheets produce numbers that don’t match LIMS. Antidote: implement validated calculations in ELN and LIMS; watermark exports as uncontrolled. Version drift lets obsolete templates linger. Antidote: effective-dated templates under Document Control, block new work on old versions. Status blindness records work on out-of-cal instruments. Antidote: status interlocks. ELN as release authority bypasses LIMS. Antidote: push reportables to LIMS for comparison vs spec and disposition with approval workflows. Attachment rot breaks reproducibility. Antidote: immutable storage with checksums and retention controls.

13) How This Fits with V5 (and V5 LIMS Integration)

V5 by SG Systems Global treats ELN as the evidence engine that feeds operational truth. In V5 MES, each eBMR step can link directly to the relevant ELN entry (method, images, chromatograms, calculations). But progression is gated by LIMS truth: if results are Pending or Fail, the eBMR next-step button stays grey, and Deviations/NCs open automatically with evidence pointers. In V5 WMS, directed picking and dynamic lot allocation honor LIMS disposition so quarantine is unpickable, preventing the classic “lab pass in a notebook, release in the warehouse” failure.

Most importantly, SG Systems provides a dedicated LIMS Integration path inside V5 QMS—see V5 QMS – LIMS Integration. That capability formalizes the two decisive interlocks: (1) create sample + set QA Hold at triggers (receiving, staging, IPC), and (2) post disposition from LIMS to flip material and batch states (Released/Quarantine/Reject). ELN sits upstream, ensuring every posted result is contextualized with Part 11/Annex 11 evidence. The outcome is a clean separation of concerns: ELN captures how, LIMS decides what, MES/WMS enforce whether work may proceed.

14) Implementation Playbook (Forward and Frank)

Start with the spine. Map each experiment type (assay, impurities, micro, EM, stability) to a controlled template. Validate calculations, units, and rounding. Link instruments with IQ/OQ/PQ and Calibration Status. Wire LIMS first for sample creation and disposition; do not attempt “ELN-only release.” Connect ELN pages to eBMR steps so reviewers see context alongside LIMS truths. Make audit trails and attachments central in technical review—side-by-side raw vs calculated views cut cycle time. Finally, trend with CPV: instrument capability, analyst RFT, OOS/OOT rates, and the frequency of system-enforced blocks. If gates rarely fire, either your process is world-class—or the wiring is broken.

FAQ

Q1. How is ELN different from LIMS?
ELN records protocols, observations, raw files, and calculations with signatures and audit trails. LIMS owns specifications, result comparison, and disposition; it flips plant states through WMS/MES. ELN explains; LIMS decides.

Q2. Can ELN alone release or quarantine a lot?
No. ELN pushes reportables to LIMS. Only LIMS, integrated with WMS/MES, implements Hold/Release hard gates that physically block movement and eBMR progression.

Q3. What makes an ELN compliant with Part 11/Annex 11?
Unique accounts, role-based access, e-signatures with meaning, computer-generated audit trails, time synchronization, validated templates and calculations (CSV), secure retention, and tested backup/restore. Evidence must satisfy ALCOA+.

Q4. How should ELN integrate with instruments and CDS?
Import results with instrument identity, method/run IDs, timestamps, and checksums; store raw files immutably (typically in CDS) and link from ELN. Never summarize away originals—reviewers must see raw and processed data side-by-side.

Q5. Where does ELN fit within V5?
ELN provides rich experiment context linked to LIMS samples and eBMR steps. Hard gates are enforced by LIMS/MES/WMS, including the dedicated V5 QMS – LIMS Integration interlocks.

Related Reading
• Core Systems: LIMS | eBMR | eMMR | Batch Genealogy | Batch-to-Bin Traceability
• Integrity & Compliance: 21 CFR Part 11 | Annex 11 | GAMP 5 | ALCOA+ | Audit Trail (GxP) | CSV | ISO 13485 | ICH Q10
• Operations & Release: Hold/Release | Finished Goods Release | Label Verification & UDI Checks | EPCIS | GS1 GTIN | Directed Picking | Dynamic Lot Allocation
• Lab Practices: Gravimetric Weighing | Cleaning Validation | Cross-Contamination Control | Environmental Monitoring (EM) | Control Limits (SPC)