Testing Data Dictionary
Overview
This dictionary defines domain-specific terms used in the Bengal Tiger (BT) PCR diagnostic software testing system. It is a practitioner-focused reference intended for people writing and understanding tests -- covering analyte targets, reagent mixes, sample roles, outcome types, Westgard QC rules, and other terms encountered in day-to-day test work.
For system architecture terminology (design patterns, module boundaries, data flows), see the SDS Glossary.
See the Testing Guide for how to use these terms in Behat tests.
PCR Fundamentals
Ct (Cycle Threshold)
The cycle number at which the fluorescence signal crosses a threshold, indicating detection of the target. Lower Ct = higher concentration.
Amplification Curve
The fluorescence reading pattern across PCR cycles. Positive samples show an exponential increase; negative samples remain flat.
Baseline
The initial flat portion of the amplification curve before amplification occurs.
Target
The specific nucleic acid sequence being detected (e.g., a virus, gene, or control sequence).
Analyte Targets
| Target | Full Name | Description |
|---|---|---|
| CMV | Cytomegalovirus | Viral pathogen |
| BKV | BK Virus | Viral pathogen |
| NOR1 | Norovirus 1 | Norovirus genogroup 1 |
| NOR2 | Norovirus 2 | Norovirus genogroup 2 |
| GAPDH | Glyceraldehyde 3-phosphate dehydrogenase | Human housekeeping gene (internal control) |
| IC | Internal Control | Control target to verify PCR success |
| REFERENCE | Reference | Reference signal (e.g., ROX passive dye) |
Mix Types
A "mix" refers to the reagent mixture used to detect specific targets.
| Mix | Targets Detected | Notes |
|---|---|---|
| NOR1 | Norovirus GI + controls | First component of Norovirus panel |
| NOR2 | Norovirus GII + controls | Second component of Norovirus panel |
| CMV | Cytomegalovirus + controls | CMV detection |
| BKV | BK Virus + controls | BKV detection |
| GAPDH | GAPDH + controls | Human gene marker |
Well Positions
Wells are identified by plate position using standard 96-well or 48-well plate notation:
96-Well Plate Layout
1 2 3 4 5 6 7 8 9 10 11 12
+---+---+---+---+---+---+---+---+---+---+---+---+
A | A1| A2| A3| A4| A5| A6| A7| A8| A9|A10|A11|A12|
+---+---+---+---+---+---+---+---+---+---+---+---+
B | B1| B2| B3| B4| B5| B6| B7| B8| B9|B10|B11|B12|
+---+---+---+---+---+---+---+---+---+---+---+---+
C | C1| C2| C3| ... continues ...
...
H | H1| H2| H3| ... |H12|
+---+---+---+---+---+---+---+---+---+---+---+---+
Sample Roles
| Role | Abbreviation | Description |
|---|---|---|
| Patient | Patient | Clinical patient sample |
| Negative Extraction Control | NEC | Verifies no contamination during extraction |
| Positive Extraction Control | PEC | Verifies extraction success |
| Positive Control | POS | Known positive sample |
| High Positive Control | Hi POS | High concentration positive |
| Low Positive Control | Lo POS | Low concentration positive |
| Negative Control | NC | Known negative sample |
| Standard 2 | S2 | Calibration standard (level 2) |
| Standard 4 | S4 | Calibration standard (level 4) |
| Standard 6 | S6 | Calibration standard (level 6) |
| Calibration Control 1 | CC1 | Calibration control (level 1) |
| Calibration Control 2 | CC2 | Calibration control (level 2) |
Outcomes
Final Outcomes
| Outcome | Description |
|---|---|
| Detected | Target pathogen was detected |
| Not Detected | Target pathogen was not detected |
| Control Passed | QC control passed |
| Control Failed | QC control failed |
| RXT | Re-extract sample required |
| Review required | Manual review needed |
| Pass | Control/validation passed |
| Fail | Control/validation failed |
Error Outcomes
| Outcome | Description |
|---|---|
| Mixes missing or in error | Required mix not uploaded or has error |
| The positive control has failed | POS control didn't amplify properly |
| An associated extraction control has failed | Extraction control issue |
| MINEXTRACT error | Minimum extraction requirements not met |
| This well is missing the required associated extraction controls | Missing controls |
| Crossover Passed | Crossover validation passed |
Reanalysis Status Messages
| Status | Description |
|---|---|
| Reanalysis required (Missing mixes uploaded) | New mixes available, reanalysis needed |
| Results for wells in this run may be affected by recently edited wells | Edits require reanalysis |
| All wells ready for export | Run complete, ready for export |
Classifications (dxai_cls)
| Classification | Abbreviation | Description |
|---|---|---|
| Positive | Pos | Amplification detected |
| Negative | Neg | No amplification detected |
| Indeterminate | Ind | Cannot determine (requires review) |
Fluorescent Dyes
| Dye | Color | Typical Use |
|---|---|---|
| FAM | Blue | Primary target detection |
| CALORANGE | Orange | Internal control |
| ROX | Red | Passive reference |
| VIC | Green | Secondary target |
Westgard Rules
Quality control statistical rules for validating control samples.
| Rule | Description |
|---|---|
| 1-2s | One control > 2 SD from mean (warning) |
| 1-3s | One control > 3 SD from mean (reject) |
| 2-2s | Two consecutive controls > 2 SD (same direction) |
| R-4s | Range between controls > 4 SD |
| 4-1s | Four consecutive controls > 1 SD (same direction) |
| 10x | Ten consecutive controls on same side of mean |
Resolution Types
Actions that can be applied to wells requiring resolution:
| Resolution | Description |
|---|---|
| Re-extract all samples | Request re-extraction of all affected samples |
| Approve | Manually approve the result |
| Reject | Reject the result |
| Override | Override the calculated result |
Configuration Files
Kit configuration files (.xlsx) define:
- Assay parameters
- Target definitions
- Control rules
- Outcome logic
- Westgard rule settings
Common Configuration Files
| File | Description |
|---|---|
Viracor_PROD.xlsx | Production Viracor configuration |
Viracor v3.xlsx | Viracor version 3 |
Viracor v30.xlsx | Viracor version 30 |
Viracor v30 pp based.xlsx | Pre-production version 30 |
QUEST_PP_OLD_RULES.xlsx | Quest pre-production (legacy rules) |
Run States
| State | Description |
|---|---|
| Uploaded | Run file uploaded, not yet processed |
| Processed | Analysis complete |
| Reanalysis required | Changes require re-processing |
| Ready for export | All validations passed, can be exported |
| Exported | Results have been exported |
Thermocycler
The PCR device that performs the amplification reaction.
| Field | Description |
|---|---|
thermocycler_id | Device serial number |
| Supported devices | TaqMan 48, TaqMan 96, etc. |
File Types
| Extension | Type | Location |
|---|---|---|
.feature | Cucumber/Behat test | exports/cucumber/ |
.json | Run file or manual tests | support_files/ or exports/manual/ |
.xlsx | Kit configuration | support_files/ |
.side | Selenium IDE test | exports/ghostinspector/ |
.csv | Jira export | Root directory |
Jira Integration
Issue Keys
- Format:
BT-xxxx(e.g., BT-5001, BT-5855) - BT = Bengal Tiger project prefix
Tags in Tests
@REQ_BT-xxxx- Links to requirement@TEST_BT-xxxx- Links to test case
Issue Types
- Test - Test case definition
- Requirement - Feature requirement
- Bug - Defect report
- Story - User story
Combined Outcomes
Some assays require results from multiple mixes to determine final outcome:
Norovirus Example
- Requires both NOR1 and NOR2 results
BOTH_NOR_POS- Both NOR1 and NOR2 positiveMISSING_MIXES- One mix not yet uploaded
Cross-Run Analysis
Tests where results depend on data from multiple run files, tracked by accession number.
Crossover Wells
Wells that receive fluorescence signal from adjacent wells due to optical bleed-through.
| Term | Description |
|---|---|
is crossover | Boolean indicating crossover well |
| Crossover Passed | Crossover validation successful |
| Crossover Failed | Crossover validation failed |
Quantification
Numerical measurement of target concentration.
| Term | Description |
|---|---|
quantity | Copy number or concentration value |
| Quant | Abbreviation for quantification |
| Standard curve | Calibration curve for quantification |
| Efficiency | PCR efficiency (ideally ~100%) |
| R2 | Correlation coefficient of standard curve |