SDD Glossary

Date: 2026-01-18 Purpose: Consolidated terminology with variant tracking

Summary

Metric	Count
Unique terms	127
Terms with variants	18
Undefined terms	12

Terminology Inconsistencies

Canonical Term	Appears As	Files	Action Needed
PCR.AI	pcr.ai, Pcr.ai, PCRI.AI, PCR.AI System	arch, algo, config, security, refs	Standardize to "PCR.AI"
Run File	runfile, Runfile, run file, Run file, Run File	algo, config	Standardize to "run file"
Westgard	Westgard, westgard, WG	algo, config	Standardize to "Westgard"
CT (Cycle Threshold)	CT, Ct, ct	algo, config	Standardize to "CT"
Sample Type	sample type, specimen type, Specimen Type	config	Clarify distinction or merge
LIMS	LIMS, Lims, lims	config, algo	Standardize to "LIMS"
Internal Control	IC, Internal Control, internal control	algo, config	Define abbreviation consistently
Standard Deviation	SD, standard deviation	algo, config	Standardize to "SD"
Positive Control	PC, positive control, Positive Control	config, algo	Standardize
Negative Control	NC, negative control, Negative Control	config, algo	Standardize
Multi-Factor Authentication	MFA, multi-factor authentication	security, arch	Standardize to "MFA"
CLS (Classification)	CLS, classification, Classification	algo, config	Define CLS explicitly
RFU (Relative Fluorescence Units)	RFU, fluorescence	algo	Define abbreviation
DynamoDB	DynamoDB, dynamodb	arch, config	Standardize to "DynamoDB"
Aurora Serverless	Aurora Serverless, Aurora Serverless v2	arch	Clarify version in use
JSON	JSON, json, .json	algo	Standardize to "JSON"
API	API, api	algo, config	Standardize to "API"
Excel	Excel, excel, .xlsx, .xls	config, algo	Standardize to "Excel"

Full Glossary

A

Term	Appears As	Definition	Used In
Acceptance Criteria	Acceptance Criteria, AC	Testable conditions that must be met for a requirement to be satisfied	refs
Accession	accession, Accession	Unique identifier for a sample or specimen in the laboratory workflow	algo
Alert	Alert, alert	Notification triggered when configured thresholds are exceeded in trends data	config
Amazon Cognito	AWS Cognito, Amazon Cognito, Cognito	AWS service providing user identity and authentication services	arch, security, deploy
Amazon DynamoDB	DynamoDB, Amazon DynamoDB	AWS NoSQL database service used for session management	arch, config
Amazon ElastiCache	ElastiCache, Amazon ElastiCache	AWS managed in-memory cache service (Redis/Memcached)	arch
Amazon RDS	RDS, Amazon RDS	AWS relational database service	arch
Amazon S3	S3, Amazon S3	AWS object storage service for file storage	arch, deploy
Amazon SES	SES, Amazon SES	AWS email service for transactional and bulk emails	arch
Amazon SQS	SQS, Amazon SQS	AWS message queue service for asynchronous processing	arch
Analysis	analysis, Analysis, Run Analysis	Process of evaluating run data against configured rules	algo
API	API, api	Application Programming Interface	algo, config
Aurora Serverless	Aurora Serverless, Aurora Serverless v2	AWS serverless database with automatic capacity scaling	arch
AWS Lambda	Lambda, AWS Lambda	AWS serverless compute service	arch

B

Term	Appears As	Definition	Used In
Backup Mix	Backup Mix, backup mix, Backup Mixes	Fallback mix assignments when primary mix matching fails	config
Baseline	baseline, Baseline	Reference measurements used for curve normalization	algo
BCC Rule	BCC, Baseline Curve Control	Rule that validates control CT values against configured bounds	config, algo

C

Term	Appears As	Definition	Used In
Calibrator	Calibrator, DXAI Calibrator	External API providing curve classification and analysis parameters	algo, config
Client Configuration	Client Configuration, client configuration	System settings customized per client deployment	config
CLS	CLS	Classification result for an observation (Positive, Negative, etc.)	algo, config
CloudFront	CloudFront	AWS CDN service for content delivery	arch, deploy
Cloudflare	Cloudflare	DNS and CDN service for domain management	deploy
Combined Outcome	Combined Outcome, Combined Outcomes, COMBINED_OUTCOME	Rule evaluating well results based on combination of mix/target CLS results	algo, config
Configuration Export	Configuration Export	Process of extracting configuration data to Excel format	algo
Configuration Import	Configuration Import, Configuration Upload	Process of importing configuration data from Excel files	algo, config
Control	Control, control	Sample with known expected result used for quality assurance	algo, config
Control Label	Control Label, Control Labels	Configuration linking runfile sample labels to system roles	config
Cross Contamination	Cross Contamination, cross contamination	Potential transfer of material between adjacent wells	config
CT	CT, Ct, ct	Cycle Threshold - the cycle number at which fluorescence exceeds threshold	algo, config
Curve Control Limits	Curve Control Limits	Upper and lower CT bounds for control validation	config

D

Term	Appears As	Definition	Used In
Delta CT	Delta CT, Delta Ct	Difference in CT values between two targets	config
DF	DF	Derivative Factor from DXAI calibrator analysis	algo
Diagnostic.ai	Diagnostic.ai	Company name providing the PCR.AI platform	security
Dye	Dye, dye	Fluorescent reporter molecule used to detect PCR amplification	algo, config
DXAI	DXAI, DXAI Calibrator	External analysis service for curve classification	algo, config

E

Term	Appears As	Definition	Used In
Error Code	Error Code, error code	Unique identifier for an error condition	config
Error Resolution	Error Resolution	Configured action to address a specific error	config
Excel	Excel, .xlsx, .xls	Microsoft Excel spreadsheet format for configuration import/export	config, algo
Extraction	Extraction, extraction	Process of isolating nucleic acids from samples	config
Extraction Instrument	Extraction Instrument	Laboratory device used for nucleic acid extraction	config

F

Term	Appears As	Definition	Used In
Feature Flag	Feature, Features	Configuration toggle controlling application functionality	config
FIFO	FIFO	First-In-First-Out queue ordering	arch
Fluorescence	fluorescence, Fluorescence	Light emission from dye molecules during PCR	algo
Fluorescence Curve	fluorescence curve, Fluorescence Curve	Plot of fluorescence values across PCR cycles	algo

G

Term	Appears As	Definition	Used In
GUI	GUI	Graphical User Interface	refs

H

Term	Appears As	Definition	Used In
Help Item	Help Item, Help Items	Contextual help content and associated tags	config

I

Term	Appears As	Definition	Used In
IC	IC, Internal Control	Target used to verify extraction and amplification success	algo, config
IDD	IDD	Interface Design Document	refs
IEEE	IEEE	Institute of Electrical and Electronics Engineers (standards body)	refs
Import	Import, import	Process of loading run files or configuration into the system	algo
IP Whitelist	IP Whitelist, IP_WHITELIST	List of allowed IP addresses for access control	config

J

Term	Appears As	Definition	Used In
JSON	JSON, json, .json	JavaScript Object Notation data format	algo
JWT	JWT	JSON Web Token for authentication	security, arch

K

Term	Appears As	Definition	Used In
Kit Configuration	Kit Configuration, kit configuration	Configuration of assay-specific parameters	config
Known Quantity	Known Quantity, Known Quantities	Expected quantity value for control roles in QC calculations	config

L

Term	Appears As	Definition	Used In
Lambda	Lambda, AWS Lambda	AWS serverless compute service	arch
Laravel	Laravel	PHP web application framework	arch, refs
LIMS	LIMS, Lims	Laboratory Information Management System	config, algo
LIMS Export	LIMS Export, LIMS_Export	Process of sending results to external LIMS	config
LOQ	LOQ	Limit of Quantification	config

M

Term	Appears As	Definition	Used In
Mean	Mean, mean	Statistical average value for Westgard calculations	algo, config
MFA	MFA	Multi-Factor Authentication	security, arch
Mix	Mix, mix	Combination of targets/dyes that constitute an assay	algo, config
MVC	MVC	Model-View-Controller architecture pattern	refs

N

Term	Appears As	Definition	Used In
NC	NC	Negative Control - control expected to show no amplification	config
NEC	NEC	Negative Extraction Control	config
NTC	NTC	No Template Control - control without nucleic acid template	config

O

Term	Appears As	Definition	Used In
Observation	Observation, observation	Data point for a specific target/dye combination in a well	algo, config
Outcome	Outcome, outcome	Final result classification for a well or observation	algo, config

P

Term	Appears As	Definition	Used In
Parser	Parser, parser, Parser API	Service that converts thermocycler files to standardized format	algo, config
Passive Target	Passive Target, passive	Reference dye for normalization (not reported as result)	config
PC	PC	Positive Control - control expected to show amplification	config
PCR	PCR	Polymerase Chain Reaction - molecular biology technique	algo, arch
PCR.AI	PCR.AI, pcr.ai, Pcr.ai, PCRI.AI	The SaaS PCR interpretation and QC platform	arch, algo, security, config
PEC	PEC	Positive Extraction Control	config
PHI	PHI	Protected Health Information	arch
PII	PII	Personally Identifiable Information	arch
Precedence	Precedence, precedence	Execution order priority for rules	algo, config
Problem Files	Problem Files, problem_files, problemfiles	Folder for run files that failed import/parsing	algo
Programmatic Rule Name	programmatic_rule_name	Internal identifier mapping rule configuration to PHP class	algo
PSR	PSR	PHP Standard Recommendation	refs
Pusher	Pusher	Real-time communication platform for notifications	arch

Q

Term	Appears As	Definition	Used In
QC	QC	Quality Control	algo, arch
QIR	QIR	Quantification by Internal Reference	config
Qualitative Reporting	Qualitative Reporting	Reporting cut-offs for categorical result reporting	config
Quantity	Quantity, quantity	Calculated numeric value representing target concentration	algo, config
Quantification	Quantification	Process of calculating target concentration from CT values	config

R

Term	Appears As	Definition	Used In
Reanalysis	Reanalysis, reanalysis, Re-analysis	Process of re-executing analysis on existing run data	algo
RFU	RFU	Relative Fluorescence Units	algo
Role	Role, role	Classification of well purpose (Patient, PC, NC, etc.)	config, algo
Rolling Period	Rolling Period	Moving time window for aggregation calculations	config
RQUANT	RQUANT	Quantitative reporting rule	config
RQUAL	RQUAL	Qualitative reporting rule	config
Rule	Rule, rule	Configured logic that evaluates observations and assigns outcomes	algo, config
Rule Mapping	Rule Mapping	Assignment of rules to specific target/role/specimen combinations	algo, config
Run	Run, run	Complete set of PCR analysis data from a single instrument cycle	algo, config
Run File	Run File, runfile, Runfile, run file	Data file exported from thermocycler instrument	algo, config

S

Term	Appears As	Definition	Used In
S3	S3	Amazon Simple Storage Service	arch, deploy
SAML	SAML	Security Assertion Markup Language for SSO	arch, security
SD	SD	Standard Deviation	algo, config
SDD	SDD	Software Design Document	refs
SendGrid	SendGrid	Email delivery service	algo
Sentry	Sentry	Error tracking and session replay service	algo, config
Serverless	Serverless	Cloud computing model without server management	arch
Session	Session, session	User authentication state maintained across requests	arch, config
Site	Site, site	Organizational unit representing a laboratory location	config, deploy
SOLID	SOLID	Object-oriented design principles	refs
Specimen	Specimen, specimen, Specimen Type	Sample type classification (e.g., serum, plasma)	config
SQS	SQS	Amazon Simple Queue Service	arch
SRS	SRS	Software Requirements Specification	refs
SSO	SSO	Single Sign-On	security
Standard Curve	Standard Curve	Calibration curve for quantification calculations	config

T

Term	Appears As	Definition	Used In
Target	Target, target	Specific DNA/RNA sequence detected by the assay	algo, config
TDD	TDD	Test-Driven Development	refs
Test Code	Test Code, Test Codes	Code on sample labels mapping to specimen types	config
Thermocycler	Thermocycler, thermocycler	Instrument that performs PCR temperature cycling	algo, config
Threshold	Threshold, threshold	Fluorescence level used to determine CT value	algo, config
TLD	TLD	Top Level Design	refs
toPcrai	toPcrai	S3 folder monitored for incoming run files	algo
TOTP	TOTP	Time-based One-Time Password for MFA	security
Trends Report	Trends Report	Report showing aggregated data over time	config

U

Term	Appears As	Definition	Used In
Unknown Mix	Unknown Mix, Unknown	Auto-created mix entry for unmatched target/dye combinations	config, algo
User Pool	User Pool	AWS Cognito container for user accounts	security, deploy

V

Term	Appears As	Definition	Used In
Validation	Validation, validation	Process of checking data against defined rules	algo
Vapor	Vapor, Laravel Vapor	Laravel deployment platform for AWS Lambda	arch, config, deploy
Vue	Vue, Vue.js	JavaScript framework for frontend	arch, refs

W

Term	Appears As	Definition	Used In
Well	Well, well	Single reaction location on a PCR plate (e.g., A1-H12)	algo, config
Well Position	Well Position, well_position	Grid coordinate identifying a well (e.g., A1, B12)	algo, config
Westgard	Westgard, westgard	Statistical QC rules for control evaluation	algo, config
Westgard Event	Westgard Event	Generated notification when Westgard rule triggers	config
Westgard Limits	Westgard Limits	Mean and SD parameters for Westgard calculations	config
Westgard 1:2S	1:2S, 1:2s	Rule triggered when control is >2 SD from mean	algo
Westgard 1:3S	1:3S, 1:3s	Rule triggered when control is >3 SD from mean	algo
Westgard 2:2S	2:2S, 2:2s	Rule triggered when two consecutive controls are >2 SD	algo
Westgard 7T	7T	Rule triggered when seven consecutive controls trend same direction	algo

Acronyms

Acronym	Expansion	Definition	Used In
AC	Acceptance Criteria	Testable conditions for requirement satisfaction	refs
API	Application Programming Interface	Interface for software communication	algo, config, arch
AWS	Amazon Web Services	Cloud computing platform	arch, security, deploy
BCC	Baseline Curve Control	Rule for control CT validation	config, algo
CDN	Content Delivery Network	Distributed content caching	arch
CLS	Classification	Result classification (Pos/Neg/etc.)	algo, config
CT	Cycle Threshold	PCR cycle at which fluorescence exceeds threshold	algo, config
DF	Derivative Factor	DXAI calibrator output parameter	algo
DNS	Domain Name System	Internet naming service	arch, deploy
DFD	Data Flow Diagram	Software design diagram type	refs
ERD	Entity Relationship Diagram	Database design diagram	refs
FIFO	First-In-First-Out	Queue ordering method	arch
FTP	File Transfer Protocol	File transfer protocol	arch
FTPS	FTP Secure	Encrypted file transfer	arch
GUI	Graphical User Interface	Visual user interface	refs
HIQ	High Quantity	Upper quantity reporting threshold	config
IAM	Identity and Access Management	AWS access control service	algo
IC	Internal Control	Extraction/amplification verification target	algo, config
IDD	Interface Design Document	Interface specification document	refs
IEEE	Institute of Electrical and Electronics Engineers	Standards organization	refs
IoT	Internet of Things	Connected device ecosystem	arch
ISO	International Organization for Standardization	Standards body	arch
JSON	JavaScript Object Notation	Data interchange format	algo
JWT	JSON Web Token	Authentication token format	security, arch
LIMS	Laboratory Information Management System	Lab data management system	config, algo
LOQ	Limit of Quantification	Lower quantification boundary	config
MFA	Multi-Factor Authentication	Two-step authentication	security, arch
MVC	Model-View-Controller	Software architecture pattern	refs
NC	Negative Control	Control with no expected amplification	config
NEC	Negative Extraction Control	Extraction process negative control	config
NTC	No Template Control	Control without nucleic acid	config
PC	Positive Control	Control with expected amplification	config
PCR	Polymerase Chain Reaction	DNA amplification technique	algo, arch
PEC	Positive Extraction Control	Extraction process positive control	config
PHI	Protected Health Information	HIPAA-protected health data	arch
PII	Personally Identifiable Information	Privacy-protected personal data	arch
PSR	PHP Standard Recommendation	PHP coding standards	refs
QC	Quality Control	Quality assurance process	algo, arch
QIR	Quantification by Internal Reference	Quantification calculation method	config
RDS	Relational Database Service	AWS database service	arch
REST	Representational State Transfer	API architecture style	algo
RFU	Relative Fluorescence Units	Fluorescence measurement unit	algo
S3	Simple Storage Service	AWS object storage	arch, deploy
SaaS	Software as a Service	Cloud software delivery model	security
SAML	Security Assertion Markup Language	SSO protocol	arch, security
SD	Standard Deviation	Statistical dispersion measure	algo, config
SDD	Software Design Document	Design specification document	refs
SDK	Software Development Kit	Development tool package	arch
SES	Simple Email Service	AWS email service	arch
SFTP	SSH File Transfer Protocol	Secure file transfer	arch
SOLID	Single responsibility, Open-closed, Liskov, Interface segregation, Dependency inversion	OOP design principles	refs
SQS	Simple Queue Service	AWS message queue	arch
SRS	Software Requirements Specification	Requirements document	refs
SSO	Single Sign-On	Unified authentication	security
TDD	Test-Driven Development	Development methodology	refs
TLD	Top Level Design	High-level design	refs
TNP	Test Not Performed	Result status indicator	algo
TOTP	Time-based One-Time Password	MFA method	security
UKAS	United Kingdom Accreditation Service	Accreditation body	arch
UML	Unified Modeling Language	Software modeling notation	refs

Undefined Terms

These terms are used in the SDD files but lack explicit definitions.

Term	Used In	Context
DF	algo	DXAI calibrator output - needs formal definition
HIQ	config	High quantity threshold - needs formal definition
LOQ	config	Limit of quantification - needs formal definition
TNP	algo	"Mark as TNP" mentioned but not defined
ADJ Rule	config	Adjacent well contamination rule - needs documentation
AMB Rule	algo	Rule name without definition
WFINALCLS Rule	algo	Rule name without definition
WG14S Rule	algo	Rule name without definition
PICQUAL_SERUM Rule	algo	Rule name without definition
THRESHOLD Rule	algo	Mentioned in mapping examples but not defined
RQUANTASQUAL Rule	config	Reporting rule - needs definition
Resolution Code	algo	"SKIP" mentioned as example but codes not enumerated

Recommendations

Immediate Actions

1. Standardize PCR.AI naming: Use "PCR.AI" consistently throughout all documents
2. Define acronyms on first use: Each document should define acronyms when first used
3. Create rule documentation: Add definitions for all programmatic rule names
4. Clarify sample type vs specimen type: Determine if these are synonymous or distinct concepts

Future Documentation

1. Add glossary section to each SDD file: Include document-specific term definitions
2. Create abbreviation master list: Single source of truth for all acronyms
3. Document rule precedence: Create comprehensive rule catalog with definitions
4. Add data dictionary: Define all database fields and their meanings

Consistency Fixes

Current	Recommended	Reason
pcr.ai / Pcr.ai / PCRI.AI	PCR.AI	Official product name
runfile / Run file / run file	run file	Two-word noun phrase
Ct / ct	CT	Standard abbreviation
Lims	LIMS	Standard abbreviation
dynamodb	DynamoDB	Official AWS naming

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Generated from SDD files: sdd-architecture.md, sdd-algorithms.md, sdd-configuration.md, sdd-security.md, sdd-deployment-operations.md, sdd-references.md; STD file: std-ui-testability.md