Lab Automation Value Sets
Modern laboratories increasingly rely on robotic systems, automated workflows, and self-driving experimentation. This view collects value sets from across the lab automation, bioprocessing, assay, specimen processing, and computing domains that are needed to describe automated laboratory operations end-to-end.
Coverage Summary
| Domain | Schema Sources | Enums | Ontologies |
|---|---|---|---|
| Robotic Systems and Devices | lab_automation/autonomous_labs, lab_automation/devices | 5 | OBI |
| Labware and Consumables | lab_automation/labware | 4 | |
| Liquid Handling and Operations | lab_automation/operations | 2 | |
| Protocols and Orchestration | lab_automation/protocols | 6 | |
| Standards and Integration | lab_automation/standards | 4 | |
| Thermal Cycling and PCR | lab_automation/thermal_cycling | 5 | |
| Sequencing Platforms | bio/sequencing_platforms | 4 | OBI, GENEPIO |
| Specimen Processing | bio/specimen_processing | 5 | OBI, NCIT |
| Bioprocessing and Scale-Up | bioprocessing/biomanufacturing, bioprocessing/scale_up | 6 | OBI, CHEBI |
| Assays | bio/assays/* | 12+ | OBI, BAO |
Assays
Laboratory assays are the core measurements that automated systems perform. This section covers both broad ontology-backed dynamic enums and curated domain-specific static enums with companion annotations for microschema coupling.
Dynamic Enums (Ontology-backed)
- OBIAssayEnum -- all OBI assay subclasses (OBI:0000070)
- BAOBioassayEnum -- all BAO bioassay subclasses (BAO:0000015)
Domain-Specific Static Enums
- EnzymologyAssayEnum -- enzyme activity, kinetics, inhibition, substrate specificity
- ImmunologyAssayEnum -- ELISA, flow cytometry, western blot, immunoprecipitation
- ProteinEngineeringAssayEnum -- SPR, BLI, thermal shift, display technologies
- ToxicologyAssayEnum -- cytotoxicity, genotoxicity, ADME, dose-response
NF-OSI Assay Enums
- SequencingAssayEnum -- RNA-seq, ATAC-seq, ChIP-seq, whole genome sequencing
- ImagingAssayEnum -- confocal, electron microscopy, MRI, live-cell imaging
- MassSpectrometryAssayEnum -- LC-MS, MALDI, proteomics, metabolomics
- CellBasedAssayEnum -- viability, proliferation, migration, reporter assays
- ClinicalBehavioralAssayEnum -- behavioral testing, clinical assessments
Robotic Systems and Devices
Autonomous labs combine robotic hardware, AI experiment planners, and high-throughput screening platforms. These enums describe the components of an automated laboratory and the experimental design methods that drive them.
Enums
- AutonomousLabComponentType -- robotic handlers, automated synthesizers, HTS platforms, AI planners
- LabAutomationWorkflowType -- closed-loop optimization, self-driving experimentation
- ExperimentalDesignMethodType -- Bayesian optimization, active learning, DOE
- LaboratoryDeviceTypeEnum -- liquid handlers, centrifuges, plate readers, thermal cyclers
- RoboticArmTypeEnum -- flexible channel, multi-channel, gripper arms
Labware and Consumables
Standardized labware is essential for robotic interoperability. These enums cover microplate formats, container types, and surface treatments.
Enums
- MicroplateFormatEnum -- 6 through 1536-well plate formats
- ContainerTypeEnum -- microplates, deep well plates, tube racks, reservoirs
- PlateMaterialEnum -- polystyrene, polypropylene, glass
- PlateCoatingEnum -- tissue culture treated, protein binding surfaces
Liquid Handling and Operations
Liquid handling is the backbone of lab automation. These enums describe pipetting operations and sample processing steps performed by robotic systems.
Enums
- LiquidHandlingOperationEnum -- aspirate, dispense, transfer, serial dilution, plate stamping
- SampleProcessingOperationEnum -- centrifugation, incubation, thermal cycling, washing, detection
Protocols and Orchestration
Automated workflows require protocol management, scheduling, and error handling. These enums describe how protocols are executed and orchestrated across instruments.
Enums
- WorkflowOrchestrationTypeEnum -- static, dynamic, event-driven, parallel processing
- SchedulerTypeEnum -- priority-based, FIFO, resource-aware, deadline-driven
- ProtocolStateEnum -- pending, running, paused, completed, failed
- ExecutionModeEnum -- automated, manual, semi-automated, simulation, dry run
- WorkflowErrorHandlingEnum -- retry, abort, skip and continue, rollback
- IntegrationSystemEnum -- LIMS, ELN, MES, SCADA
Standards and Integration
Lab automation standards ensure interoperability between instruments from different vendors. These enums cover communication protocols, labware standards, and integration features.
Enums
- AutomationStandardEnum -- SiLA 2, LabOP, Autoprotocol, CLSI standards
- CommunicationProtocolEnum -- gRPC, REST API, OPC UA, Modbus
- LabwareStandardEnum -- ANSI/SLAS microplate standards, SBS footprint
- IntegrationFeatureEnum -- barcode tracking, audit trail, electronic signatures
Thermal Cycling and PCR
PCR and qPCR are among the most automated laboratory procedures. These enums describe cycler types, reaction configurations, and detection methods.
Enums
- ThermalCyclerTypeEnum -- standard, real-time qPCR, digital PCR, gradient
- PCROperationTypeEnum -- standard PCR, RT-qPCR, multiplex, touchdown, digital PCR
- DetectionModeEnum -- SYBR Green, TaqMan, molecular beacon, FRET
- PCRPlateTypeEnum -- 96-well, 384-well, tube strips
- ThermalCyclingStepEnum -- denaturation, annealing, extension, melt curve
Sequencing Platforms
Next-generation sequencing is a core automated workflow. These enums describe instrument platforms, chemistries, library preparations, and data formats.
Enums
- SequencingPlatform -- Illumina, PacBio, Oxford Nanopore, Element, MGI
- SequencingChemistry -- sequencing by synthesis, SMRT, nanopore
- LibraryPreparation -- genomic DNA, RNA-seq, single-cell, metagenomics
- SequenceFileFormat -- FASTQ, BAM, CRAM, VCF, GFF3
Specimen Processing
Sample preparation is the critical first step in any automated pipeline. These enums describe how specimens are collected, preserved, and processed.
Enums
- SpecimenCollectionMethodEnum -- biopsy, venipuncture, swab, lavage
- SpecimenPreparationMethodEnum -- FFPE, cryopreservation, flash freezing, RNAlater
- SpecimenTypeEnum -- tissue, blood, plasma, serum, urine, CSF
- AnalyteTypeEnum -- DNA, RNA, protein, cfDNA
- SourceMaterialTypeEnum -- primary tumor, blood-derived, cell lines, xenografts
Bioprocessing and Scale-Up
Automated biomanufacturing scales from microfluidic devices to commercial fermenters. These enums cover reactor types, operating modes, and purification.
Enums
- BiomanufacturingScaleType -- micro through commercial scale
- BioreactorTypeEnum -- stirred tank, airlift, wave bag, photobioreactor
- FermentationModeEnum -- batch, fed-batch, continuous, perfusion
- DownstreamProcessEnum -- centrifugation, filtration, chromatography, extraction
- SterilizationMethodEnum -- steam in place, autoclave, filter sterilization
- BioprocessOptimizationType -- media optimization, PAT, digital twin modeling