1.0
2016-12-01
REPRODUCE-ME Ontology
Sheeba Samuel
Birgitta König-Ries
Christoph Biskup
Kathrin Groeneveld
repr
The REPRODUCE-ME ontology describes a scientific experiment taking into focus the use-case of microscopy. The ontology describes the lifecycle of an experiment from its input to its result. The ontology describes the property of a microscopic image and its acquisition. It also describes terms from the OME data model. The Experiment describes the activities, entities, agents, steps, plans, variables, locations and time that is related to an experiment.
hasAnnotation
hasOriginalFile
hasPixels
hasPixelsType
hasPlate
hasPlateAcquisition
hasProperty
hasRenderingdef
hasScreen
hasSetting
hasStatus
Relates an entity to its unit.
hasUnit
isAccessibleTo is a property which describes that an Entity is accessible or available to an Agent.
isAccessibleTo
An entity is part of another entity if one of its part belong to the other entity.
isPartOf
isRelatedTo
An entity which has used another entity as reference.
reference
storedAt
A process which used a method to achieve something.
usedMethod
A relationship between an entity to its creator agent.
wasCreatedBy
A relationship between an entity to its distributor agent.
wasDistributedBy
An experiment material which is extracted from another material.
wasExtractedFrom
An entity which is updated by another entity or an agent.
wasUpdatedBy
Absorption Coefficient
The wavelength of the absorption maximum.
Absorption Maximum
The excitation spectrum.
Absorption Spectrum Field
Time at which an entity was last accessed.
accessedAtTime
Action
Active
Alpha
Annealing Temperature
Annealing Temperature
Archived
Bit size
Blue
Bool Value
Client Path
Coefficient
Column index of the Well.
Column
All components of the solution with the corresponding concentrations.
Components
Compression
Count
Current Patch
The current version of an entity.
Current Version
The id of the dataset object in OMERO.
datasetid
The date of the purification of the material.
Date of Purification
Default Event Type
Default Sample
Default T
Default Z
Description of an entity.
Description
Discriminator
The original name or ID of the material used in the lab from whom the material was received.
Distributor Product Id
Doc String
Double Value
Duration
The Email of an agent.
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Experimenter_Email
E-Mail
The wavelength of the emission maximum.
Emission Maximum
The emission spectrum.
Emission Spectrum File Id
Entity Type
Event
The wavelength of the excitation maximum.
Excitation Maximum
The excitation spectrum file.
Excitation Spectrum File Id
External Description
External Identifier
Link to the FASTA database.
FASTA Link
Finished
First Name of the Person.
First Name
Green
The name of the group.
Group Name
Hash
A unique identifier of an entity.
Id
Input End
Input Start
The Institution of an Agent.
Institution
The keywords used to tag an entity.
Keywords
Time at which an entity was last activated.
lastActivatedAtTime
The Last Name of an Agent.
Last Name
LDAP
Length
LifeTime
Linearization Site
Long Value
Lookup Table
Maximum Field Count
Message
The methodology used.
Methodology
The Middle Name of an Agent.
Middle Name
MIME Type
Time at which a thing was modified.
modifiedAtTime
The name of a thing.
Name
Namespaces
NCBI Genbank Id
Noise Reduction
NS
oligonucleotidesequencelength
OME Name
OMERO Id
Optical Axis Averaged
Origin describes the name of the creator of the vector.
Origin
Other Links
Owner
The unique identifier of an owner.
Owner ID
Partial
Path
PDB Id
Previous Patch
Previous Version
Product Id
Protocol Description
Protocol Identifier
quantumyield
Reagent Identifier
Reagent Set Description
Reagent Set Identifier
The time the material was received.
Received At Time
Red
The Paper which was referenced in an experiment.
Reference Paper
The DOI of the paper which was referenced in an experiment.
Reference Paper DOI
The PubMed Id of the paper which was referenced in an experiment.
Reference Paper PUBMed Id
Repo
The return value of a function.
Return Value
Row
Scheduled for
Sequence of Oligonucleotide
Series
SHA 1
Size
The current state of an object.
State
The current status of an object.
Status
Time at which status of an entity or an event changed.
statusChangedAtTime
Sub File Ids
Submitted
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ImagingEnvironment_Temperature
Temperature
Template prefix
Term value
Text Value
Time to Idle
Time To Live
Time value
Type
The unique identifier of an entity.
Unique id
Unique Id
Where the solution is used.
Use of Solution
User Agent
The IP address of a user's system.
User IP
User Name
Vector Effect
Version
Wave Increment
Wave start
AIM
APD
Axon Raw Format (ARF)
AVI (Audio Video Interleave)
Absorption Spectrum
Acquisition of an Image.
Acquisition
Acquistion Mode
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel_AcquisitionMode
Data that provides additional information of an experiment.
Additional Information
Adler-32
AequoriaVictoria
Air Pressure
Alicona 3D
A person or an organisation responsible for receiving the experiment aliquots.
AliquotsReceiver
Amersham Biosciences Gel
Amira Mesh
Amnis FlowSight
Amplification
AmplificationGain
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Detector_AmplificationGain
AmplificationLevel
AnalogVideo
Analyze 7.5
Andor Bio-Imaging Division (ABD) TIFF
Andor SIF
Animal
Animated PNG
A description added to a thing which provides comment, note or description.
Annotation
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Annotation
Annotation
Annotation Map Value
Aperio AFI
Aperio SVS TIFF
Applied Precision CellWorX
Arc
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Arc
Arc Type
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Arc_Type
A parameter.
For example, an argument of parameter of a function.
Argument
Attenuation
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#LightSourceSettings_Attenuation
BD Pathway
BMP
The Bacterial Resistance used to transform a bacteria.
BacterialResistance
A subtype of a microorganism bacteria
BacterialStrain
BandPass
Bath Solution
Preparation of Bath Solution for an experiment.
BathSolutionPreparation
BathSolutionPreparationStandardOperatingProcedure
Binning
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Binning
BioRad
Bio-Rad Gel
#Bio-Rad SCN
BIO-Formats is an image translation library which reads and writes life sciences image file formats. It converts the proprietary microscopy data to a open standard model called OME data model, particularly into the OME-TIFF file format, which then can be used by other tools.
Bio-Formats
BrightField
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel_AcquisitionMode
BrightField
Bruker MRI
Burleigh
CAS number is a uniquely numerical identifier assigned by Chemical Abstracts Service (CAS) to every chemical substance.
CASNumber
CCD
CHO
CMOS
CO2Percent
COS7
CRC-32
CalibratedMagnification
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Objective_CalibratedMagnification
Canon DNG
CellH5
CellVoyager
Cellomics
A component of an Image.
Channel
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel
Annotation added to the channel object in OMERO.
Channel Annotation
Channel Binding
ChannelFluorophore
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel_Fluor
ChannelSetting
CheckSum Algorithm
A pure substance with constant chemical composition and properties
used in an experiment.
Chemical
ChemicalPreparation
The procedure to replicate specimen.
Cloning
Colocalization
ColumnNamingConvention
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plate_ColumnNamingConvention
Columns
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plate_Columns
Compound
Concentration
Configuration
Configuration of the microscope used in the lab.
Microscope Configuration
A person who has the role of being a contact person for a certain thing.
ContactPerson
Contrast Method
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel_ContrastMethod
Correction
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Objective_Correction
CorrectionCollar
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ObjectiveSettings_CorrectionCollar
CorrelationSpectroscopy
CultureCells
CutIn
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#TransmittanceRange_CutIn
CutInTolerance
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#TransmittanceRange_CutInTolerance
CutOut
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#TransmittanceRange_CutOut
CutOutTolerance
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#TransmittanceRange_CutOutTolerance
DIC
DICOM
Deoxyribonucleic acid which is carries genetic instructions for the many functions like growth, development and reproduction.
DNA
DNAAmplificationResult
DNAAmplificationStandardOperatingProcedure
DNAPreparation
Darkfield
A type or format of a thing.
DataType
Dataset
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Dataset
Annotation added to the dataset object in OMERO.
Dataset Annotation
DB Patch
DeltaT
DeltaVision
The activity of describing things.
Describe
The text which is used to provide information about a thing.
Description
Detector
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Detector
Annotation added to the instrument detector.
Detector Annotation
Detector Settings
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#DetectorSettings
Detector Type
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Detector_Type
Dichroic
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Dichroic
Annotation added to the instrument Dichroic.
Dichroic Annotation
DichroicFilter
Dimension Order
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_DimensionOrder
Dissection
Distributor is a person who is responsible for the distribution of materials.
Distributor
Dye
E.T
EBCCD
ECAT7
EM-CCD
EPS (Encapsulated PostScript)
ElectronicGain
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Detector_Gain
Electrophysiology
ElectrophysiologyMicroscope
EmissionSpectrum
EmissionWavelength
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel_EmissionWavelength
EncodedProtein
Environment Attribute
To setup the environment to perform an experiment.
EnvironmentSetup
EnvironmentSetupSetting
Epifluorescence
The resistance of Eukaryotic Cells.
EukaryoticCellResistance
Event
Event Type
Evotec/PerkinElmer Opera Flex
Excimer
ExcitationSpectrum
ExcitationWavelength
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel_ExcitationWavelength
Experiment is an entity which describes the collective activity conducted in a science lab.
Experiment
ExperimentEnvironmentSetup
The materials or things used in an experiment.
For example, a specimen.
Experiment Material
A procedure to prepare experiment materials.
Experiment Material Preparation
To setup the execution environment of an experiment.
ExperimentSetup
Experiment Type
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Experiment_Type
Data used in an experiment.
Experimental Data
Experimenter is a person who is the owner of the Experiment and has its responsibility.
Experimenter
Annotation added to the Experimenter object in OMERO.
Experimenter Annotation Link
Experimenter Group
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ExperimenterGroup
Annotation added to the Experimenter group object in OMERO.
Experimenter Group Annotation
Configuration of an experimenter group.
Experimenter Group Config
ExposureTime
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plane_ExposureTime
The procedure of expression of materials.
Expression
The activity to express protein molecules.
ExpressionOfProtein
ExpressionOfProteinStandardOperatingProcedure
The procedure used for the expression of experiment materials like Vectors, Protein.
ExpressionSystem
ExternalIdentifier
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plate_ExternalIdentifier
FEI
FEI TIFF
FISH
FITS (Flexible Image Transport System)
FLIP
FP
FRAP
FRET
FSM
FTIR
Family
FieldIndex
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plate_FieldIndex
Filament
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Filament
Filament Type
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Filament_Type
A storage to store data. For example, a computer file.
File
File-Size-64
Fileset
Annotation added to the fileset object in OMERO.
Fileset Annotation
Fileset Entry
Filter
Annotation added to the instrument filter.
Filter Annotation
FilterSetting
Filter Type
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Filter_Type
FilterWheel
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Filter_FilterWheel
Filterset
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#FilterSet
The filters placed in the emission light path.
Filterset Emission Filter
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#FilterSet_EmissionFilterRef
The filters placed in the excitation light path.
Filterset Excitation Filter
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#FilterSet_ExcitationFilterRef
Fixation
FixationStandarOperatingProcedure
Fluorescence
FluorescenceCorrelationSpectroscopy
FluorescenceLifetime
FluorescenceLifetimeExperiment
A protein composed of 238 amino acid residues (26.9 kDa) that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range.
Fluoroscent Protein
FluorescentProteinPreparation
Fluorophore
FluroscentProteinSpectra
FourDPlus
FreeElectron
FrequencyMultiplication
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Laser_FrequencyMultiplication
A programming language code snippet in a script which describes a procedure or a routine.
Function
Function Activation is when a function is activated or run.
Function Activation
GCContent
GIF (Graphics Interchange Format)
Gas
Gatan Digital Micrograph
Gatan Digital Micrograph 2
Generic Excitation Source
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#GenericExcitationSource
Generic Excitation Source Map
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#GenericExcitationSource_Map
Group Experimenter Map
The growth condition of a specimen.
GrowthCondition
Halogen
Hamamatsu Aquacosmos NAF
Hamamatsu HIS
Hamamatsu ndpi
Hamamatsu VMS
HeLa
HeatInactivation
Hek293
Hg
HgXe
Hitachi S-4800
HoffmanModulation
Human
Humidity
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ImagingEnvironment_Humidity
I2I
ICS (Image Cytometry Standard)
IMAGIC
IMOD
INR
IPLab
ImagePro Workspace
IVision
Illumination
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel_IlluminationType
Imacon
An image or picture generated in an experiment by a device.
For example, a microscopic image with metadata.
Image
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Image
The process of acquiring image from device.
ImageAcquisition
Annotation added to the image object in OMERO.
Image Annotation
The file format of an Image.
Format
ImagePro Sequence
The properties of an image while its acquisition.
ImageSetting
The experiment environment when the image was captured.
Imaging Environment
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ImagingEnvironment
Imaging Environment Map
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ImagingEnvironment_Map
ImagingMethod
Imaris
Immersion
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Objective_Immersion
Immunocytochemistry
Immunofluorescence
A job performed to import data.
For example, in OMERO, its the job to import images.
Import Job
Improvision Openlab Raw
ImprovisionTIFF
Imspector OBF
InCell 1000/2000
InCell 3000
Incandescent
Incubation
IncubationStandardOperatingProcedure
A device used to capture images.
Instrument
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Instrument
Annotation added to the instrument object.
Instrument Annotation
InstrumentSetting
Integration
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#DetectorSettings_Integration
IntensifiedCCD
Inveon
InverseFRAP
Inverted
IonImaging
Iris
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Objective_Iris
IsolationOfProtein
JEOL
JPEG
JPEG 2000
JPK
JPX
A task or a piece of work.
For example, OMERO performs the task of script execution or import of metadata to the system.
Job
Annotation added to the original file object in OMERO.
Job Original File
An Interactive Notebook computation engine that executes the code written in a programming language.
Kernel
Khoros VIFF (Visualization Image File Format) Bitmap
Kodak BIP
LCM
LEO
Leica LAS AF LIF (Leica Image File Format)
LIM (Laboratory Imaging/Nikon)
LaVision Imspector
Lambert Instruments FLIM
Laser
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Laser
LaserScanningConfocalMicroscopy
LaserSetting
LaserTuneable
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Laser_Tuneable
Laser Type
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Laser_Type
Leica
Leica SCN
Lens Numerical Aperture
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Objective_LensNA
Li-Cor L2D
LifetimeImaging
Light Emitting Diode
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#LightEmittingDiode
Light Path
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#LightPath
Annotation added to the light path object in OMERO.
Light Path Annotation
The filters placed in the emission light path.
Light Path Emission Filter
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#LightPath_EmissionFilterRef
The filters placed in the excitation light path.
Light Path Excitation Filter Link
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#LightPath_ExcitationFilterRef
Light Settings
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#LightSourceSettings
Light Source
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#LightSource
Annotation added to the instrument lightsource.
Light Source Annotation Link
A log file records all the events, interactions or messages generated in a system.
Log
Logical Channel
LogicalChannelSetting
LongPass
LotNumber
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ManufacturerSpec_LotNumber
MD5-128
MIAS (Maia Scientific)
MINC MRI
MNG (Multiple-image Network Graphics)
MRC (Medical Research Council)
ManufactuerSpec
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ManufacturerSpec
The person/organisation responsible for manufacturing a component.
Manufacturer
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ManufacturerSpec_Manufacturer
MapAnnotation
The step where materials are prepared for the experiment.
MaterialPreparationStep
A Material Transfer Aggrement defines the rights that governs the transfer of materials between agents.
Material Transfer Agreement
Medium
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Laser_LaserMedium
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ObjectiveSettings_Medium
MetaMorph 7.5 TIFF
MetaMorph Stack (STK)
A job performed to import metadata.
For example, in OMERO, its the job to import metadata of images.
Metadata Import Job
Metadata Import Job Version Info
MetalVapor
The procedure used to perform a process.
Method
MethylationSensitivity
Micro-Manager
A microbeam operation applied to an image.
Microbeam Manipulation
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#MicrobeamManipulation
Microbeam Manipulation Type
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#MicrobeamManipulation_Type
Microscope
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Microscope
Microscope Type
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Microscope_Type
MinoltaMRW
Model
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ManufacturerSpec_Model
Modification
A part of a computer program or a software.
Module
The molecular formula of a chemical substance.
MolecularFormula
Molecular Imaging
The molecular weight of a chemical substance.
MolecularWeight
MultiPass
MultiPhotonMicroscopy
Murmur3-128
Murmur3-32
NIfTI
NRRD (Nearly Raw Raster Data)
NearFieldScanningOpticalMicroscopy
NeutralDensity
NeutralDensityFilter
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel_NDFilter
Nikon
Nikon EZ-C1 TIFF
NEF (Nikon Electronic Format)
Nikon Elements TIFF
Nikon NIS-Elements ND2
NominalMagnification
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Objective_NominalMagnification
NonLinear
A comment or description of an experiment.
Note
Interactive Notebook is a notebook for interactive computation and allow users to run code.
For example, Jupyter Notebook
Notebok
A cell is a multiline text input field in an Interactive Notebook which can either be code cells where code can be excuted or markdown cells where a descriptive text can be provided or raw cells where output can directly be entered.
For example, a Jupyter Notebook cell.
NotebokCell
The step to note the description of things.
Noting
OME-TIFF
OME-XML
OMERO Pyramid
Objective
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Objective
Annotation added to the instrument objective.
Objective Annotation
Objective Settings
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ObjectiveSettings
Oblique
ObliqueIllumination
Offset
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Detector_Offset
Short DNA or RNA molecules.
OligoNucleotide
OligonucleotidePreparation
Olympus CellR/APL
Olympus FluoView FV1000
Olympus SIS TIFF
Olympus ScanR
Oocyte
Operating System
OTF
OpticalTrapping
Organ
Organism
A step to collect original information of materials like the provenance of a thing.
OriginInformationCollection
The original attribution of a thing belongs to the OriginalCreator.
OriginalCreator
Original File
Annotation added to the original file object in OMERO.
Original File Annotation
Output
A person who owns a certain thing.
Owner
Oxford Instruments
PALM
PCORAW
PCX (PC Paintbrush)
PGIDocumentation
PGM
PICT (Macintosh Picture)
PMT
PNG (Portable Network Graphics)
Adobe Photoshop PSD
PerkinElmer Columbus
Perkin Elmer Densitometer
PerkinElmer Nuance
PerkinElmer Operetta
PerkinElmer UltraVIEW
PetrophagaLorioti
Phase
Photoablation
Photoactivation
Photobleaching
Photodiode
Photometric Interpretation
Photoshop TIFF
PhysicalSizeX
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_PhysicalSizeX
PhysicalSizeY
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_PhysicalSizeY
PhysicalSizeZ
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_PhysicalSizeY
PicoQuant Bin
PinholeSize
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel_PinholeSize
Pipette Solution
The step of preparing Pipette Solution.
PipetteSolutionPreparation
PipetteSolutionPreparationStandardOperatingProcedure
A job performed for management of pixel data.
Pixel Data Job
Pixels
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels
Pixels Original File Map
PixelsSetting
Pixels Type
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_Type
Plane Information
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plane
Annotation added to the Plane object in OMERO.
Plane Information Annotation
PlaneSetting
A small circular DNA strand usually found in the cytoplasm.
Plasmid
PlasmidMap
PlasmidPreparation
The step to prepare Plasmid.
PlasmidPreparationStep
Plate
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plate
The process of plate acquisition.
Plate Acquisition
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#PlateAcquisition
Annotation added to the Plate Acquiistion process in OMERO.
Plate Acquisition Annotation
Annotation added to the Plate object in OMERO.
Plate Annotation
PlateSetting
PockelCell
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Laser_PockelCell
PockelCellSetting
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel_PockelCellSetting
PolarizedLight
PositionX
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plane_PositionX
PositionY
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plane_PositionY
PositionZ
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plane_PositionZ
Power
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#LightSource_Power
Prairie Technologies TIFF
Step of preparing something.
Preparation
An important person responsible for a ResearchProject.
Principal Investigator
Programming Language
Project
Annotation added to the Project object in OMERO.
Project Annotation
Biomoelcules responsible for performing variety of functions in an organism.
Protein
ProteinMap
ProteinPreparation
Step to prepare Protein.
ProteinPreparationStep
ProtocolDescription
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Screen_ProtocolDescription
ProtocolIdentifier
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Screen_ProtocolIdentifier
A printed work or a file describing the work of one or more agents.
Publication
Pulse
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Laser_Pulse
The step for the purification of protein.
PurificationOfProtein
PurificationOfProteinStandardOperatingProcedure
The purity of a substance.
Purity
Quesant
QuickTime Movie
RHK
RNA
RNAAmplificationResult
RNAAmplificationStandardOperatingProcedure
RNA Injection
RNAInjectionStandardOperatingProcedure
RNAPreparation
ROI
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ROI
Annotation added to the ROI (Region of Interest) object in an image.
ROI Annotation
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ROIRef
Rat
The overall review provided by an agent to a thing.
Rating
ReactionCondition
ReadOutRate
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#DetectorSettings_ReadOutRate
A chemical or a physical parameter used in an experiment.
Reagent
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Reagent
Annotation added to the Reagent object in OMERO.
Reagent Annotation
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ReagentRef
ReagentSetDescription
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Screen_ReagentSetDescription
ReagentSetIdentifier
RefractiveIndex
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ObjectiveSettings_RefractiveIndex
Rendering Def
Rendering Model
RepetitionRate
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Laser_RepetitionRate
Group is an organization which belongs to a department of an institution consisting of people responsible for research and education.
Research Group
A person or collaborative group working on a research plan to achieve certain goals.
ResearchProject
Restriction Enzyme
RestrictionEnzymePreparation
RestrictionSite
The output of a step.
Result
RowNamingConvention
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plate_RowNamingConvention
Rows
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plate_Rows
SBIG
Becker & Hickl SPCImage
SHA1-160
SM Camera
SPIDER
SPIM
STED
STORM
SamplesPerPixel
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel_SamplesPerPixel
Screen
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Screen
Annotation added to the Screen object in OMERO.
Screen Annotation
ScreenExperiment
Annotation added to the screen plate object in OMERO.
Screen Plate
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Screen_PlateRef
ScreenSetting
A computer program written to perform a task in a scripting language.
Script
A job performed for the execution of scripts.
For example, in OMERO, its the job to execute scripts.
Script Job
SecondHarmonicGenerationImaging
Seiko
Semiconductor
SequenceOfOligonucleotide
Sequencing
SerialNumber
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ManufacturerSpec_SerialNumber
A period of activity between a user is logged in and logged out of a system. For example, A OMERO session, JupyterNotebook session.
Session
Annotation added to the Session object in OMERO.
Session Annotation
A setting of a system in a session.
SessionSetting
The parameters or the situation in which the experiment was performed.
Setting
Setup of an experiment.
SetupInformation
Shape
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Shape
ShortPass
SignificantBits
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_SignificantBits
SimplePCI and HCImage
SimplePCI & HCImage TIFF
SingleMoleculeImaging
A dimension of a thing.
Size
SizeC
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_SizeC
SizeT
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_SizeT
SizeX
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_SizeX
SizeY
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_SizeY
SizeZ
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_SizeZ
Slice
3i SlideBook
SlitScanConfocal
SolidState
A homogeneous mixture of substances.
For example, a chemical solution used in an experiment.
Solution
SolutionPreparation
SolutionPreparationStandardOperatingProcedure
A substance to dissolve other substances.
Solvent
Specimen is a part of a thing used in an Experiment or a study to determine the character of the whole thing.
Specimen
SpecimenPreparation
SpecimenPreparationStandardOperatingProcedure
SpecimenSubclassification
SpectralImaging
SpectralImagingExperiment
Spectroscopy
SpinningDiskConfocal
Stage Label
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#StageLabel
A set of steb-by-step instructions to carry out a complex routine.
Standard Operating Procedure
Status
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plate_Status
StockSolution
The Structural Formula of a chemical substance.
StructuralFormula
StructuredIllumination
The Bio-Format supported file formats.
SupportedFileFormat
SweptFieldConfocal
TCS
TIFF (Tagged Image File Format)
TIRF
A label attached to something to identify it.
For example, an experiment tag to identify and categorize the experiments.
Tag
The process of tagging with tags.
Tagging
Targa
Temperature
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#ImagingEnvironment_Temperature
Text
TheC
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plane_TheC
TheT
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plane_TheT
TheZ
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plane_TheZ
Thumbnail
TillPhotonics TillVision
TimeIncrement
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_TimeIncrement
TimeLapse
Topometrix
TotalInternalReflection
Transfection
TransfectionStandardOperatingProcedure
Transmittance
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#TransmittanceRange_Transmittance
Transmittance range
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#TransmittanceRange
Transmitted
Trestle
A run or execution of an activity.
For example, one execution of a script.
Trial
Tuneable
U2OS
UBM
Uncaging
Unisoku
A standard quantity of measurement.
Unit
A job performed to upload data to a server.
For example, in OMERO, its the job to upload data to the OMERO server.
Upload Job
Upload Job version Information
Upright
VG SAM
Varian FDF
Vector
VectorMap
VectorPreparation
The step for the preparation of Vector.
VectorPreparationStep
Veeco AFM
Verification
The input used to verify a material.
VerificationInput
VisiTech XYS
Volocity
Volocity Library Clipping
Voltage
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Detector_Voltage
WA-TOP
Wavelength
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Laser_Wavelength
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#LightSourceSettings_Wavelength
Well
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Well
Annotation added to the Well object in OMERO.
Well Annotation
WellOriginX
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plate_WellOriginX
WellOriginY
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Plate_WellOriginY
Annotation added to the Well Reagent object in OMERO.
Well Reagent
Well Sample
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#WellSample
WideField
Woolz
WorkingDistance
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Objective_WorkingDistance
XYCTZ
XYCZT
XYTCZ
XYTZC
XYZCT
XYZTC
Xe
Zeiss AxioVision ZVI (Zeiss Vision Image)
Zeiss Axio CSM
Zeiss AxioVision TIFF
Zeiss CZI
Zeiss LSM (Laser Scanning Microscope) 510/710
Zoom
http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Detector_Zoom
Complementary DNA source
cDNASource
cellSens VSI
A numerical scale used to express the acidity or alkalinity of a solution.
pH