Overview of the NIDM Experiment Component
This section provides an explanation of ...
NIDM-Experiment: Types and relations
Project
| NIDM-Experiment Concept | PROV type | Identifier |
|---|---|---|
| nidm:'Model Specification' | prov:Activity | nidm:ModelSpecification |
| nidm:'Project' | nidm:Project | |
| nidm:'Group' | prov:'Entity' | nidm:Group |
| nidm:'Protocol' | nidm:Protocol | |
| nidm:'Specified Plan' | nidm:SpecifiedPlan |
nidm:'Model Specification'
nidm:'Model Specification': Model specification is an activity in which the model designer creates the model that describes an experiment.
nidm:'Model Specification' is a prov:Activity.
nidm:'Project'
nidm:'Project': A project is a coordinated set of activities designed to generate data acquisition objects, with the ultimate goal of discovery or hypothesis testing.
nidm:'Project' is a prov:Activity and has the following child: sio:'clinical trial'.
sio:'clinical trial'
nidm:'Group'
nidm:'Group': A group is a collection of subjects or objects formed by the assignment of membership through the selection of one or more common characteristics.
nidm:'Group' is a prov:'Entity' and has the following children: sio:'control group', sio:'intervention group'.
nidm:'Protocol'
nidm:'Protocol': An protocol is a performed plan that contains information necessary to acquire the desired data during a session and the acquisition device parameters that are to be used in that acquisition.
nidm:'Specified Plan'
nidm:'Specified Plan': A specified plan is a plan that describes how the acquisition activity is to be carried out.
nidm:'Specified Plan' is a prov:'Entity'.
nidm:Model
nidm:Model:
nidm:Model is.
nidm:OrganismType
Acquisition
| NIDM-Experiment Concept | PROV type | Identifier |
|---|---|---|
| nidm:'Behavioral Data Acquisition' | prov:Activity | nidm:BehavioralDataAcquisition |
| nidm:'Demographics Data Acquisition' | nidm:DemographicsDataAcquisition | |
| nidm:'Image Data Reconstruction' | nidm:ImageDataReconstruction | |
| nidm:'Informed Consent Acquisition' | nidm:InformedConsentAcquisition | |
| nidm:'Series' | nidm:Session | |
| nidm:'Acquisition Method' | prov:'Entity' | nidm:AcquisitionMethod |
| nidm:'Acquisition Modality' | nidm:AcquisitionModality | |
| nidm:'Acquisition Object' | nidm:AcquisitionObject | |
| nidm:'Acquisition Object Quality' | nidm:AcquisitionObjectQuality | |
| nidm:'Auxiliary File' | nidm:AuxiliaryFile | |
| nidm:'Auxiliary File Collection' | nidm:AuxiliaryFileCollection | |
| nidm:'Clinical Assessment Acquisition Object' | nidm:ClinicalAssessmentAcquisitionObject | |
| nidm:'DICOM Tag Collection' | nidm:DICOMTagCollection | |
| nidm:'Image Contrast Type' | nidm:ImageContrastType | |
| nidm:'Image Usage Type' | nidm:ImageUsageType | |
| nidm:'Performed Plan' | nidm:PerformedPlan | |
| nidm:'Pulse Sequence' | nidm:PulseSequence | |
| nidm:'Raw Acquisition Object' | nidm:RawAcquisitionObject | |
| nidm:'Reconstructed Acquisition Object' | nidm:ReconstructedAcquisitionObject | |
| nidm:'Session Object' | nidm:SessionObject | |
| nidm:'Presentation Software' | prov:Agent | nidm:PresentationSoftware |
nidm:'Behavioral Data Acquisition'
nidm:'Behavioral Data Acquisition': A behavioral data acquisition is an activity in which an acquisition object containing information on aspects of the behavior of a subject in response to a predefined task is collected.
nidm:'Demographics Data Acquisition'
nidm:'Demographics Data Acquisition': A demographics data acquisition is an acquisition activity that collects information from a person in the investigation subject role that aids in grouping that subject with other subjects.
nidm:'Demographics Data Acquisition' is a nidm:'Acquisition'.
nidm:'Image Data Reconstruction'
nidm:'Image Data Reconstruction': Image data reconstruction is an activity in which raw data is transformed into a matrix of values that represent the spatial distribution of intensity based on some image contrast type.
nidm:'Image Data Reconstruction' is a prov:Activity.
nidm:'Informed Consent Acquisition'
nidm:'Informed Consent Acquisition': Informed Consent Acquisition is an acquisition in which a subject is asked to agree to participate in the performance of one or more acquisitions and to the plan for the disposition of the resulting acquisition object(s).
nidm:'Informed Consent Acquisition' is a nidm:'Acquisition'.
nidm:'Series'
nidm:'Series': An activity during which data is acquired from a subject by an experimenter during a single unbroken time period.
nidm:'Series' is a prov:Activity.
nidm:'Acquisition Method'
nidm:'Acquisition Method': An acquisition method is a specific form of a procedure that was used to gather data from a subject.
nidm:'Acquisition Method' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Amperometry', nidm:'Arterial Spin Labeling', nidm:'Current Clamp', nidm:'Dynamic Contrast Enhanced', nidm:'Dynamic Susceptibility Contrast', nidm:'Electrocorticography', nidm:'Electroencephalography', nidm:'Field Potential', nidm:'Multi-unit Recording', nidm:'Parallel Imaging', nidm:'Patch Clamp', nidm:'Sharp Electrode', nidm:'Simultaneous Multislice Method', nidm:'Single-unit Recording', nidm:'Voltage Clamp'.
nidm:'Amperometry'
nidm:'Amperometry': Amperometry is an extracellular acquisition method in electrophysiology in which an electrode is brought near a cell to detect the release of ions by vesicles.
nidm:'Arterial Spin Labeling'
nidm:'Arterial Spin Labeling': Arterial spin labeling is a magnetic resonance imaging acquisition method that measures perfusion using the flow of saturated blood into a predefined area by comparing the image intensity obtained in the slice with and without the saturation pulse.
nidm:'Arterial Spin Labeling' is a nidm:'Acquisition Method'.
nidm:'Current Clamp'
nidm:'Current Clamp': A current clamp is an intracellular electrophysiology acquisition method in which current is injected into a cell and the voltage generated by the cell is recorded.
nidm:'Dynamic Contrast Enhanced'
nidm:'Dynamic Contrast Enhanced': Dynamic contrast enhanced is a magnetic resonance imaging acquisition method in which T1-weighted images are acquired both before and then sequentially after a contrast agent has been injected in order to quantify metrics related to the permeability of the blood-brain barrier.
nidm:'Dynamic Contrast Enhanced' is a nidm:'Acquisition Method'.
nidm:'Dynamic Susceptibility Contrast'
nidm:'Dynamic Susceptibility Contrast': Dynamic sysceptibility contrast is a magnetic resonance imaging acquisition method in which T2*-weighted images are acquired sequentially after a contrast agent has been injected in order to quantify metrics related to blood volume and flow.
nidm:'Dynamic Susceptibility Contrast' is a nidm:'Acquisition Method'.
nidm:'Electrocorticography'
nidm:'Electrocorticography': Electrocorticography (ECoG) is an electrophysiological acquisition method in which the electrical activity of the brain is measured using electrodes that are placed directly on the cortical surface of the brain.
nidm:'Electroencephalography'
nidm:'Electroencephalography': Electroencephalography (EEG) is an electrophysiological acquisition method in which the electrical activity of the brain is measured using electrodes that are placed on the surface of the head.
nidm:'Electroencephalography' is a nidm:'Acquisition Method'.
nidm:'Field Potential'
nidm:'Field Potential': The field potential is an extracellular electrophysiology acquisition method in which an electrode is used to measure the voltage that is generated by synaptic activity (in neural tissue).
nidm:'Multi-unit Recording'
nidm:'Multi-unit Recording': Multiunit recording is an extracellular electrophysiological acquisition method in which an acquisition object is gathered using multiple recording devices.
nidm:'Parallel Imaging'
nidm:'Parallel Imaging': Parallel imaging is an acquisition method used in magnetic resonance imaging to acquire the k-space data in which multiple coils are employed and the signals from each coil are disambiguated using the coil sensitivity profile.
nidm:'Patch Clamp'
nidm:'Patch Clamp': Patch clamp is an intracellular electrophysiological acquisiiton method in which a micropipette tip is brought near a cell and scution applied drawing a section of cell membrane into the tip in order that ion movement or the intracellular environment can be studied.
nidm:'Sharp Electrode'
nidm:'Sharp Electrode': Sharp electrode is intracellular electrophysiological acquisition method used for measuring the potential of the intracellular environment with minimal disturbance of that environment, in which a pipette, filled with electrolyte and with a very small opening, is inserted into the cell and the potential measured.
nidm:'Simultaneous Multislice Method'
nidm:'Simultaneous Multislice Method': Simultaneous multislice is an acquisition method in magnetic resonance imaging used to acquire the k-space in which data from multiple slices are acquired at the same time and the coil sensitivity profiles are used to separate the data from each slice.
nidm:'Simultaneous Multislice Method' is a nidm:'Acquisition Method'.
nidm:'Single-unit Recording'
nidm:'Single-unit Recording': Single-unit recording is an extracellular electrophysiological acquisition method, in which a thin electrode is introduced into the extracellular space of a sample or subject and the action potential from a single neuron is recorded.
nidm:'Single-unit Recording' is a nidm:'Acquisition Method'.
nidm:'Voltage Clamp'
nidm:'Voltage Clamp': Voltage clamp is an intracellular electrophysiological acquisition method in in which the cell membrane potential is fixed to a set value and the ionic current that crosses the cell membrane at that potential is measured.
nidm:'Acquisition Modality'
nidm:'Acquisition Modality': An acquisition modality is a description of the general type of experiment that was used to gather data from a subject.
nidm:'Acquisition Modality' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Electrophysiology Recording', nidm:'Magnetic Resonance Imaging', nidm:'Magnetoencephalography', nidm:'Nuclear Magnetic Resonance Spectroscopic Imaging', nidm:'Nuclear Magnetic Resonance Spectroscopy', nidm:'Positron Emission Tomography', nidm:'X-ray Computed Tomography'.
nidm:'Electrophysiology Recording'
nidm:'Electrophysiology Recording': Electrophysiology Recording is an acquisition modality in which electrical signals are recorded from one or more electrodes inserted into living tissue.
nidm:'Electrophysiology Recording' is a nidm:'Acquisition Modality' and has the following children: nidm:'Extracellular Electrophysiology Recording', nidm:'Intracellular Electrophysiology Recording'.
nidm:'Extracellular Electrophysiology Recording'
nidm:'Extracellular Electrophysiology Recording': Extracellular Electrophysiology Recording is an acquisition modality in which one or more electrodes are inserted into living tissue and the electrical signals from adjacent cells are recorded.
nidm:'Extracellular Electrophysiology Recording' is a nidm:'Electrophysiology Recording'.
nidm:'Intracellular Electrophysiology Recording'
nidm:'Intracellular Electrophysiology Recording': Intracellular Electrophysiology Recording is an activity in which electrical measurements of the interior cell environment are made.
nidm:'Intracellular Electrophysiology Recording' is a nidm:'Electrophysiology Recording'.
nidm:'Magnetic Resonance Imaging'
nidm:'Magnetic Resonance Imaging': Magnetic Resonance Imaging is an acquisition modality in which radiofrequency electromagnetic radiation is used to excite nuclei of the sample or subject and the characteristics of the detected signal are used to generate intensity contrast between different spatial locations.
nidm:'Magnetic Resonance Imaging' is a nidm:'Acquisition Modality'.
nidm:'Magnetoencephalography'
nidm:'Magnetoencephalography': Magnetoencephalography is an acquisition modality in which the magnetic fields, resulting from electrical activity in the brain, are detected and used to elucidate the time course of brain electrical activity.
nidm:'Magnetoencephalography' is a nidm:'Acquisition Modality'.
nidm:'Nuclear Magnetic Resonance Spectroscopic Imaging'
nidm:'Nuclear Magnetic Resonance Spectroscopic Imaging': Nuclear magnetic resonance spectroscopic imaging is an acquisition modality in which radiofrequency electromagnetic radiation is used to excite nuclei of the sample or subject, the characteristics of the detected signal are used to generate intensity contrast over a restricted (usually grid-like) area, and the resulting signal is displayed as a spectrum for each one of the spatially-resolved areas.
nidm:'Nuclear Magnetic Resonance Spectroscopic Imaging' is a nidm:'Acquisition Modality'.
nidm:'Nuclear Magnetic Resonance Spectroscopy'
nidm:'Nuclear Magnetic Resonance Spectroscopy': Nuclear magnetic resonance spectroscopy is an acquisition modality in which radiofrequency electromagnetic radiation is used to excite nuclei of the sample or subject, the characteristics of the detected signal are used to generate signal intensity contrast over an entire selected volume, and the resulting signal is displayed as a signal spectrum rather than as matrix meant to be a representation of the underlying object.
nidm:'Nuclear Magnetic Resonance Spectroscopy' is a nidm:'Acquisition Modality'.
nidm:'Positron Emission Tomography'
nidm:'Positron Emission Tomography': Positron emission tomography is an acquisition modality in which a positron-emitting radioactive tracer is introduced into the subject and the gamma rays emitted after a positron-electron collision are detected and their originating position calculated.
nidm:'Positron Emission Tomography' is a nidm:'Acquisition Modality'.
nidm:'X-ray Computed Tomography'
nidm:'X-ray Computed Tomography': X-ray Computed tomography is an acquisition modality in which an x-ray beam is scanned across a subject and the resulting data is reconstructed into two-dimensional slices or a three-dimensional volume in which the contrast is generated by the differential absorption of x-rays.
nidm:'X-ray Computed Tomography' is a nidm:'Acquisition Modality'.
nidm:'Acquisition Object'
nidm:'Acquisition Object': An acquisition object is an entity that is gathered from a subject during an acquisition activity.
nidm:'Acquisition Object' is a prov:'Entity' and has the following children: neuro:assessment-instrument, neuro:instrument-variable, nidm:'Clinical Assessment Acquisition Object', nidm:'Demographics Acquisition Object', nidm:'Raw Acquisition Object', nidm:'Reconstructed Acquisition Object'.
nidm:'Acquisition Object Quality'
nidm:'Acquisition Object Quality': An acquisition object quality is an quality that describes an essential feature of an object that is gathered from a subject during an acquisition activity.
nidm:'Acquisition Object Quality' is a prov:'Entity' and has the following children: nidm:'Acquisition Method', nidm:'Acquisition Modality', nidm:'Image Contrast Type', nidm:'Image Usage Type', nidm:'fMRI Design Type', nidm:'k-space Traversal Scheme'.
nidm:'Auxiliary File'
nidm:'Auxiliary File': An auxiliary file is an information-bearing object that is either used to inform the execution of an experiment or that is generated during the execution of the experiment.
nidm:'Auxiliary File' is a prov:'Entity' and has the following children: nidm:'Stimulus Presentation File', nidm:'Stimulus Response File', nidm:'b-value File', nidm:'b-vector File'.
nidm:'Auxiliary File Collection'
nidm:'Auxiliary File Collection': An auxiliary file collection is a grouping that contains the URI's of files that are necessary for the execution of the experiment or the processing of the data.
nidm:'Auxiliary File Collection' is a prov:'Entity'.
nidm:'Clinical Assessment Acquisition Object'
nidm:'Clinical Assessment Acquisition Object': A clinical assessment object is an acquisition object that contains information on aspects of the medical condition of the subject.
nidm:'Clinical Assessment Acquisition Object' is a nidm:'Acquisition Object'.
nidm:'DICOM Tag Collection'
nidm:'DICOM Tag Collection': A DICOM tag collection is a group of identifiers and their values that are stored in the headers of DICOM-formatted acquisition objects and that record the acquisition and reconstruction parameters for that acquisition object.
nidm:'DICOM Tag Collection' is a prov:'Entity'.
nidm:'Image Contrast Type'
nidm:'Image Contrast Type': Image Contrast Type is an acquisition object quality that denotes the physical properties on which differences in image intensity, in an image, are based.
nidm:'Image Contrast Type' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Diffusion Weighted', nidm:'Flow Weighted', nidm:'Proton Density Weighted', nidm:'Susceptibility Weighted', nidm:'T1 Weighted', nidm:'T2 Weighted', nidm:'T2-Star Weighted'.
nidm:'Diffusion Weighted'
nidm:'Diffusion Weighted': Diffusion weighted is an image contrast type in which differences in voxel intensity are based on the brownian-motion behavior of the species that generates the detected signal from that voxel.
nidm:'Flow Weighted'
nidm:'Flow Weighted': Flow weighted is an image contrast type in which differences in voxel intensity are based on the bulk motion behavior of the species that generates the detected signal from that voxel.
nidm:'Proton Density Weighted'
nidm:'Proton Density Weighted': Proton density weighted is a image contrast type in magnetic resonance imaging in which differences in voxel intensity reflect underlying differences in the number of protons in those voxels.
nidm:'Proton Density Weighted' is a nidm:'Image Contrast Type'.
nidm:'Susceptibility Weighted'
nidm:'Susceptibility Weighted': Susceptibility weighted is a magentic resonance imaging image-contrast type in which differences in voxel intensity reflect differences in magnetic susceptibilty of the underlying sample.
nidm:'Susceptibility Weighted' is a nidm:'Image Contrast Type'.
nidm:'T1 Weighted'
nidm:'T1 Weighted': T1 weighted is an image contrast type in which differences in voxel intensity reflect differences in the spin-lattice relaxation time of the probe in the underlying sample.
nidm:'T2 Weighted'
nidm:'T2 Weighted': T2 weighted is an image contrast type in which differences in voxel intensity reflect differences in the spin-spin relaxation time of the probe in the underlying sample.
nidm:'T2-Star Weighted'
nidm:'T2-Star Weighted': T2-star weighted is an image contrast type in which differences in voxel intensity reflect differences in the spin-spin relaxation time of the probe as well as the field inhomogeneities in the underlying sample.
nidm:'Image Usage Type'
nidm:'Image Usage Type': Image Usage Type is an acquisition object quality that denotes to what purpose the acquired object will be employed.
nidm:'Image Usage Type' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Anatomical', nidm:'Diffusion Tensor', nidm:'Functional', nidm:'Quantitative Susceptibility Mapping', nidm:'Stimulus Response File', nidm:'Susceptibility Weighted Imaging'.
nidm:'Anatomical'
nidm:'Anatomical': Anatomical is a description of the usage of a given acquisition object, indicating that the purpose of the object is to provide information on the anatomy of the object on which the acquisition was performed.
nidm:'Diffusion Tensor'
nidm:'Diffusion Tensor': Diffusion tensor is an image usage type that denotes that the acquisition object collected can be use to construct the diffusion tensor of the imaged tissue.
nidm:'Functional'
nidm:'Functional': Functional is a description of the usage of a given acquisition object, indicating that the purpose of the object is to provide information on the biological function of some aspect of the object on which the acquisition was performed.
nidm:'Quantitative Susceptibility Mapping'
nidm:'Quantitative Susceptibility Mapping': Quantitative susceptibility mapping is a magentic resonance imaging image-usage type in which differences in voxel intensity reflect quantitative differences magnetic susceptibilty of the underlying sample.
nidm:'Quantitative Susceptibility Mapping' is a nidm:'Image Usage Type'.
nidm:'Stimulus Response File'
nidm:'Stimulus Response File': A stimulus response file is an auxiliary file that contains the recorded response of the subject to an experimental stimulus the course of a task-based assessment activity.
nidm:'Susceptibility Weighted Imaging'
nidm:'Susceptibility Weighted Imaging': Susceptibility weighted imaging is a magentic resonance imaging image-usage type in which differences in voxel intensity reflect differences in magnetic susceptibilty of the underlying sample, but are not caculated values.
nidm:'Susceptibility Weighted Imaging' is a nidm:'Image Usage Type'.
nidm:'Performed Plan'
nidm:'Performed Plan': A performed plan is a plan that is actually implemented during an acquisition activity.
nidm:'Performed Plan' is a prov:'Entity' and has the following child: nidm:'Protocol'.
nidm:'Pulse Sequence'
nidm:'Pulse Sequence': A pulse sequence is a collection of commands sent to the magnetic resonance imaging or nuclear magnetic resonance hardware to control the excitation of the subject or sample and the acquisition of data.
nidm:'Pulse Sequence' is a prov:'Entity'.
nidm:'Raw Acquisition Object'
nidm:'Raw Acquisition Object': A raw acquisition object is an acquisition object that has not yet undergone any further processing steps such asthe image reconstruction process.
nidm:'Raw Acquisition Object' is a nidm:'Acquisition Object'.
nidm:'Reconstructed Acquisition Object'
nidm:'Reconstructed Acquisition Object': A reconstructed acquisition object is an acquisition object that has undergone an image reconstruction activity resulting in a matrix of values that when viewed form an image.
nidm:'Reconstructed Acquisition Object' is a nidm:'Acquisition Object' and has the following child: dctype:Image.
nidm:'Session Object'
nidm:'Session Object': A session object is an entity that represents one or more acquisitions that take place during the same temporal epoch (session).
nidm:'Session Object' is a prov:'Entity'.
A nidm:'Session Object' has attributes:
- rdfs:label: (OPTIONAL) Human readable description of the nidm:'Session Object'.
- dct:hasPart: (OPTIONAL)
nidm:'Presentation Software'
nidm:'Presentation Software': Presentation software is a software agent that provides the stimulus to the subject during a functional imaging (MRI, MEG, EEG) or behavioral data acquisition activity.
nidm:'Presentation Software' is a prov:Agent.
nidm:Computer
nidm:DataAcquisitionDeviceOperator
nidm:InformedConsentAdministrator
Modality
| NIDM-Experiment Concept | PROV type | Identifier |
|---|---|---|
| nidm:'Series' | prov:Activity | nidm:Session |
| nidm:'Task' | nidm:Task | |
| nidm:'Stimulus Presentation File' | prov:'Entity' | nidm:StimulusPresentationFile |
| nidm:'Stimulus Response File' | nidm:StimulusResponseFile | |
| nidm:'k-space Traversal Scheme' | nidm:k-spaceTraversalScheme |
nidm:'Series'
nidm:'Series': An activity during which data is acquired from a subject by an experimenter during a single unbroken time period.
nidm:'Series' is a prov:Activity.
nidm:'Task'
nidm:'Task': A task is an activity that is performed by a subject to elucidate some aspect of human behavior or underlying process.
nidm:'Task' is a prov:Activity.
nidm:'Stimulus Presentation File'
nidm:'Stimulus Presentation File': A stimulus presentation file is an auxiliary files that contains the presentation timing and/or location of the experimental stimulus (e.g., words, pictures) that are shown to the subject in a task-based assessment activity.
nidm:'Stimulus Presentation File' is a nidm:'Auxiliary File'.
nidm:'Stimulus Response File'
nidm:'Stimulus Response File': A stimulus response file is an auxiliary file that contains the recorded response of the subject to an experimental stimulus the course of a task-based assessment activity.
nidm:'k-space Traversal Scheme'
nidm:'k-space Traversal Scheme': The k-space traversal scheme is an acquisition object quality that describes, in a magnetic resonance imaging acquisition, the path in k-space along which the signal is acquired.
nidm:'k-space Traversal Scheme' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Cartesian', nidm:'Echo Planar', nidm:'Inside-out Spiral', nidm:'Outside-in Spiral', nidm:'Rectilinear'.
nidm:'Amperometry'
nidm:'Amperometry': Amperometry is an extracellular acquisition method in electrophysiology in which an electrode is brought near a cell to detect the release of ions by vesicles.
nidm:'Anatomical'
nidm:'Anatomical': Anatomical is a description of the usage of a given acquisition object, indicating that the purpose of the object is to provide information on the anatomy of the object on which the acquisition was performed.
nidm:'Cartesian'
nidm:'Cartesian': Cartesian is a k-space traversal scheme in MRI in which the path of the data acquisition follows a straight line parallel to one axis of the defined k-space and perpendicular to the other k=space axis.
nidm:ComputedTomography
nidm:'Current Clamp'
nidm:'Current Clamp': A current clamp is an intracellular electrophysiology acquisition method in which current is injected into a cell and the voltage generated by the cell is recorded.
nidm:'Diffusion Tensor'
nidm:'Diffusion Tensor': Diffusion tensor is an image usage type that denotes that the acquisition object collected can be use to construct the diffusion tensor of the imaged tissue.
nidm:'Diffusion Weighted'
nidm:'Diffusion Weighted': Diffusion weighted is an image contrast type in which differences in voxel intensity are based on the brownian-motion behavior of the species that generates the detected signal from that voxel.
nidm:DynamicContrastEnhancement
nidm:'Dynamic Susceptibility Contrast'
nidm:'Dynamic Susceptibility Contrast': Dynamic sysceptibility contrast is a magnetic resonance imaging acquisition method in which T2*-weighted images are acquired sequentially after a contrast agent has been injected in order to quantify metrics related to blood volume and flow.
nidm:'Dynamic Susceptibility Contrast' is a nidm:'Acquisition Method'.
nidm:'Echo Planar'
nidm:'Echo Planar': Echo planar is a k-space traversal scheme used to acquire the k-space data in magnetic resonance imaging in which the entirety of k-space is continuously traversed for each repetition of the pulse sequence.
nidm:'Electrocorticography'
nidm:'Electrocorticography': Electrocorticography (ECoG) is an electrophysiological acquisition method in which the electrical activity of the brain is measured using electrodes that are placed directly on the cortical surface of the brain.
nidm:'Electroencephalography'
nidm:'Electroencephalography': Electroencephalography (EEG) is an electrophysiological acquisition method in which the electrical activity of the brain is measured using electrodes that are placed on the surface of the head.
nidm:'Electroencephalography' is a nidm:'Acquisition Method'.
nidm:'Extracellular Electrophysiology Recording'
nidm:'Extracellular Electrophysiology Recording': Extracellular Electrophysiology Recording is an acquisition modality in which one or more electrodes are inserted into living tissue and the electrical signals from adjacent cells are recorded.
nidm:'Extracellular Electrophysiology Recording' is a nidm:'Electrophysiology Recording'.
nidm:'Field Potential'
nidm:'Field Potential': The field potential is an extracellular electrophysiology acquisition method in which an electrode is used to measure the voltage that is generated by synaptic activity (in neural tissue).
nidm:'Finger Tapping Test'
nidm:'Finger Tapping Test': The Finger Tapping Test is an assessment instrument in which a subject is asked to press a button as many times as possible in a set duration, the results of which can be used to assess motor efficiency and motor function.
nidm:'Flow Weighted'
nidm:'Flow Weighted': Flow weighted is an image contrast type in which differences in voxel intensity are based on the bulk motion behavior of the species that generates the detected signal from that voxel.
nidm:'Functional'
nidm:'Functional': Functional is a description of the usage of a given acquisition object, indicating that the purpose of the object is to provide information on the biological function of some aspect of the object on which the acquisition was performed.
nidm:'Inside-out Spiral'
nidm:'Inside-out Spiral': Inside-out spiral is a k-space traversal scheme in which the path along which magnetic resonance imaging k-space data is acquired is in the shape of a spiral and the data at the center of k-space is acquired first.
nidm:'Inside-out Spiral' is a nidm:'k-space Traversal Scheme'.
nidm:'Intracellular Electrophysiology Recording'
nidm:'Intracellular Electrophysiology Recording': Intracellular Electrophysiology Recording is an activity in which electrical measurements of the interior cell environment are made.
nidm:'Intracellular Electrophysiology Recording' is a nidm:'Electrophysiology Recording'.
nidm:'Magnetic Resonance Imaging'
nidm:'Magnetic Resonance Imaging': Magnetic Resonance Imaging is an acquisition modality in which radiofrequency electromagnetic radiation is used to excite nuclei of the sample or subject and the characteristics of the detected signal are used to generate intensity contrast between different spatial locations.
nidm:'Magnetic Resonance Imaging' is a nidm:'Acquisition Modality'.
nidm:'Multi-unit Recording'
nidm:'Multi-unit Recording': Multiunit recording is an extracellular electrophysiological acquisition method in which an acquisition object is gathered using multiple recording devices.
nidm:'Nuclear Magnetic Resonance Spectroscopy'
nidm:'Nuclear Magnetic Resonance Spectroscopy': Nuclear magnetic resonance spectroscopy is an acquisition modality in which radiofrequency electromagnetic radiation is used to excite nuclei of the sample or subject, the characteristics of the detected signal are used to generate signal intensity contrast over an entire selected volume, and the resulting signal is displayed as a signal spectrum rather than as matrix meant to be a representation of the underlying object.
nidm:'Nuclear Magnetic Resonance Spectroscopy' is a nidm:'Acquisition Modality'.
nidm:'Outside-in Spiral'
nidm:'Outside-in Spiral': Outside-inSpiral is a k-space traversal scheme in which the path, along which magnetic resonance imaging k-space data is acquired, is spiral and the data further away from the center of k-space is acquired first.
nidm:'Outside-in Spiral' is a nidm:'k-space Traversal Scheme'.
nidm:ParallelImagingMethod
nidm:'Patch Clamp'
nidm:'Patch Clamp': Patch clamp is an intracellular electrophysiological acquisiiton method in which a micropipette tip is brought near a cell and scution applied drawing a section of cell membrane into the tip in order that ion movement or the intracellular environment can be studied.
nidm:'Positron Emission Tomography'
nidm:'Positron Emission Tomography': Positron emission tomography is an acquisition modality in which a positron-emitting radioactive tracer is introduced into the subject and the gamma rays emitted after a positron-electron collision are detected and their originating position calculated.
nidm:'Positron Emission Tomography' is a nidm:'Acquisition Modality'.
nidm:'Proton Density Weighted'
nidm:'Proton Density Weighted': Proton density weighted is a image contrast type in magnetic resonance imaging in which differences in voxel intensity reflect underlying differences in the number of protons in those voxels.
nidm:'Proton Density Weighted' is a nidm:'Image Contrast Type'.
nidm:'Rectilinear'
nidm:'Rectilinear': Rectilinear is a k-space traversal scheme in magnetic resonance imaging in which the path in k-space over which the data is acquired is linear and aligned perpendicular to either the phase-encoding or frequency-encoding direction.
nidm:'Sharp Electrode'
nidm:'Sharp Electrode': Sharp electrode is intracellular electrophysiological acquisition method used for measuring the potential of the intracellular environment with minimal disturbance of that environment, in which a pipette, filled with electrolyte and with a very small opening, is inserted into the cell and the potential measured.
nidm:'Simultaneous Multislice Method'
nidm:'Simultaneous Multislice Method': Simultaneous multislice is an acquisition method in magnetic resonance imaging used to acquire the k-space in which data from multiple slices are acquired at the same time and the coil sensitivity profiles are used to separate the data from each slice.
nidm:'Simultaneous Multislice Method' is a nidm:'Acquisition Method'.
nidm:'Single-unit Recording'
nidm:'Single-unit Recording': Single-unit recording is an extracellular electrophysiological acquisition method, in which a thin electrode is introduced into the extracellular space of a sample or subject and the action potential from a single neuron is recorded.
nidm:'Single-unit Recording' is a nidm:'Acquisition Method'.
nidm:'Stimulus Response File'
nidm:'Stimulus Response File': A stimulus response file is an auxiliary file that contains the recorded response of the subject to an experimental stimulus the course of a task-based assessment activity.
nidm:'Susceptibility Weighted'
nidm:'Susceptibility Weighted': Susceptibility weighted is a magentic resonance imaging image-contrast type in which differences in voxel intensity reflect differences in magnetic susceptibilty of the underlying sample.
nidm:'Susceptibility Weighted' is a nidm:'Image Contrast Type'.
nidm:'Susceptibility Weighted Imaging'
nidm:'Susceptibility Weighted Imaging': Susceptibility weighted imaging is a magentic resonance imaging image-usage type in which differences in voxel intensity reflect differences in magnetic susceptibilty of the underlying sample, but are not caculated values.
nidm:'Susceptibility Weighted Imaging' is a nidm:'Image Usage Type'.
nidm:'T1 Weighted'
nidm:'T1 Weighted': T1 weighted is an image contrast type in which differences in voxel intensity reflect differences in the spin-lattice relaxation time of the probe in the underlying sample.
nidm:'T2-Star Weighted'
nidm:'T2-Star Weighted': T2-star weighted is an image contrast type in which differences in voxel intensity reflect differences in the spin-spin relaxation time of the probe as well as the field inhomogeneities in the underlying sample.
nidm:'T2 Weighted'
nidm:'T2 Weighted': T2 weighted is an image contrast type in which differences in voxel intensity reflect differences in the spin-spin relaxation time of the probe in the underlying sample.
nidm:'Voltage Clamp'
nidm:'Voltage Clamp': Voltage clamp is an intracellular electrophysiological acquisition method in in which the cell membrane potential is fixed to a set value and the ionic current that crosses the cell membrane at that potential is measured.
nidm:bValueFile
nidm:bVectorFile
Assessments
| NIDM-Experiment Concept | PROV type | Identifier |
|---|
nidm:BarnesScale
nidm:'Calgary Depression Scale'
nidm:'Calgary Depression Scale': The Calgary Depression Scale is an assessment instrument consisting of a series of questions specifically developed to assess the level of depression in schizophrenia.
nidm:'Category Fluency Test'
nidm:'Category Fluency Test': The Category Fluency test is an assessment instrument in which subjects are asked to produce as many words belonging to three specific categories (e.g., animals, fruits and vegetables) in a given period of time and thereby provides a measure of the integrity of the subjects brain lexical system.
nidm:'Clinical Global Impression'
nidm:'Clinical Global Impression': The Clinical Global Impression scale(s) are assessment instruments that assign a rating number to the severity or improvement of the patient condition or to the efficacy of a given treatment at the time of assessment.
nidm:CombinedAssessment
nidm:'Continuous Performance Test'
nidm:'Continuous Performance Test': A Continuous Performance Test is an assessment instrument that measures sustained and selective attention by having the subject perform a task continuously for a given duration of time.
nidm:DelayedSemanticVerbalLearningTest
nidm:DelayedVisualFiguralLearningTest
nidm:EdinburghHandnessTest
nidm:'Facial Emotion Discrimination Test'
nidm:'Facial Emotion Discrimination Test': The Facial Emotion Discrimination Test is an assessment instrument in which subjects are shown pairs of facial images and the asked to determine whether the emotion conveyed by the faces are the same or different.
nidm:FagerstromSmokingTest
nidm:'Letter Fluency Test'
nidm:'Letter Fluency Test': The Letter Fluency test is used to evaluate the spontaneous production of words beginning with a given letter within a limited amount of time (60 seconds).
nidm:'Letter Number Span Test'
nidm:'Letter Number Span Test': In this test of auditory working memory, sequences of mixed letters and numbers are verbally presented and the subject is required to reorganize them into a progressive or ascending order and then report the reordered sequence to the examiner.
nidm:'Maze Solving Test'
nidm:'Maze Solving Test': Using a pen, in the Maze Solving test, subjects attempt to find their way out of a maze by tracing a path while trying to avoid making mistakes, such as tracing to a dead end.
nidm:'North American Reading Test'
nidm:'North American Reading Test': A method of estimating verbal IQ in patients based upon their ability to read and correctly pronounce irregular words that do not necessarily follow common or intuitive rules of phonography and orthography.
nidm:'Positive and Negative Syndrome Scale'
nidm:'Positive and Negative Syndrome Scale': The Positive and Negative Syndrome Scale is an assessment instrument used for typological and dimensional assessment.
nidm:'Premorbid Adjustment Scale'
nidm:'Premorbid Adjustment Scale': The Premorbid Adjustment Scale (PAS) is an assessment instrument that evaluates the degree of achievement of developmental goals at each of several periods of a subject's life before the onset of schizophrenia.
nidm:SemanticVerbalLearningTest
nidm:'Simpson Angus Rating Scale'
nidm:'Simpson Angus Rating Scale': The Simpson Angus Rating Scale is an assessment instrument used to evaluate the presence and severity of parkinsonian symptomatology and focuses on rigidity rather than bradykinesia.
nidm:SocioeconomicScale
nidm:'Spatial Memory Span'
nidm:'Spatial Memory Span': The Spatial Memory Span is an assessment instrument that assesses the capacity of an individual for holding a visual-spatial sequence in working memory.
nidm:'Stroop Test'
nidm:'Stroop Test': This test measures the ease with which a person can shift his or her perceptual set to conform to changing demands and suppress a habitual response in favor of an unusual one. The subject is assessed on his or her ability to read color names compared to the ability to read the color of ink that is not congruent with the color name of the printed words.
nidm:'Symbol Digit Association Test'
nidm:'Symbol Digit Association Test': The Symbol Digit Association Test is an assessment instrument in which the subject is asked to match a presented number with the associated symbol from rows of symbols and digits using a table that displays a pairing of each symbol with a corresponding number.
nidm:'Trails A'
nidm:'Trails A': Trails A is an assessement instrument in which the subject is asked to draw lines connecting consecutively numbered circles.
nidm:'Trails A' is.
nidm:'Trails B'
nidm:'Trails B': Trails B is an assessement instrument in which the subject is asked to draw lines connecting circles with consecutively numbered and lettered circles.
nidm:'Trails B' is.
nidm:VisualFiguralLearningTest
nidm:'Wisconsin Card Sorting Test'
nidm:'Wisconsin Card Sorting Test': The Wisconsin Card Sorting Test is an assessment instrument in which a subject is asked to place cards under one of the four stimulus cards that he or she believes would be a correct strategy, while receiving feedback from the test administrator as to whether the last card was placed correctly or not (though the changes the sorting strategy throughout the test).
Other
| NIDM-Experiment Concept | PROV type | Identifier |
|---|---|---|
| nidm:'Acquisition' | prov:Activity | nidm:Acquisition |
| nidm:'Clinical Data Acquisition' | nidm:ClinicalDataAcquisition | |
| nidm:'Series' | nidm:Series | |
| nidm:'Demographics Acquisition Object' | prov:'Entity' | nidm:DemographicsAcquisitionObject |
| nidm:'fMRI Design Type' | nidm:NIDM_0000155 | |
| nidm:'b-value File' | nidm:b-ValueFile | |
| nidm:'b-vector File' | nidm:b-VectorFile |
nidm:'Acquisition'
nidm:'Acquisition': An acquisition is an activty in which data about a subject is gathered.
nidm:'Acquisition' is a prov:Activity and has the following children: neuro:instrument-based-assessment, neuro:variable-assessment, nidm:'Behavioral Data Acquisition', nidm:'Clinical Data Acquisition', nidm:'Demographics Data Acquisition', nidm:'Informed Consent Acquisition'.
neuro:instrument-based-assessment
neuro:instrument-based-assessment: An INSTRUMENT-BASED ASSESSMENT is a SUBJECT DATA ACQUISITION that captures some required information concerning the subject and involves the integration of data from instruments: TEST(-INSTRUMENTS) and/or QUESTIONNAIRES. When the purpose of the patient's examination is the assessment of her/his behavior, the examiner uses questionnaires rather than tests to rate the level of intensity/severity of a behavioral trait. Then, the appropriate action is a BEHAVIOURAL INTERVIEW rather than a BEHAVIOURAL TEST which is less adapted.
INSTRUMENT-BASED ASSESSMENTS are divided among TEST-BASED ASSESSMENTS and QUESTIONNAIRE-BASED ASSESSMENTS according to the kind of instrument which is administrated and therefore to the specific roles played by the subject and the healthcare professional in the assessment.
neuro:instrument-based-assessment is a nidm:'Acquisition' and has the following children: neuro:questionnaire-based-assessment, neuro:test-based-assessment.
neuro:questionnaire-based-assessment
neuro:questionnaire-based-assessment: A Questionnaire-based assessment is an Instrument-based assessment which involves the integration of data from questionnaires. A questionnaire-based assessment involves sets of questions (items), carried out in a structured way (known as structured interview) or semi-structured way, to provide normative data. Interview-based measures and rating scales are designed to be completed by clinicians, subjects, parents, caregivers. The scoring of each item contributes to the measure of the explored domain (e.g. Depression).
“A directed conversation with the subject aimed at eliciting information for psychiatric diagnosis, evaluation, treatment planning, etc. The interview may be conducted by a social worker or psychologist.” (Source: MSH/MH). (Concept: [CUI C0021819] Interview, Psychological, Semantic Type: Diagnostic Procedure).
QUESTIONNAIRE-BASED ASSESSMENTS are divided among PSYCHOLOGICAL INTERVIEWS, BEHAVIOURAL INTERVIEWS, and NEUROCLINICAL INTERVIEWS according to the kind of questionnaire that is used.
neuro:questionnaire-based-assessment is a prov:Activity and has the following children: neuro:behavioural-interview, neuro:neuroclinical-interview, neuro:psychological-interview.
neuro:behavioural-interview
neuro:behavioural-interview: A behavioural interview is a Questionnaire-based assessment carried out during a behavioral examination.
neuro:behavioural-interview is a prov:Activity.
neuro:neuroclinical-interview
neuro:neuroclinical-interview: A neuroclinical interview is a Questionnaire-based assessment carried out during a neurological examination.
neuro:neuroclinical-interview is a prov:Activity.
neuro:psychological-interview
neuro:psychological-interview: A psychological interview is a Questionnaire-based assessment carried out during a psychological examination.
neuro:psychological-interview is a prov:Activity.
neuro:test-based-assessment
neuro:test-based-assessment: A Test-based assessment is an Instrument-based assessment which involves the integration of data from tests. A Test-based assessment is conducted as a formal testing session to provide normative data.
TEST-BASED ASSESSMENTS are divided among PSYCHOLOGICAL TESTS, BEHAVIOURAL TESTS and NEUROCLINICAL TESTS according to the kind of instrument that is used.
neuro:test-based-assessment is a prov:Activity and has the following children: neuro:behavioural-test, neuro:neuroclinical-test, neuro:psychological-test.
neuro:behavioural-test
neuro:behavioural-test:
neuro:behavioural-test is a prov:Activity.
neuro:neuroclinical-test
neuro:neuroclinical-test: “The Neuroclinical examination (Neurological test) is the usual clinical approach to the study of the brain functions. The Neurological test includes extensive study of the brain's chief product-behavior. [...] The neurologist examines the strength, efficiency, reactivity, and appropriateness of the patient's responses to commands, questions, discrete stimulation of particular neural subsystems, and challenges to specific muscle groups and motor patterns. […] In the neurological examination of behavior, the clinician reviews behavior patterns generated by neuroanatomical subsystems, measuring patients' responses in relatively coarse graduations or nothing their absence" (Lezak et al., 2004).
neuro:neuroclinical-test is a prov:Activity.
neuro:psychological-test
neuro:psychological-test: "[…] psychological assessment […] involves the intensive study of behavior by means of interviews and standardized scaled tests and questionnaires that provide relatively precise and sensitive indices of behaviour." (Lezak et al., 2004).
PSYCHOLOGICAL TESTS are divided among NEUROPSYCHOLOGICAL TESTS and EXPERIMENTAL PSYCHOLOGY TESTS according to the kind of instrument that is used.
neuro:psychological-test is a prov:Activity and has the following children: neuro:experimental-psychology-test, neuro:neuropsychological-test.
neuro:experimental-psychology-test
neuro:experimental-psychology-test:
neuro:experimental-psychology-test is and has the following child: neuro:psychophysical-test.
neuro:psychophysical-test
neuro:neuropsychological-test
neuro:neuropsychological-test: "Neuropsychological assessment is a method of examining the brain by studying its behavioural product. Since the subject matter of neuropsychological assessment is behavior, it relies on many of the same techniques, assumptions, and theories as does psychological assessment. The distinctive character of neuropsychological assessment lies in a conceptual frame of reference that takes brain function as its point of departure. Regardless of whether a behavioral study is undertaken for clinical or research purposes, it is neuropsychological so long as the questions that prompted it, the central issues, the findings, or the inferences drawn from them ultimately relate to brain function" (Lezak et al., 2004).
neuro:variable-assessment
neuro:variable-assessment: A variable assessment is an activity that results in a value assigned to a specific item on an assessment instrument question or test.
neuro:variable-assessment is a nidm:'Acquisition' and has the following children: neuro:coded-variable-assessment, neuro:numerical-variable-assessment.
neuro:coded-variable-assessment
neuro:coded-variable-assessment:
neuro:coded-variable-assessment is a prov:Activity.
neuro:numerical-variable-assessment
neuro:numerical-variable-assessment:
neuro:numerical-variable-assessment is a prov:Activity.
nidm:'Clinical Data Acquisition'
nidm:'Clinical Data Acquisition': A clinical data acquisition is an activity in which an acquisition object containing information on aspects of the medical condition of the subject is collected.
nidm:'Clinical Data Acquisition'
nidm:'Clinical Data Acquisition': A clinical data acquisition is an activity in which an acquisition object containing information on aspects of the medical condition of the subject is collected.
nidm:'Series'
nidm:'Series': A series is an activity in which data is acquired such that one acquisition takes place during the same temporal epoch.
nidm:'Series' is a prov:Activity.
nidm:'Demographics Acquisition Object'
nidm:'Demographics Acquisition Object': A demographics acquisition object is an object that contains the demographic information acquired from a person in the investigation subject role.
nidm:'Demographics Acquisition Object' is a nidm:'Acquisition Object'.
nidm:'fMRI Design Type'
nidm:'fMRI Design Type': The type of stimulus presentation used in the data acquisition, one of block-based design, event-related design or mixed design.
nidm:'fMRI Design Type' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Block-Based Design', nidm:'Event-Related Design', nidm:'Mixed Design'.
nidm:'Block-Based Design'
nidm:'Block-Based Design': A block-based design is a fMRI design comprised of epochs of stimulus and/or behavior.
nidm:'Event-Related Design'
nidm:'Event-Related Design': An event-related design is a fMRI design comprised of discrete events of stimulus and/or behavior.
nidm:'Mixed Design'
nidm:'Mixed Design': A mixed design is a fMRI design comprised of both epochs & discrete events of stimulus and/or behavior.
nidm:'b-value File'
nidm:'b-value File': A b-value file is an auxiliary file, used in a diffusion-weighted magnetic resonance imaging acquisition activity, that contains the b-values used to control the diffusion-sensitization weighting.
nidm:'b-vector File'
nidm:'b-vector File': A b-vector file is an auxiliary file, used in a diffusion-weighted magnetic resonance imaging acquisition activity, that contains the direction vectors used to control the direction of the diffusion-sensitization weighting.
nidm:'Block-Based Design'
nidm:'Block-Based Design': A block-based design is a fMRI design comprised of epochs of stimulus and/or behavior.
nidm:'Event-Related Design'
nidm:'Event-Related Design': An event-related design is a fMRI design comprised of discrete events of stimulus and/or behavior.
nidm:'Mixed Design'
nidm:'Mixed Design': A mixed design is a fMRI design comprised of both epochs & discrete events of stimulus and/or behavior.