v.1.2 (July, 2009) - New classes have been added from NeuroLex wiki since the February release (Class ID: nlx_inv_20090401 to 20090610). v 2.0 (August, 2011) - NIF-Investigation now imports NIF-Resource.owl, NIF-Government-Granting-Agency.owl, and NIF-Scientific-discipline.owl as part of its direct imports. Imports Cognitive paradigm ontology (CogPO). v 2.1 (April, 2012) - Modified the hierarchy of 'Data set'. all the subclasses of 'Data set' are kept as 'Information content entity'. The reason for this chage was to provide a cleaner hierarchy for NIF Resource descriptor. v2.2 (October, 2012) - New classes added under Electron microscopic imaging assay. Definition changed for Segmentation Software from NITRC. v2.3 (December, 2012) - Addition of NEMO (v.2.98) as an imported module. Addition of Cognitive Atlas Ontology (CogAt v.0.3) as an import. Note that we have only imported the 'concepts' and excluded the 'task' classes for now. Newly defined classes: Neuroimaging and Immunolabeling.
Adapted from IMOD user manual. Kremer JR, Mastronarde DN, McIntosh JR. Computer visualization of three-dimensional image data using IMOD. J Struct Biol. 1996 Jan-Feb;116(1):71-6.
A reconstruction algorithm for electron tomography. In R-weighted backprojection, each horizontal line of input data is filtered to weight each spatial frequency proportional to its radius in Fourier space. This is radial weighting, and the filter is referred to as a radial filter.
A subject group consisting of individuals that display a canonical phenotype for the phenotype under investigation in a scientific study. Membership in this group does not imply that the subject displays no abberrant phenotypes. For example, an adult that displays no symptoms of respiratory disease may serve as a normal control in a study even though the subject posssess a rare blood type.
A behavioral paradigm in which subjects view images of moving body parts (Brain Map).
A behavioral paradigm in which subjects recall items from episodic memory (autobiographical history, long-term event memories).
A quantitative value representing the difference of two underlying quantitative values.
A behavioral paradigm that requires subjects to hold their breath one or more times.
The time interval between successive initial excitation pulses in one full playout of a pulse sequence. This is also often used in reference to the time it takes to acquire the entire volume being imaged (e.g., the brain, the ventral surface of the brain).
The amount of time that exists between successive pulse sequences applied to the same slice. It is delineated by initiating the first RF pulse of the sequence then repeating the same RF pulse at a time t. Variations in the value of TR have an important effect on the control of image contrast characteristics. Short values of TR (< 1000 ms) are common in images exhibiting T1 contrast, and long values of TR (> 1500 ms) are common in images exhibiting T2 contrast. TR is also a major factor in total scan time.
A subject group that has received an identical treatment to the experimental group but without the active agent under study.
A behavioral paradigm where subjects are stimulated with Chinese acupuncture, a procedure in which thin needles are passed through the skin to specific points.
A behavioral paradigm in which the subject are asked to respond to an auditory stimuli (tone or word discrimination, with or without distractors), during the performance of an unrelated task. Also often co-coded with Tone Monitor/Discrimination.
A behavioral paradigm in which a subject views stimuli (words, pictures, letters) and are instructed to memorize them.
Uniform measurement standard used to characterize a quantitative value.
Role played by individual investigators during the course of an investigation
A behavioral paradigm in which subjects are presented with paired stimuli (usually involving presentation of an eye puff with an auditory tone) in an attempt to study associative learning.
* A procedure for critical evaluation; a means of determining the presence, quality, or truth of something. (NCI) * Administration of tests, and analysis and interpretation of test scores in order to measure differences between individuals or between test performances of the same individual on different occasions. (PSY)
An assessment is the process of evaluating organism attributes via an assessment instrument that results in an assessment measure which may be interpreted in a phenotypical domain.
The preferred unit of magnetic flux density. One tesla is equal to 10,000 gauss. The Tesla unit value is defined as a field strength of 1 Weber per meter 2, where 1 Weber represents 1 x 108 (100,000,000) flux lines. Named after the 20th century, Serbian-American electrical engineer and inventor, Nikola Tesla.
A subject group that has received an identical surgical procedure to the experimental group but without the treatment under study.
A standardized brain atlas published by Talairach and Tournoux.
moved under the new Item_recognition_paradigm class (BB).
A behavioral paradigm that involves the presentation of sets of target items and the recognition of some of those items vs unfamiliar items presented serially (probe items).
Is an assessment that measures the ability of an individual to name as many items as possible within a specified amount of time. May measure letter (or phonemic, e.g., F-A-S) or category (e.g., animals) fluency.
An antibody produced by clones of cells such as those isolated after hybridization of activated B lymphocytes with neoplastic cells. These hybrids are often referred to as hybridomas. (MeSH)
A type of image where pixel values represent a quantity measure over 2 spatial dimensions.
An assessment of neurological function associated with certain behaviors often used in diagnosing brain dysfunction or damage and central nervous system disorders or injury. (adapted from MeSH)
Brain Map uses this designtation only when letters are used as stimuli; however there is some confusion about whether other stimuli may be used in the Sternberg paradigm
A delayed matching-to-sample paradigm that uses letters or numbers as stimuli (Sternberg S. High-speed scanning in human memory. Science. 1966 Aug 5;153(736):652-4).
Need to clarify what a Sternberg paradigm involves
Immunoglobulins which arise from more than one clone of B-lymphocyte cells. Polyclonal antibodies are usually present when antisera from a conventional immunization is used. (www.brendan.com/Glossary.htm)
A type of 3D image collected using an MRI device.
Biochemical specimen preparation protocol
Changed name from the ambiguous Biochemical_protocol to Biochemical_specimen_preparation_protocol (BB).
A confocal microscope that that uses a laser that is scanned in a raster pattern across the specimen to excite fluorescence or otherwise visualize the specimen one point at a time. Out of focus light is removed by an aperture inserted in the transmitted light path; 2 or 3 dimensional likenesses are then reconstructed by computer; relatively noninvasive, applicable to thick sections and living tissue. (CSP)
An oddball discrimination paradigm where subjects view letters or objects and indicate when they see a target stimulus.
A chemical substance or formulation regulated as a medical device that is delivered by various routes of administration into the body of a patient undergoing a diagnostic imaging procedure to temporarily enable or enhance the capability of a specified diagnostic imaging. (UMD)
Substances used in radiography that allow visualization of certain tissues. (CSP)
Substances used in radiography that allow visualization of certain tissues. (MeSH)
A behavioral phenotype where the subject preferentially uses the left hand for tasks requiring the use of a single hand or a dominant hand.
Microscopy contrast enhancement protocol
Should really be importing the FlyBase biological imaging ontology, now that it is so mature. Unfortunately, this is currently only available in OBO format. It really needs to be incorporated directly or through import into OBI (BB:2006-10-10).
Changed preferred Label from Contrast_enhancement_protocol to Microscopy_contrast_enhancement_protocol.
A type of 2D image collected using an MRI device.
A laterality measure where there is no overall dominance in the use of right or left hand in the performance of tasks that require one hand or a dominant hand.
Should look to FBbi for content here, hopefully brought into BIRNLex-Main via import.
A behavioral paradigm that requires the subject respond to stimuli that are dissimilar to the majority of stimuli presented
administration of a drug via injection into a muscle. (CSP)
Forceful administration into a muscle of liquid medication, nutrient, or other fluid through a hollow needle piercing the muscle and any tissue covering it. (MeSH)
A cognitive phenotype measuring an individual's facility with producing spoken language.
A type of temporal characteristic value where the time measured is that between the occurance of two events.
A measure of the mass of the entire body of the organism.
Blood Oxygenation Level Dependent signal
Haemoglobin is diamagnetic when oxygenated but paramagnetic when deoxygenated. Local changes in the relative concentration of oxyhemoglobin and deoxyhemoglobin and changes in local cerebral blood volume in addition, mean that the magnetic resonance (MR) signal of blood is slightly different depending on the level of oxygenation. Higher BOLD signal intensities arise from decreases in the concentration of deoxygenated hemoglobin since the blood magnetic susceptibility now more closely matches the tissue magnetic susceptibility. (from Wikipedia).
Participant in a research project or experiment, who is not the primary investigator, who performs portions of the research project or who makes significant intellectual contributions to the research project.
What is this and how would it differ from Phenotype_attribute (BB)?
An impairment in cognition, specifically memory performance, that is frequently associated with aging and, in some cases, pre-clinical Alzheimer's disease. The degree and type of impairment distinguishes MCI from dementia in that MCI patients exhibit deficits in tests of memory, but perform normally on standard tests measuring other cognitive domains.
The time between the initial pulse and the end of the data acquisition. Note that there may be an additional delay placed at the end of the acquisition to achieve a certain repetition time (TR)
The time the MRI scanner takes to collect an MRI image.
FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data (http://www.fmrib.ox.ac.uk/fsl/).
Participant in a research project, who may or may not be the principal investigator, who assumes the responsiblity for completion of a project. Responsibilities may include research design, performance of experiments or supervision of other experimenters and communication of results.
Dynamic Causal Modeling: As published by Friston, Harrison, and Penny (Neuroimage, 2003, 19, 1273-1302), this is a method for "identifying non-linear input-state-output systems", as applied to determining effective connectivity in fMRI data. The emphasis is on determining the effects of the experimental inputs on the coupling or co-activations of various brain regions (psychophysiological interactions), rather than the effects of the experimental inputs on the activation of each brain region separately.
The time interval between excitation and data acquisition of the center of k-space. This is also referred to as echo time and typically measured in units of milliseconds. (Huettel, Song, & McCarthy, 2004).
This is an imaging parameter which helps determine image contrast. It represents the time in milliseconds between the application of the 90degree pulse and the peak of the echo signal in Spin Echo and Inversion Recovery pulse sequences
The observable physical characteristics typical of the male or female of the species.
This list contains terms from Brain Map and BIRN; right now it is presented as a fairly flat list of paradigms. Functional classifications were deliberately avoided. This list contains many pre-coordinated terms which will be reconsidered in the future (JT).
In the behavioural sciences, e.g. Psychology, Biology, Neurosciences, an experimental paradigm is an experimental setup (i.e. a way to conduct a certain type of experiment) that is defined by certain fine-tuned standards and often has a theoretical background. Within an Experimental Paradigm, the behavioral paradigm describes the behavioral aspects of the experiment: what stimuli are presented to the subject when, and under what conditions, and what the subject's responses are supposed to be.
Substances intended to detect and/or measure, in some cases producing or modifying other substances, a specific analyte of interest (e.g., enzymes, hormones). Substances used as reagents must be sufficiently pure to appropriately perform a specific analytical test. Reagents are typically used in the clinical laboratory for clinical chemistry, immunochemistry, hematology, microbiology (e.g., culture), infectious immunology, and molecular biology (e.g., nucleic acid technology) tests. (UMD)
A scaling factor applied to a given independent variable in a polynomial equation. Such characteristic values are often linked to physical significant proporties of real-world systems that are modeled by polynomial equations.
AFNI (which might be an acronym for Analyis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X (http://afni.nimh.nih.gov/afni/).
An n-dimensional quantity representing a value that has both an amplitude and a direction. A vector quantity can have 1 or more dimensions. The overall amplitude of a multi-dimensional vector quantity is the square-root of the sum of the sqaures of the amplitudes in each individual dimension.
A behavioral paradigm where sets of target items are presented at the outset and the recognition of one or more of those items vs unfamiliar items is tested using a probe item.
A well defined set of rules that can be expressed using formal mathematical expression and thereby implemented in a computing environment.
This had been subclassed previously from the obi:independent_continuant, which has since been subsumed into bfo:independent_continuant. Just as with Experiment, it is not appropriate to have something as concrete as a participating research institution so high up in the more abstract layers of the ontology. I think it can live here under bfo:object_aggregate for now and possibly even stay here (BB:2006-10-10).
The organization to which an individual researcher or groups of researchers belong and where the research is usually conducted, usually a university or medical facility.
Check with BFO researchers whether this is an appropriate location in BFO for this class. Institutions are definitely entities they've had to handle before.
How does this related to Phenotype_attribute and to PaTO expressions (BB)?
A behavioral paradigm in which subjects view three or more items.. After a brief delay a probe item is presented and subjects are asked to recall if the probe item was presented in the the previous list. Stimuli can be words, pictures, or abstract patterns. If the stimuli are letters, the task is coded as a Sternberg Task.
Transmission electron microscopic imaging assay
We may want to eventually include the 1/e mathematical definition of relaxation time.
a type of temporal characteristic value where the time measured is that required to return to an equilibrium state following a well-defined stimulus.
A probe for identifying macromolecules that is a specific, characterizable, poisonous chemical, often a protein, with specific biological properties, produced by microbes, higher plants, or animals, that react with specific components of cells or tissues.
Is a neuropsychological assessment of conceptual abilities and visuo-motor sequencing. Part A measures subjects ability to draw lines to connect consecutively numbered circles on a work sheet. Part B measures subjects draw lines between consecutively numbered and lettered circles by alternating between the two sequences (e.g., 1-A-2-B-3-C ...).
An instrument used to obtain a magnified image of small objects and reveal details of structure not otherwise distinguishable.
Used in various techniques, staining is the artificial coloration of a substance that enhances the contrast of tissues, genes, cells, or microorganisms(etc.), to be viewed under the microscope. In biochemistry it involves adding a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. Staining can serve the same purpose as fluorescent tagging. (Adapted from Wikipedia)
BIRNLex should make use of OBO Flybase bioimaging (FBbi ontology) (see the EBI Ontology Browser), once it is available in OWL. Though we could use the OBO to OWL converts, this is problematic.
a type of temporal characteristic value where the time meansured is the time required to return to an equilibrium state following a well-defined external stimulus.
Behavioral phenotype used to describe an individual who currently smokes tobacco products.
Immunoglobulin that is used as a reagent to localize a signal through an immunological reaction.
antibody used for immunocytochemical protocol
Is a neuropsychological assessment of cognitive function that is a widely used for measuring cognitive impairment. Developed in 1975 by Marshall Folstein and his colleagues (Citation)
A behavioral phenotype used to describe an individual who is currently not smoking tobacco products but has at some time in the past.
May have to adapt this definition or alter class to reflect that fact some atlases are collections of data sets.
A type of anatomical data set contains a collection of anatomical maps.
Franklin-Paxinos C57Bl/6J Adult Mouse Brain Atlas in stereotaxic coordinates (2001).
LONI Minimum Deformation C57Bl/6 Mouse Brain Atlas
NeuroTerrain C57Bl/6 Adult Mouse Brain Atlas
GENSAT is an image data set but not a map, and, therefore, not an atlas data set. Query Atlas and SMART Atlas are tools that use atlas data sets.
Phalloidin is a toxin from the Death Cap mushroom that binds actin, inhibiting its depolymerization. Phalloidin binds specifically F-actin and is therefore a very convenient tool to investigate the distribution of F-actin since fluorescent analogs can be synthesized that retain actin binding. (Wikipedia)
Optical microscope with a multiphoton attachment, where fluorescence excitation is produced by two or more photons of light of longer wavelength that the fluorophore. On their own, these photons possess insufficient energy to excite the fluorophore but under certain conditions, the two photons can interact to produce excitation in a narrow focal plane.
Not sure whether this is the same as study; needs clarification (MM).
Moved this to bfo:process. It was formerly a subclass of occurrent, which is too deep in the hierarchy for an object as concrete as an experiment. We need to determine how to use the study & investigation classes from OBI under bfo:process (BB).
A set of actions and observations, performed to verify or falsify a hypothesis or research a causal relationship between phenomena. The experiment is a cornerstone in empirical approach to knowledge. (adapted from wikipedia.org)
The original BIRNLex had its own occurrent class called "Evolves through time". This was subsumbed into fugo:occurrent, which itself has now been subsumed into bfo:occurrent.
A type of 2D MRI image collected using an T2 Weighted MRI imaging protocol.
A type of data set describing anatomical objects.
Behavioral phenotype used to describe an individual who does not currently smoke tobaccor products. This term describes only current behavior and does not imply that the individual never smoked.
An experimental design in which conditions of interest are continued for up to 30 s, and the time course is modeled as a constant state during those "blocks" of time.
The process by which an experimental agent is delivered to an organism or part of organism.
A standardized brain atlas developed by the Montreal Neurological Institute.
in fMRI results, the coefficient from the General Linear Model which reflects the strength of the relationship between the data and the modeled effect. Usually one beta value per voxel per modeled effect.
A mathematical operation that describes the action of a linear system on a signal.
For fMRI, the time course of an experimental design's conditions beginning and ending is often convolved with the Hemodynamic Response Function (HRF) to model fMRI data.
This BONFIRE ID is actually from vascular perfusion fixation, but I think this entity should be listed under agent delivery process rather than as a type of fixation (MM).
Method of agent delivery where the agent is pumped through the vasculature of the animal.
A process for delivering an agent to an object of study in which the object is physically submersed in the agent.
immersion of a tissue sample into fixative
A role played by a continuant in an investigational protocol designed to prepare a Biomaterial_entity for experimental manipulation.
An MRI scanning pulse sequence that is used to acquire structural data whose tissue contrast parameter is T1-weighted.
definition mtd, modified from kgh's other anatomical definitions.
An imaging protocol typically using short TE and TR times whose contrast and brightness are predominately determined by T1 signals. This leads to high contrast between white and gray matter and is the basis for high-resolution anatomical brain imaging.
Injection of a dye or some other indicator agent into a cell using a micropipette to delineate cell morphology or the distribution of a signal across a single cell. May be in fixed or live tissue.
Agents employed in the preparation of histologic or pathologic specimens for the purpose of maintaining the existing form and structure of all of the constituent elements. Great numbers of different agents are used; some are also decalcifying and hardening agents. They must quickly kill and coagulate living tissue. (MeSH)
Reagents used for coagulation and/or precipitation of protoplasmatic substances (i.e., fixation), making them resistant to further changes either from the reagents to which they are subjected or from autolysis and putrefaction before microscopic sections can be prepared. Several substances are used as fixatives, including formaldehyde, mercury chloride, and glutaraldehyde solutions; some include decalcifier additives. (UMD)
Is transverse relaxation time truly a synonym for this entity under all conditions (BB: 2007-03-09)?
Spin-spin or transverse relaxation time. The time constant for loss of phase coherence among spins oriented at an angle to the static magnetic field due to interactions between the spins. Results in a loss of transverse magnetization and the MRI signal.
The time constant, T2, which determines the rate at which excited protons reach equilibrium, or go out of phase with each other. A measure of the time taken for spinning protons to lose phase coherence among the nuclei spinning perpendicular to the main field due to interaction between spins, resulting in a reduction in the transverse magnetization. The transverse magnetization value will drop from maximum to a value of about 37% of its original value in a time of T2.
Changed name to singular from plural to comply with univocity constraint (BB).
A behavioral paradigm in which the subject is asked to draw lines, circles or more complex figures using a pen or stylus.
A crosslinking fixative. Glutaraldehdye is a pentanedial; 5-carbon saturated chain with a highly reactive aldehyde group on each end (MM).
A general purpose reagent is a chemical reagent that has general laboratory application, that is used to collect, prepare, and examine specimens from the human body for diagnostic histopathology, cytology, and hematology, and that is not labeled or otherwise intended for a specific diagnostic application. General purpose reagents include cytological preservatives, decalcifying reagents, fixatives and adhesives, tissue processing reagents, isotonic solutions, and pH buffers. (SPN)
One of the protein CROSS-LINKING REAGENTS that is used as a disinfectant for sterilization of heat-sensitive equipment and as a laboratory reagent, especially as a fixative. (MSH)
pentanedial; 5-carbon saturated chain with a highly reactive aldehyde group on each end; used as a protein crosslinking agent, fixative, disinfectant, and mutagen. (CSP)
This is a placeholder for a ChEBI class (BB: 2007-03-05).
The time constant for loss of phase coherence among spins oriented at an angle to the static magnetic field due to a combination of magnetic field inhomogeneities and the spin-spin relaxation. Results in a rapid loss of transverse magnetization and the MRI signal.T2* < T2. This is the basis for EPI and thus fMRI.
What organism characteristic could not be described as a phenotype attribute? (Age). How does this relate to PaTO? Will instances of this class include PaTO expressions? If so, and given that PaTO expressions include qualities, this appears to be a circular class - well, not quite circular, but probably inappropriate. PaTO expressions will be used to describe instances in data repositories and will include pointers to classes in BIRNLex.(BB).
The technique of using FIXATIVES in the preparation of cytologic, histologic, or pathologic specimens for the purpose of maintaining the existing form and structure of all the constituent elements. (MeSH)
A fixative and contrast agent which is a lustrous powder, yellow to light-brown in color, that is found in tree bark (particularly oak), fruits, leaves, and tea. It is used medicinally as an astringent, commercially in tanning hides, and as a dye mordant. (Saunders Dictionary and Encyclopedia of Laboratory Medicine and Technology, 1984).
A lustrous powder, yellow to light-brown in color, that is found in tree bark (particularly oak), fruits, leaves, and tea. It is used medicinally as an astringent, commercially in tanning hides, and as a dye mordant. (Saunders Dictionary and Encyclopedia of Laboratory Medicine and Technology, 1984). It is also used as a histological fixative and stain. (MeSH)
Participant in a research project who directs a research project or program. The principal investigator (the PI) usually writes and submits the grant application, oversees the scientific and technical aspects of the grant, and has responsibility for the management of the research. www.medterms.com
A cross linking fixative consisting of a very low molecular weight polymer of formaldehyde, or a mixture of polyoxymethylene glycols, in the form of a white solid which easily depolymerizes by heating to yield formaldehyde gas and water vapor. Often used by histologists to refer to formaldehyde that has been prepared freshly from paraformaldehyde (MM).
is an assessment which consists of a questionnaire that measures nicotine use (Fagerstrom citation)
An oddball discrimination paradigm that involves responding to auditory stimuli that are dissimilar to the majority of auditory stimuli presented.
A type of image where pixel values represent a quantity measure over 3 spatial dimensions.
A behavioral paradigm in which a subject fixate on a target and are instructed to make a saccadic eye movement to a stimulus (modified from Brain Map by OTF)
This term is equivalent to "saccade paradigm" in Brain Map
Behavioral phenotype used to describe an individual who has never smoked tobacco products.
method for procuring pure cells from specific microscopic regions of tissue sections; laser beam focally activates a special transfer film which bonds specifically to cells identified and targeted by microscopy within the tissue section, when the film is removed, the chosen cells are tightly held within the focally expanded polymer for microdissection. (CSP)
A sample of a specimen consisting of a thin plane produced through the use of a microtome or other cutting device, usually produced for the purposes of histological processing and/or microscopic examination.
A type of 2D MRI image collected using an T1 Weighted MRI imaging protocol.
Positron Emission Tomography imaging protocol
* A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance (for example, 2-fluoro-2-deoxy-D-glucose (FDG), which is similar to a naturally occurring sugar, glucose, with the addition of a radioactive fluorine atom). When living tissue containing the positron emitter is bombarded by electrons, gamma radiation produced by collisions of electrons and positrons is detected by a scanner, revealing in fine detail the tissue location of the metabolically-active substance administered. (NCI04) (NCI) * An imaging technique using compounds labelled with short-lived positron-emitting radionuclides (such as carbon-11, nitrogen-13, oxygen-15 and fluorine-18) to measure cell metabolism. It has been useful in study of soft tissues such as CANCER; CARDIOVASCULAR SYSTEM; and BRAIN. SPECT is closely related to PET, but uses isotopes with longer half-lives and resolution is lower. (MSH) * For this type of scan, a person is given a substance that reacts with tissues in the body to release protons (parts of an atom). Through measuring the different amounts of protons released by healthy and cancerous tissues, a computer creates a picture of the inside of the body. PET images show the chemical functioning of an organ or tissue, unlike X-ray, CT, or MRI which show only body structure. Also called PET scan. (NCI) * detection of gamma rays emitted from tissues after administration of a natural substance such as glucose or fatty acids into which positron emitting isotopes have been incorporated; the paths of the gamma rays, which result from collisions of positrons and electrons, are interpreted by a computer algorithm, and the resultant tomogram represents local concentrations of the isotope containing substance. (CSP)
An imaging protocol where images are acquired using a Positron Emission Tomography device.
A behavioral manifestation of cerebral dominance in which there is preferential use and superior functioning of either the left or the right side, as in the preferred use of the right hand or right foot. (MeSH)
This concept ID maps to the term "handedness" and "laterality" in the UMLS. We distinguish in BIRNLex between use of dominant hand (handedness) and other forms of behavioral laterality.
A behavioral paradigm in which subjects fixate a target and are instructed to make a saccade in the opposite direction of a stimulus (modified from Brain Map by OTF)
A transformation that applies an algorithm with specified parameters on a data set on a specific computing platform.
a type of quantitative value measured in units of time.
A behavioral paradigm that assesses a response to non-attended stimuli which are dissimilar to the majority of stimuli presented
* MRI uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. (NCI) * Non-invasive method of demonstrating internal anatomy based on the principle that atomic nuclei in a strong magnetic field absorb pulses of radiofrequency energy and emit them as radiowaves which can be reconstructed into computerized images. The concept includes proton spin tomographic techniques. (MSH) * non-invasive method of demonstrating internal anatomy based on the principle that atomic nuclei in a strong magnetic field absorb pulses of radiofrequency energy and emit them as radiowaves which can be reconstructed into computerized images; concept includes proton spin tomographic techniques. (CSP)
An imaging protocol where images are acquired using a Magnetic Resonance Imaging device.
A behavioral attribute defined by the unequal distribution of fine motor skill between the left and right hands. Individuals more skilled with the right hand are called 'right-handed', and those more skilled with the left are 'left-handed'. A few people are equally skilled with both, and are termed 'ambidextrous'. (adapted from Wikipedia)
behavioral paradigm that assesses a response to non-attended stimuli which are dissimilar to the majority of stimuli presented.
Intermediate voltage electron microscope
Transmission electron microscope cabable of operating at an accelerating voltage in the range of 300-400 KeV
The component (MZ) of the net magnetization vector in the direction of the static magnetic field. After RF excitation, this vector returns to its equilibrium value at a rate characterized by the time constant T1
A behavioral phenotype where the subject preferentially uses the right hand for tasks requiring the use of a single hand or a dominant hand.
A behavioral paradigm in which a subject reads aloud with fingers.
Brain Map lists only a Braille reading paradigm but BIRNLex is dividing this into overt and covert Braille reading paradigms
transmission electron microscope cabable of operating an accelerating voltage in the range of 500- 1000 KeV
A behavioral paradigm in which subjects are required to utilize problem-solving skills and logic to determine the correct solution; feedback is sometimes given.
a type of temporal characteristic value where the time meansured is the time requird for the longitudinal magnetization to return to its equilibrium value after excitation due to the exchange of energy between the nuclear spins and the lattice.
Software delivered in source or binary form as a collection of independent modules whereby the kit components can be used independently of each other or included as part of another program (derived from NCBC Software Ontology) (BB:2007-03-07).
An application or program that is used for any form of signal processing for which the input is an image, such as photographs, magnetic resonance images, or frames of video; the output of image processing can be either an image or a set of characteristics or parameters related to the image.
Transmission electron microscope capable of operating at an accelerating voltage of > 1 MeV
An MRI scanning pulse sequence that is used to acquire structural data whose tissue contrast parameter is T2-weighted.
An imaging protocol typically using longer TE and TR times whose contrast and brightness are predominately determined by T2 signals (2007-03-07)
A behavioral paradigm in which a subject makes a rapid eye movement relative to an initial target (JB).
BIRN uses this term to refer to any paradigm involving a saccadic eye movement. These paradigms include both saccdic movements to and away from the target. Note that this usage differs from that in Brain Map.
Moved as a subclass of Data processing software from Data analysis software.
A magnetic resonance imaging protocol that is sensitive to the diffusion of water molecules and measures this diffusion in 6 or greater directions. (February 9, 2009)
Moved as a subclass of 'Diffusion-weighted imaging protocol' from 'Structural MRI protocol'.
Diffusion Tensor Imaging: an imaging technique that enables the measurement of the restricted diffusion of water in tissue. The principal application is in the imaging of white matter where the location, orientation, and anisotropy of the tracts can be measured. The architecture of the axons in parallel bundles, and their myelin sheaths, facilitate the diffusion of the water molecules preferentially along their main direction. Such preferentially oriented diffusion is called anisotropic diffusion. If we apply diffusion gradients (i.e. magnetic field variations in the MRI magnet) in at least 6 directions, it is possible to calculate, for each voxel, a tensor (i.e. a symmetric positive definite 3by3 matrix) that describes the 3-dimensional shape of diffusion. The fiber direction is indicated by the tensor's main eigenvector. (from Wikipedia).
A behavioral paradigm in which a subject is asked to read either silently (covert) or aloud (overt)
This list contains precoordinated terms that will be addressed at a future date.
This term does not differentiate between lexical and semantic parsing by the subject
Subject group that serves as a standard for comparison in experimental studies. It is similar in relevant characteristics to the experimental group but do not receive the experimental intervention. (MeSH)
Algorithm used to compute a reconstruction from a set of images, e.g., R-weighted back projection.
Behavioral paradigm in which the subject ingests food.
Echo Planar Imaging: the utilization of rapid gradient reversal pulses of the readout gradient resulting in a series of gradient echo signals to reduce fast dephasing or signal loss. This is the primary imaging method for fMRI.
The component of the net magnetization vector at right angles to the main magnetic field. Precession of the transverse magnetization at the Larmor frequency is responsible for the detectable NMR signal. In the absence of externally applied RF energy, the transverse magnetization will decay to zero with a characteristic time constant of T2, or more strictly T2*.
I think this class should be retired and we should just go with at the level of resource descriptors. Does a user really care what the underlying technology or data model is? (Maryann Martone)
A normalized data set constructed according to a specific entity-relation data model.
A resource that provides software that assists in measuring, recording, and collecting information about a physical phenomenon or physical property of an object (under investigation). Examples include the temperature or temperature change of a room, the reaction time of a response, digital picture acquisition.
A resource that provides a programming tool that generates documentation intended for programmers (API documentation) or end users (End-user Guide), or both, from a set of specially commented source code files, and in some cases, binary files.
A resource that provides an application or program that is used to gather, model, and transform data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making.
A resource that provides an application or program that is used for the study of the visual representation of data, defined as information which has been abstracted in some schematic form, including attributes or variables for the units of information.
Integrated Software development environment
A resource that provides the entire environment (applications, servers, network) that provides comprehensive facilities to computer programmers for software development. An SDE typically includes an integrated development environment (IDE, comprising source code editor, compiler, build automation, debugger), requirement management tools, design modeling tools, documentation generation tools, code analysis tools, and so on.
A resource that provides a computer program (or set of programs) that transforms source code written in a computer language (the source language) into another computer language (the target language, often having a binary form known as object code). The most common reason for wanting to transform source code is to create an executable program. A \\u201ccompiler\\u201d is primarily used for programs that translate source code from a high-level programming language to a lower level language (e.g., assembly language or machine language), and is likely to perform many or all of the following operations: lexical analysis, preprocessing, parsing, semantic analysis, code generation, and code optimization.
A resource that provides a performance analysis tool that measures the behavior of a program as it executes, particularly the frequency and duration of function calls. The profiling process helps to determine which subroutines (or just snippets of code) take longest to execute and which subroutines are called most often. Code profilers are used when you suspect that some part of your code is called very often and maybe there is a need to optimize it, which could significantly improve the overall performance. Profilers use a wide variety of techniques to collect data, including hardware interrupts, code instrumentation, instruction set simulation, operating system hooks, and performance counters.
A resource that provides a software environment created to investigate the quality of the product or service under test, with respect to the context in which it is intended to operate. This includes, but is not limited to, the process of executing a program or application with the intent of finding software bugs.
Software application for the generation of the 'Segmentation' of input data into regions of 'homogeneous' characteristic. Various characteristics can be utilized to influence the selection of regions as targets for the segmentation (NITRC).
Software application that performs image spatial transformation for the purposes of image 'Registration'. (NITRC)
Added: synonyms, definition and new label. (April 2, 2009)
A resource that provides a software system designed to support interoperable machine-to-machine interaction over a network. Web services are frequently Web APIs that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services.
Single Photon Emission Computed Tomography imaging protocol
* A method of computed tomography that uses radionuclides which emit a single photon of a given energy. The camera is rotated 180 or 360 degrees around the patient to capture images at multiple positions along the arc. The computer is then used to reconstruct the transaxial, sagittal, and coronal images from the 3-dimensional distribution of radionuclides in the organ. The advantages of SPECT are that it can be used to observe biochemical and physiological processes as well as size and volume of the organ. The disadvantage is that, unlike positron-emission tomography where the positron-electron annihilation results in the emission of 2 photons at 180 degrees from each other, SPECT requires physical collimation to line up the photons, which results in the loss of many available photons and hence degrades the image. (MSH) * method of computed tomography that uses radionuclides which emit a single photon of a given energy: the camera is rotated 180 or 360 degrees around the subject to capture images at multiple positions along the arc; the computer is then used to reconstruct the transaxial, sagittal, and coronal images from the three-dimensional distribution of radionuclides in the organ. (CSP)
Scanning electron microscopy imaging protocol
Transmission electron microscopy imaging protocol
Scanning transmission electron microscopy imaging protocol
A protocol that specifies the process of immunohistochemistry. Immunohistochemistry is the process of localizing proteins in cells of a tissue section exploiting the principle of antibodies binding specifically to antigens in biological tissues. It takes its name from the roots "immuno," in reference to antibodies used in the procedure, and "histo," meaning tissue (compare to immunocytochemistry). (from wikipedia)
Note: Some use the term "immunohistochemistry" to refer to protocols that employ an enzymatic chromagen as opposed to a particulate or fluorescent marker. Going back to the original Greek (histo=tissue), we have chosen the current definition. (Maryann Martone)
A resource that provides a system for the management of multiple revisions of the same unit of information. It is most commonly used in engineering and software development to manage ongoing development of digital documents like application source code, art resources such as blueprints or electronic models, and other projects that may be worked on by a team of people.
A structural MRI protocol is an MRI protocol that provides information to qualitatively and quantitatively describe the shape, size, and integrity of gray and white matter structures in the brain.
Light transmission optical imaging protocol
fluorescence/chemiluminescence/phosphorescence optical imaging protocol
An imaging protocol that produces images using a microscopy in multiphoton mode.
Added: definition and synonyms (April 2, 2009)
Laser scanning confocal imaging protocol
Fluorescence resonance energy transfer imaging protocol
Differential interference contrast imaging protocol
Differential interference contrast microscopy
Total internal reflection imaging protocol
Electron Energy Loss Spectroscopy imaging protocol
Computer Axial Tomography imaging protocol
Extracellular electrode recording protocol
Intracellular electrode recording protocol
Amperometric electrode recording protocol
Single electrode extracellular recording protocol
Current clamp voltage recording protocol
Voltage clamp current recording protocol
Single-electrode voltage clamp recording protocol
Whole-cell voltage clamp recording protocol
Multiple-electrode voltage clamp recording protocol
Cell-attached single-channel recording protocol
Cell-detached single-channel recording protocol
Cell-detached inside-out single-channel recording protocol
Cell-detached outside-out single-channel recording protocol
Reconstituted bilayer single-channel patch recording protocol
Reconstituted bilayer electrical recording protocol
Ion-sensitive electrode recording protocol
pH-sensitive electrode recording protocol
Electroencephalography recording protocol
A mathematical description of a inter-connected and/or dynamic biological system.
A mathematical description of the structure or function of nerve cells and/or their cellular compartments.
A mathematical description of the structure of nerve cells and/or their cellular compartments.
A mathematical description of the physiological funcion of nerve cells and/or their cellular compartments.
A mathematical description of the temporal and voltage dependencies of particular, ion-selective membrane currents.
A mathematical description of the complex physical and temporal dependencies between a set of related biological entities and their immediated environment.
A coordinate-based mathematical description of a collection of biological structures.
A mathematical description of the structure of organs and organ regions.
Finite element decomposition of anatomical structure
Wavelet-based multi-resolution decomposition of anatomical structure
A mathematical description of the temporal dependencies of a related set of biological cells
A mathematical description of the temporal activity dependence of a related set of neuronal cells typically composed of nerve cell models, specific intercellular transmission relations (neurochemical and electrotonic), and enviormental influences.
A mathematical description of the temporal activity dependence of an extended set of tissues and cells across an entire organism.
A mathematical description of the relatedness of a set of nucleic acid or amino acid sequences based on a correlative comparison of the sequences or properties derived from those sequences.
A mathematical description of the phylogenetic relatedness of a set of nucleic acid sequences based on a correlative comparison of linear sequence.
A mathematical description of the solvent interaction properties of an amino acid sequence based on the biophysical properties of the amino acid side chain moeties. Such models are used to indicate putative internal hydrophobic domains and transmembrane spanning regions in polypeptides.
A mathematical description of the related structural domains of a collection of amino acid sequence based on the consensus sequences with defined structural properties (e.g., alpha helix, beta sheet, etc.). These models are typically used to infer phylogenetic relatedness of proteins (families/superfamilies) based on structural properties.
A mathematical separation and/or combination of time-series data typically performed in real-time and utilizing Fourier transform methods to manipulate the distinct frequency components of a set of an input data stream to produce an output data stream.
Graphical pipeline construction software
A resource that provides an application or program with the capability to exchange data with different programs via a common set of exchange formats, to read and write the same file formats, and to use the same protocols. According to ISO/IEC 2382-01, Information Technology Vocabulary, Fundamental Terms, interoperability is "the capability to communicate, execute programs, or transfer data among various functional units in a manner that requires the user to have little or no knowledge of the unique characteristics of those units".
A collection of unstructured, scientific literature.
Any text-based algorithm used to match strings against a controlled lexicon and/or infer syntactic structure or semantic conent from a corpus of unstructured text.
Natural language processing (NLP) is a subfield of artificial intelligence and linguistics. It studies the problems of automated generation and understanding of natural human languages. Natural language generation systems convert information from computer databases into normal-sounding human language, and natural language understanding systems convert samples of human language into more formal representations that are easier for computer programs to manipulate.
Part-of-speech tagging (POS tagging or POST), also called grammatical tagging, is the process of marking up the words in a text as corresponding to a particular part of speech, based on both its definition, as well as its context, i.e., relationship with adjacent and related words in a phrase, sentence, or paragraph. A simplified form of this is commonly taught school-age children, in the identification of words as nouns, verbs, adjectives, adverbs, etc. Once performed by hand, POS tagging is now done in the context of computational linguistics, using algorithms which associate discrete terms, as well as hidden parts of speech, in accordance with a set of descriptive tags.
A collection bibliographic records describing published works from the scientific literature which may or may not contain abstracts
A collection data records arranged according to some semantic framework. The semantic framework may be minimally expressive - such as a simple controlled vocabulary - of highly expressive such as a formally structured ontology. Such resources may include only a representation of universal/classes/categories or may be linked to individual instance data typed according to a set of asserted classes (i.e., a knowledgebase).
In library and information science controlled vocabulary is a carefully selected list of words and phrases, which are used to tag units of information (document or work) so that they may be more easily retrieved by a search. Controlled vocabularies solve the problems of homographs, synonyms and polysemes by ensuring that each concept is described using only one authorized term and each authorised term in the controlled vocabulary describes only one concept. In short, controlled vocabularies reduce ambiguity inherent in normal human languages where the same concept can be given different names and ensure consistency. Controlled vocabulary schemes mandate the uses of predefined, authorised terms that have been preselected by the designer of the controlled vocabulary as opposed to natural language vocabularies where there is no restriction on the vocabulary that can be used.
Systematized Nomenclature of Medicine (SNOMED)
Structured grouping of entities based on a correspondence of derived physicochemical properties.
Structural Classification of Proteins (SCOP)
A taxonomy, or taxonomic scheme, is composed of taxonomic units known as taxa (singular taxon), or kinds of things that are arranged frequently in a hierarchical structure, typically related by subtype-supertype relationships, also called parent-child relationships. In such a subtype-supertype relationship the subtype kind of thing has by definition the same constraints as the supertype kind of thing plus one or more additional constraints. For example, car is a subtype of vehicle. So any car is also a vehicle, but not every vehicle is a car. So, a thing needs to satisfy more constraints to be a car than to be a vehicle.
A formal definition of a thesaurus designed for indexing is: * a list of every important term (single-word or multi-word) in a given domain of knowledge; and * a set of related terms for each term in the list. Terms are the basic semantic units for conveying concepts. They are usually single-word nouns, since nouns are the most concrete part of speech. Verbs can be converted to nouns -- cleans to cleaning, reads to reading, and so on. Adjectives and adverbs, however, seldom convey any meaning useful for indexing. When a term is ambiguous, a "scope note" can be added to ensure consistency, and give direction on how to interpret the term. Naturally, not every term needs a scope note, but their presence is of considerable help in using a thesaurus correctly and reaching a correct understanding of the given field of knowledge. Term relationships are links between terms that often describe synonyms, near-synonyms, or hierarchical relations. Synonyms and near-synonyms are indicated by a Related Term (RT). The way the term "Cybernetics" is related to the term "Computers" is an example of such a relationship. Hierarchical relationships are used to indicate terms which are narrower and broader in scope. A Broader Term (BT) is a more general term, e.g. "Apparatus" is a generalization of "Computers". Reciprocally, a Narrower Term (NT) is a more specific term, e.g. "Digital Computer" is a specialization of "Computer". BT and NT are reciprocals; a broader term necessarily implies at least one other term which is narrower. Thesaurus designers are generally careful to ensure that BT and NT indicate class relationships, as distinguished from part-whole relationships. Some thesauri also include Use (USE) and Used For (UF) indicators when an authorized term is to be used for another, unauthorized, term; for example the entry for the authorized term "Frequency" could have the indicator "UF Pitch". Reciprocally, the entry for the unauthorized term "Pitch" would have the indicator "USE Frequency".
In both computer science and information science, an ontology represents a set of concepts within a domain and the relationships between those concepts. It is used to reason about the objects within that domain. Ontologies are used in artificial intelligence, the semantic web, software engineering, biomedical informatics and information architecture as a form of knowledge representation about the world or some part of it. Ontologies generally describe: * Individuals: the basic or "ground level" objects * Classes: sets, collections, or types of objects[1] * Attributes: properties, features, characteristics, or parameters that objects can have and share * Relations: ways that objects can be related to one another * Events: the changing of attributes or relations
Descriptive Ontology for Linguistic and Cognitive Engineering (DOLCE)
OBO Ontology of Phenotypic Qualities (PATO)
A collection research data arranged according to a structured semantic framework.
Clinical research (translational) knowledge base
Clinical research translational knowledge base
A collection clinical biomedical subject data - individual records or reduced information - arranged according to a structured semantic framework. Includes diagnosis, treatment, and/or outcomes information.
An open source license is a copyright license for computer software that makes the source code available under terms that allow for modification and redistribution without having to pay the original author. Such licenses may have additional restrictions such as a requirement to preserve the name of the authors and the copyright statement within the code. One popular (and sometimes considered normative) set of open source software licenses are those approved by the Open Source Initiative (OSI) based on their Open Source Definition (OSD).
The GNU General Public License (GNU GPL or simply GPL) is a widely used free software license, originally written by Richard Stallman for the GNU project. The GPL is the most popular and well-known example of the type of strong copyleft license that requires derived works to be available under the same copyleft. Under this philosophy, the GPL is said to grant the recipients of a computer program the rights of the free software definition and uses copyleft to ensure the freedoms are preserved, even when the work is changed or added to. This is in distinction to permissive free software licenses, of which the BSD licenses are the standard examples.
A resource that provides an application or program that is based on the process of imitating a real phenomenon with a set of mathematical formulas. It is, essentially, a program that allows the user to observe an operation through simulation without actually running the program.
Note as of 2006, the BSD License is equivalent to the MIT License
Any non open source license with restrictions on the source code.
A written or printed work of fiction or nonfiction, usually on sheets of paper fastened or bound together within covers, or an electronic facsimile thereof.
Discussion among a group in some forum, public, private, or electronic, which may or may not be moderated, for example, a single discussion thread in a listserv (NLM).
Listserv or discussion group (as an entity, as opposed to a single discussion thread which uses the value "discussion") (NLM).
A web portal is a site that functions as a point of access to information on the World Wide Web. Portals present information from diverse sources in a unified way. Popular portals are MSN, Yahoo, and AOL. Aside from the search engine standard, web portals offer other services such as news, stock prices, infotainment and various other features. Portals provide a way for enterprises to provide a consistent look and feel with access control and procedures for multiple applications, which otherwise would have been different entities altogether. A personal portal is a site on the World Wide Web that typically provides personalized capabilities to its visitors, providing a pathway to other content. It is designed to use distributed applications, different numbers and types of middleware and hardware to provide services from a number of different sources. In addition, business portals are designed to share collaboration in workplaces. A further business-driven requirement of portals is that the content be able to work on multiple platforms such as personal computers, personal digital assistants (PDAs), and cell phones.
A portal where either the aggregated resources are restricted to those describing or associated with the organization or access to the portal is limited to members of the organization.
A portal where either the aggregated resources are restricted to those describing or associated with an institutional department or access to the portal is limited to members of that department.
A portal where either the aggregated resources are restricted to those describing or associated with a specific laboratory or access to the portal is limited to members of that laboratory.
A portal where the aggregated resources are restricted to those describing or related to a particular topic.
A portal where the aggregated resources are restricted to those describing or related to a particular disease.
A portal where the aggregated resources are restricted to those describing or related to a particular disease and are specifically targetted to provide information to the community of patients and the families of patients diagnosed with that disease.
A portal where the aggregated resources are restricted to those describing or related to a particular disease and are specifically targetted to provide information to the community of basic and clinical researchers studying that specific disease.
A web site containing a curated set of links typically focussed on a particular topic or set of related topics.
Those elements defined as a part of the PubMed DTD and used by many literature citation databases
Chemical compositional analysis instrument
High-pressure liquid chromotography instrument
Gravity-driven liquid chromotography instrument
Size exclusion liquid chromotography instrument
Size exclusion chromotography instrument
Ion-exchange liquid chromotography instrument
Polyacrylamide gel electrophoresis instrument
1D polyacrylamide gel electrophoresis instrument
2D polyacrylamide gel electrophoresis instrument
Reverse-phase high-pressure liquid chromotography instrument
Calorimetry is the science of measuring the heat of chemical reactions or physical changes. Calorimetry involves the use of a calorimeter. The word calorimetry is derived from the Latin word calor, meaning heat. Scottish physician and scientist Joseph Black, who was the first to recognize the distinction between heat and temperature, is said to be the founder of calorimetry.[1] Indirect calorimetry calculates heat that living organisms produce from their production of carbon dioxide and nitrogen waste (frequently ammonia in aquatic organisms, or urea in terrestrial ones), OR from their consumption of oxygen. Lavoisier noted in 1780 that heat production can be predicted from oxygen consumption this way, using multiple regression. The Dynamic Energy Budget theory explains why this procedure is correct. Of course, heat generated by living organisms may also be measured by direct calorimetry, in which the entire organism is placed inside the calorimeter for the measurement.
Constant-pressure calorimetry instrument
Differential scanning calorimetry instrument
Differential scanning calorimetry or DSC is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference are measured as a function of temperature. Both the sample and reference are maintained at nearly the same temperature throughout the experiment. Generally, the temperature program for a DSC analysis is designed such that the sample holder temperature increases linearly as a function of time. The reference sample should have a well-defined heat capacity over the range of temperatures to be scanned. The basic principle underlying this technique is that, when the sample undergoes a physical transformation such as phase transitions, more (or less) heat will need to flow to it than the reference to maintain both at the same temperature. Whether more or less heat must flow to the sample depends on whether the process is exothermic or endothermic. For example, as a solid sample melts to a liquid it will require more heat flowing to the sample to increase its temperature at the same rate as the reference. This is due to the absorption of heat by the sample as it undergoes the endothermic phase transition from solid to liquid. Likewise, as the sample undergoes exothermic processes (such as crystallization) less heat is required to raise the sample temperature. By observing the difference in heat flow between the sample and reference, differential scanning calorimeters are able to measure the amount of heat absorbed or released during such transitions. DSC may also be used to observe more subtle phase changes, such as glass transitions. DSC is widely used in industrial settings as a quality control instrument due to its applicability in evaluating sample purity and for studying polymer curing
Isothermal titration calorimetry instrument
Isothermal Titration Calorimetry (ITC) is a biophysical technique used to determine the thermodynamic parameters of (biochemical) interactions. It is most often used to study the binding of small molecules (such as medicinal compounds) to larger macromolecules (proteins, DNA etc.). An isothermal titration calorimeter is composed of two identical cells made of a highly efficient thermal conducting material such as Hasteloy alloy or gold, surrounded by an adiabatic jacket (reviewed by O'Brien et al, 2000). Sensitive thermopile/ thermocouple circuits are used to detect temperature differences between the reference cell (filled with buffer or water) and the sample cell containing the macromolecule. Prior to addition of ligand, a constant power (<1 mW) is applied to the reference cell. This directs a feedback circuit, activating a heater located on the sample cell (VP-ITC users manual, MicroCal Inc, Northampton, MA, USA. 2001). During the experiment, ligand is titrated into the sample cell in precisely known aliquots, causing heat to be either taken up or evolved (depending on the nature of the reaction). Measurements consist of the time-dependent input of power required to maintain equal temperatures between the sample and reference cells.
Respirometry is a general term that encompass a number of techniques for obtaining estimates of the rates of metabolism of vertebrates, invertebrates, plants, tissues, cells, or microorganisms via an indirect measure of heat production (calorimetry).
United States Department of Health and Human Services granting agency
United States Department of Health and Human Services granting institution
Derived from terms used by the NIH CIT CRISP system (http://crisp.cit.nih.gov/)
is the science of determining the arrangement of atoms within a crystal from the manner in which a beam of X-rays is scattered from the electrons within the crystal. The method produces a three-dimensional picture of the density of electrons within the crystal, from which the mean atomic positions, their chemical bonds, their disorder and sundry other information can be derived. The technique of single-crystal X-ray crystallography has three basic steps. The first, and often most difficult, step is to obtain an adequate crystal of the material under study. The crystal should be sufficiently large, pure in composition and regular in structure, with no large internal imperfections such as cracks or twinning. In the second step, the crystal is placed in an intense beam of X-rays, usually of a single wavelength (monochromatic X-rays), producing the regular pattern of reflections. As the crystal is gradually rotated, previous reflections disappear and new ones appear; the intensity of every spot is recorded meticulously at every orientation of the crystal. Multiple data sets may have to be collected, with each set covering slightly more than half a full rotation of the crystal and containing tens of thousands of reflection intensities. In the third step, these data are combined computationally with complementary chemical information to produce and refine a model of the arrangement of atoms within the crystal. The final, refined model, now called a crystal structure, is usually stored in a public database.
A scintillation counter measures ionizing radiation. The sensor, called a scintillator, consists of a transparent crystal, usually phosphor, plastic (usually containing anthracene), or organic liquid (see liquid scintillation counting) that fluoresces when struck by ionizing radiation. A sensitive photomultiplier tube (PMT) measures the light from the crystal. The PMT is attached to an electronic amplifier
Liquid scintillation detection instrument
Liquid scintillation counting is a standard laboratory method in the life-sciences for measuring radiation from beta-emitting nuclides. Scintillating materials are also used in differently constructed "counters" in many other fields. Samples are dissolved or suspended in a "cocktail" containing an aromatic solvent (historically benzene or toluene, but more recently less hazardous solvents have come into favour) and small amounts of other additives known as fluors. Beta particles emitted from the sample transfer energy to the solvent molecules, which in turn transfer their energy to the fluors; the excited fluor molecules dissipate the energy by emitting light. In this way, each beta emission (ideally) results in a pulse of light. Scintillation cocktails often contain additives that shift the wavelength of the emitted light to make it more easily detected. The samples are placed in small transparent or translucent (often glass or plastic) vials that are loaded into an instrument known as a liquid scintillation counter. The counter has two photomultiplier tubes connected in a coincidence circuit. The coincidence circuit assures that genuine light pulses, which reach both photomultiplier tubes, are counted, while spurious pulses (due to line noise, for example), which would only affect one of the tubes, are ignored. Counting efficiencies under ideal conditions range from about 30% for Tritium (a low-energy beta emitter) to nearly 100% for Phosphorus-32, a high-energy beta emitter. Some chemical compounds (notably Chlorine compounds) and highly colored samples can interfere with the counting process. This interference, known as "quenching", can be overcome through data correction or through careful sample preparation. High-energy beta emitters such as P-32 can also be counted in a scintillation counter without the cocktail. This technique, known as Cherenkov counting, relies on the Cherenkov radiation being detected directly by the photomultiplier tubes. Cherenkov counting in this experimental context is normally used for quick rough measurements, since it is more liable to variation caused by the geometry of the sample.
National Institutes of Health granting agency
National Institutes of Health granting institution
The clonal cell line A10 was derived by B. Kimes and B. Brandt from the thoracic aorta of DB1X embryonic rat and possesses many of the properties characteristic of smooth muscle cells. The cells produce spontaneous action potentials at the stationary phase of the growth cycle and exhibit an increase in activity of the enzymes myokinase and creatine phosphokinase. Growth Properties: adherent
An imaging protocol where images are assembled by detecting the pattern created when a particular type of radiated energy is applied to a biomaterial object.
* RAEB: The visualization of deep structures of the body by recording the reflections of echoes of pulses of ultrasonic waves directed into the tissues. Use of ultrasound for imaging or diagnostic purposes employs frequencies ranging from 1.6 to 10 megahertz. (MSH99) (NCI) * The visualization of deep structures of the body by recording the reflections of echoes of pulses of ultrasonic waves directed into the tissues. Use of ultrasound for imaging or diagnostic purposes employs frequencies ranging from 1.6 to 10 megahertz. (MSH) * Use of ultrasound for imaging or diagnostic purposes. Employs frequencies ranging from 1.6 to 10 megahertz. (DCTD-DIP) (NCI) * high frequency sound waves used to identify and examine internal organs and structures without the invasive hazards of X xays, dyes, or fluoroscopy. (CSP)
Cross-sectional nuclear imaging protocol
Multiple electrode extracellular recording protocol
An neuropsychiatric instrument consisting of a series of patient-answer and/or clinician-answered questions designed to assess the affective state of the patient. Typically score ranges are mapped to particular stages or states along an affective continuum such as depressive state.
A evaluative instrument collecting together either individual and/or pedigree related questions and/or data values all designed to evaluate the dependence of a particular trait or disorder on genetic variability.
A evaluative instrument collecting together either individual and/or family related questions and/or data values all designed to evaluate the dependence of a particular trait or disorder on social, economic and/or familial environmental factors.
An neuropsychiatric instrument consisting of a series of patient-answer and/or clinician-answered questions designed to assess the mental state of the patient. Typically score ranges are mapped to particular stages or states along a continuum such as depressive state.
A behavioral instrument consisting of a series of patient-answer and/or clinician-answered questions along with metrics for performing specific movement related tasks both voluntary and involuntary designed to assess the state of the patients pyramidal, extrapyramidal, and reflex movement pathways.
The AIMS is an assessment of movement dysfunctions. It is a 12-item instrument assessing abnormal involuntary movements associated with antipsychotic drugs, such as tardive dystonia and chronic akathisia, as well as 'spontaneous' motor disturbance related to the illness itself. Scoring the AIMS consists of rating the severity of movement in three main anatomic areas (facial/oral, extremities, and trunk), based on a five-point scale (0=none, 4=severe).
National Institute of Mental Health. Abnormal Involuntary Movement Scale. In Guy, W., ed. (1976). ECDEU Assessment Manual. Washington DC, U.S. Department of Health, Education, and Welfare: 534.
The AIS is an assessment of anxiety, consists of 20 somatic and affective symptoms of anxiety. Each item is rated on severity from 1 to 4, where 1 indicates none and 4 indicates severe. The raw score range is from 20 - 80. This is converted to a percentage, by dividing the raw score by 80 and multiplying by 100. Low scores or percentages indicate low levels of anxiety and high scores indicate high levels of anxiety.
Zung, W.W.K. (1971). A rating instrument for anxiety disorders. Psychosomatics, 8, 6, 371-379.
The Barnes Akathisia Rating Scale is an assessment of akathisia which is a movement dysfunction. It is a four-item scale to assess the presence and severity of drug-induced akathisia. It is the most widely used comprehensive rating scale for akathisia, including both objective items (eg observed restlessness) and subjective items (eg patient's awareness of restlessness and related distress), together with a global clinical assessment of akathisia. Global assessment is made on a scale of 0 to 5 with comprehensive definitions provided for each anchor point on scale: 0=absent; 1=questionable; 2=mild akathisia; 3=moderate akathisia; 4=marked akathisia; 5=severe akathisia.
Barnes, T.R. (1989). A rating scale for drug-induced akathisia. British Journal of Psychiatry, 154, 672-676.
Note that akathisia is listed in BIRNLex as Psychomotor Aggitation (birnlex_12661) which is the prefered term given in MeSH (BB).
A survey completed by a patient, with each answer scored on a scale of 0 to 3, designed to measure presence of depression. (NCI)
Beck, A. T., Steer, R..A., Garbin, M.. G., (1988) Psychometric properties of the Beck Depression Inventory: Twenty-five years of evaluation. Clinical Psychology Review 8 (1), 77-100.
Beck, A.T., Rial, W. Y., Rickets, K. (1974). Short form of Depression Inventory: Cross-validation. Psychological-Reports 34 (3), 1184-1186.
Beck, A.T., Ward, C. H., Mendelson, M., Mock, J., & Erbaugh, J. (1961). An inventory for measuring depression. Archives of General Psychiatry 4, 561-571.
The CDSS is an assessment of depression in schizophrenia. It has been extensively evaluated in both relapsed and remitted patients and appears sensitive to change. In comparison to the Hamilton Depression Scale, it has fewer factors and less overlap with positive and negative symptoms. This lack of overlap is present both at the time of relapse and at the time of remission
Addington, D., Addington, J., Maticka-Tyndale, E., & Joyce, J. (1992). Reliability and validity of a depression rating scale for schizophrenics. Schizophrenia Research, 6, 201-208.
The SDS is a symptom assessment tool, which assesses negative symptoms in schizophrenia. Six core items of the deficit syndrome (restricted affect; diminished emotional range; poverty of speech; curbing of interests; diminished sense of purpose; and diminished social drive) are rated on a 5-point scale, 0=absent; 1=mild; 2=moderate; 3=severe; 4=very severe. Each item is also rated as to whether it is a primary symptom and a stable symptom (yes, no, n/a).
Kirkpatrick, B., Buchanan, R.W., McKenney, P.D., Alphs, L.D., Carpenter, W.T. (1989). The schedule for the deficit syndrome: An instrument for research in schizophrenia. Psychiatry Research, 30, 119-123.
An assessment of the statistical characterization of human populations or segments of human populations (e.g., characterization by age, sex, race, or income). (NCI)
The Edinburgh Handedness Inventory is a 20 or 10 item questionnaire in which participants are asked to indicate the preference in the use of hands during certain activities. Participants are instructed to indicate hand preference by a single check. For activities in which they would "never try to use the other hand unless absolutely forced to", two checks should be indicated. To score the inventory, add the number of checks in each column, whichever column total is greater is considered the individual's handedness.
Oldfield, R.C. (1971). The assessment and analysis of handedness: the Edinburgh inventory. Neuropsychologia, 9(1), 97-113.
Assessment of a demographic parameter indicating the number of years of schooling or the highest level of achievement at school. (NCI); Assessment of educational attainment or level of education of individuals. (MSH)
Assessment of an individual's cultural heritage that sets them apart from others in a variety of social relationships. (MSH); Assessment of an individual's social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Assessment of an individual's ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI);
A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (MSH); A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP)
The FIGS is structured interview for gathering diagnostic information about relatives in the pedigree being studied. FIGS data are collected from everyone interviewed about all known members of the extended family. A pedigree (including at a minimum the proband, his/her parents, grandparents, siblings, aunts, uncles, offspring, and spouse) is drawn as part of the interview. The second step of the FIGS is to ask the General Screening Questions. The third step is to complete a Face Sheet and Symptom Checklists with selected relatives.
Maxwell, M.E.: Manual for the FIGS (Family Interview for Genetics Studies). Bethesda, Md, National Institute of Mental Health, Clinical Neurogenetics Branch, Intramural Research Program, 3/30/1992
CFI is used to determine whether a person or family has high expressed emotion or low expressed emotion through a taped interview known as the Camberwell Family Interview. Answers to questions and non-verbal cues are used to determine if some one has high expressed emotion. There is another measurement that is taken from the view of the patient. It rates the patient's perception of how his family feels about him and the disorder. If the patient feels that the parents are too protective or not caring the patient feels that his parents don't care of his independence or trust his judgement. The three dimensions of high EE shown are hostility, emotional over-involvement and critical comments.
Vaughn C, Leff J. (1976) The measurement of expressed emotion in the families of psychiatric patients. Br J Soc Clin Psychol. Jun;15(2):157-65.
Assessment of status of familial relation of patient under study.
Assessment of status of the father of patient under study.
Assessment of status of the mother of patient under study.
Assessment of an individual's father's demographic parameter indicating the number of years of schooling or the highest level of achievement at school. (NCI); Assessment of an individual's father's educational attainment or level of education of individuals. (MSH)
An assessment of an individual's father's work specialties as defined by duties and required skills. Use a more specific term if possible. (PSY); An assessment of an individual's father's crafts, trades, professions, or other means of earning a living. (MSH); An assessment an individual's father's principal activity that a person does to earn money. (NCI)
Assessment of an individual's mother's demographic parameter indicating the number of years of schooling or the highest level of achievement at school. (NCI); Assessment of an individual's mother's educational attainment or level of education of individuals. (MSH)
An assessment of an individual's mother's work specialties as defined by duties and required skills. Use a more specific term if possible. (PSY); An assessment of an individual's mother's crafts, trades, professions, or other means of earning a living. (MSH); An assessment an individual's mother's principal activity that a person does to earn money. (NCI)
An assessment of an indivdual's preferred category exemplars. Assessed on items such as food, color, tv show, etc. Typically used for regression testing of databases.
An assessment of gender, the assemblage of properties that distinguish people on the basis of their societal roles. (NCI) An assessment of gender, the socially-constructed identity of male or female. (MSH); An assessment of the sex of an organism.(BIRNLex).
An assessment of a hallucination, a false sensory perception in the absence of an external stimulus, as distinct from an illusion which is a misperception of an external stimulus. (from Wikipedia) (NCI); An assessment of hallucinations, subjectively experienced sensations in the absence of an appropriate stimulus, but which are regarded by the individual as real. They may be of organic origin or associated with MENTAL DISORDERS. (MSH); An assessment of hallucinations, subjectively experienced sensations in the absence of an appropriate stimulus, but which are regarded by the individual as real; may be of organic origin, drug induced, or associated with a mental disorder. (CSP)
Assessment of behavioral manifestations of cerebral dominance in which there is preferential use and superior functioning of either the left or the right side, as in the preferred use of the right hand or right foot. (MSH); Assessment of learned or spontaneous differential dexterity with and tendency to use one hand rather than the other. (PSY); Assessment of the preferential use of the hand of one side in voluntary motor acts. (CSP)
The InterSePT Scale for Suicidal Thinking (ISST) is an assessment of current suicidal ideation in patients with schizophrenia and schizoaffective disorders.
Lindenmayer, J. P., Czobor, P., Alphs, L., Nathan, A., Anand, R., Islam, Z., Chou J.C.Y. & InterSePT Study Group. (2003). The InterSePT scale for suicidal thinking reliability and validity. Schizophrenia Research, 63,1,161-170.
An assessment of the manner in which an individual habitates, with particular reference to whom living space is shared (e.g., spouse, children, significant other, friend, other family member(s)).
Assessment of a demographic parameter indicating a person's conjugal status. Marital status categories include married, divorced, widowed, or never married. (NCI); Assessment of a demographic parameter indicating a person's status with respect to marriage, divorce, widowhood, singleness, etc. (MSH)
The PANSS is an assessment of positive and negative symptoms in schizophrenia. It is a 30-item rating instrument evaluating the presence/absence and severity of positive, negative and general psychopathology of schizophrenia. The scale was developed from the BPRS and the Psychopathology Rating Scale. All 30 items are rated on a 7-point scale (1=absent; 7=extreme).
Kay, S.R., Opler, L.A., & Fiszbein, A. (1987) The positive and negative syndrome scale (PANSS) for schizophrenia. Schizophrenia Bulletin, 13, 261-276.
Modified Positive and Negative Symptom Scale
These 4 questions in conjunction with the SANS and SAPS provide the answers to the PANSS assessment.
Kay, S.R., Opler L.A. and Fiszbein, A. (1992) Positive and negative syndrome scale (PANSS) rating manual, Multihealth Systems, Inc., Toronto, Canada.
The North American Adult Reading Test (NAART) is an assessment of verbal intellectual ability. The NAART is a reliable and valid measure of verbal intelligence, comparable in psychometric properties to the WAIS-R Vocabulary test and with equal psychometric properties in young, middle-aged and older adults. Each incorrectly pronounced word is counted as one error, score range is from 0 to 60, with 0 indicating no pronunciation errors and 60 indicating pronunciation errors on all items.
Nelson, H.E. & O'Connell, A. (1978). Denentia: The estimation of pre-morbid intelligence levels using the new adult reading test. Cortex, 14, 234-244.
Nelson, H.E. (1982). National Adult Reading Test (NART): Test Manual, Windsor, U.K.: NFER nelson.
An assessment of the number of sons or daughters of any age, including biological offspring and sometimes including unborn children, adopted children, stepchildren, foster children and children born outside of marriage; person under an age specified by law. (NCI)
An assessment of an individual's work specialties as defined by duties and required skills. Use a more specific term if possible. (PSY); An assessment of an individual's crafts, trades, professions, or other means of earning a living. (MSH); An assessment of the principal activity that a person does to earn money. (NCI)
A evaluative instrument collecting together either subject and/or clinician-answered questions related to evaluating the developmental stage of the subject.
The Premorbid Adjustment Scale (PAS) is a rating scale for use in schizophrenia. It evaluates the degree of achievement of developmental goals at each of several periods of a subject's life before the onset of schizophrenia
Cannon-Spoor,H. E., Potkin, S.G. & Wyatt, R. J. (1982) Measurement of premorbid adjustment in chronic schizophrenia. Schizophrenia Bulletin, 8, 470-484.
The Quick Mood Scale is a 12-item category scale which gives information on six factors of importance in the assessment of drug effects on the central nervous system (drowsiness, anxiety, depression, aggression, confusion and lack of coordination). Responders are instructed to give an indication of his or her mood at this moment for each of the 12 items on a 5 point likert scale (not at all, a little, moderately, very, extremely).
Woodruffe-Peacock, C., Turnbull, G.M., Johnson, M.A., Elahi, N., Preston, G.C. (1998). The quick mood scale: development of a simple mood assessment for clinical pharmacology studies. Human Psychopharmacology, 13, 53-88.
An assessment of an individual's race - an arbitrary classification of taxonomic group that is a division of a species; usually arise as a consequence of geographical isolation within a species and characterised by shared heredity, physical attributes and behavior, and in case of humans, by common history, nationality, or geographic distribution. (NCI)
Scale for the Assessment of Negative Symptoms
The SANS is an assessment of negative symptoms in schizophrenia. It assesses five symptom complexes to obtain clinical ratings of negative symptoms in patients with schizophrenia. They are: affective blunting; alogia (impoverished thinking); avolition/apathy; anhedonia/asociality; and disturbance of attention. Assessments are conducted on a six-point scale (0=not at all to 5=severe). Ratings are made on each negative symptom cluster, after consideration has been given to each of the items contained within the various complex scores. Item descriptions are not given, but anchor point descriptions are given for each score.
Andreasen, N. C. (1983). The Scale for the Assessment of Negative Symptoms (SANS). Iowa City, Iowa: The University of Iowa, 1983.
Andreasen, N.C. & Olsen, S. (1982). Negative v positive schizophrenia: definition and validation. Archives of General Psychiatry, 39, 789-794.
Structured clinical interview for DSM-IV Axis I Disorders
* The SCID is a diagnostic tool. It assesses thirty-three of the more commonly occurring psychiatric disorders described in the DSM-IV. The SCID is a semi-structured interview that allows the experienced clinician to tailor questions to fit the patient's understanding; to ask additional questions that clarify ambiguities; to challenge inconsistencies; and to make clinical judgments about the seriousness of symptoms. The main uses of the SCID are for diagnostic evaluation, research, and the training of mental-health professionals. (BIRNLex) * The Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I) is a semi-structured interview for making the major DSM-IV Axis I diagnoses. The SCID-II is a semi-structured interview for making DSM-IV Axis II: Personality Disorder diagnoses (www.scid4.org/faq/scidfaq.html).
First, M.B., Spitzer, R.L., Gibbon, M., & Williams, J.B., SCID-I/Scoresheet, Clinician version, American Psychiatric Press, Inc. 1-6
First, M.B., Spitzer, R.L., Gibbon, M., & Williams, J.B.W. (1997). Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I), Clinician Version. American Psychiatric Press, Washington, DC.
R.L. Spitzer, J.B.W. Williams, M. Gibbon and M.B. First, The structured clinical interview for DSM-III-R (SCID), Arch Gen Psychiatry 49 (1992), pp. 624-629.
Structured clinical interview for DSM-IV Axis I Disorders - non-patient
* The SCID is a diagnostic tool. It assesses thirty-three of the more commonly occurring psychiatric disorders described in the DSM-IV. The SCID is a semi-structured interview that allows the experienced clinician to tailor questions to fit the patient's understanding; to ask additional questions that clarify ambiguities; to challenge inconsistencies; and to make clinical judgments about the seriousness of symptoms. The main uses of the SCID are for diagnostic evaluation, research, and the training of mental-health professionals. (BIRNLex) * The Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I) is a semi-structured interview for making the major DSM-IV Axis I diagnoses. The SCID-II is a semi-structured interview for making DSM-IV Axis II: Personality Disorder diagnoses (www.scid4.org/faq/scidfaq.html). * SCID non-patient (overview and screening module) modified by Stanford University, 9/27/1999
Structured clinical interview for DSM-IV Axis I Disorders - patient
Scale for the Assessment of Positive Symptoms
The SAPS is an assessment of positive symptoms in schizophrenia. It accompanies the SANS.
Andreasen, N. C. (1984). The Scale for the Assessment of Positive Symptoms (SAPS). Iowa City, Iowa: The University of Iowa, 1984.
The Self-rating Anxiety Scale is a self-administered assessment of anxiety, consisting of 20 statements. The subject is instructed to rate how each statement applies to him or her within the past week. Each item is rated on a scale from None of the time, some of the time, a good part of the time, most or all of the time. The raw score range is from 20 - 80. This is converted to a percentage, by dividing the raw score by 80 and multiplying by 100. Low scores or percentages indicate low levels of anxiety and high scores indicate high levels of anxiety.
Zung, W.W.K. (1971). A rating instrument for anxiety disorders. Psychosomatics, 12, 6, 371-379.
The SAS is a 10-item instrument used to evaluate the presence and severity of parkinsonian symptomatology. It is the most commonly used rating scale for Parkinsonism in clinical trials over the past 25 years. The ten items focus on rigidity rather than bradykinesia, and do not assess subjective rigidity or slowness. Items are rated for severity on a 0-4 scale, with definitions given for each anchor point.
Simpson G.M., Angus, J.W.S.(1970). A rating scale for extrapyramidal side effects. Acta Psychiatry Scand (Suppl), 212, 11-19.
The SES assessment is a demographic measure which rates a person's socio-economic status by scoring the education and occupation levels of a patient and his/her primary and secondary caretakers
a type of quantitative value specifying the count of another entity.
Moved as a subclass of 'DTI imaging protocol attribute' from 'Cardinality value'.
the number of gradient amplitude vectors used in each complete set of diffusion-weighted data
number of imaging volumes acquired without any diffusion-weighting gradients applied
number of diffusion-weighted directions multiplied by the number of non-zero b-values
An experimental design in which the conditions of interest are brief, and the time course is modeled as a sudden on and off-set rather than a constant state.
A computational method for separating a multivariate signal into additive subcomponents supposing the mutual statistical independence of the non-Gaussian source signals. It is a special case of blind source separation. (from Wikipedia).
Applied to fMRI data, it identifies independent temporal and spatial patterns.
The general linear model (GLM) is a statistical linear model. It may be written as Y = XB + U where Y is a matrix with series of multivariate measurements, X is a matrix that might be a design matrix, B is a matrix containing parameters that are usually to be estimated and U is a matrix containing errors or noise. The residual is usually assumed to follow a multivariate normal distribution. If the residual is not a multivariate normal distribution, generalized linear models may be used to relax assumptions about Y and U. The general linear model incorporates a number of different statistical models: ANOVA, ANCOVA, MANOVA, MANCOVA, ordinary linear regression, t-test and F-test. If there is only one column in Y (i.e., one dependent variable) then the model can also be referred to as the multiple regression model (multiple linear regression). Hypothesis tests with the general linear model can be made in two ways: multivariate and mass-univariate.(WIkiPedia)
A Gaussian random field is a random field involving Gaussian probability density functions of the variables. The initial conditions of physical cosmology generated by quantum mechanical fluctuations during cosmic inflation are thought to be a Gaussian random field with a nearly scale invariant spectrum.(WIkiPedia)
A Region of Interest, often abbreviated ROI, is a selected subset of samples within a dataset identified for a particular purpose. The concept of an ROI is commonly used in medical imaging. For example, the boundaries of a tumor may be defined on an image or in a volume, for the purpose of measuring its size. The endocardial border may be defined on an image, perhaps during different phases of the cardiac cycle, say end-systole and end-diastole, for the purpose of assessing cardiac function.There are three fundamentally different means of encoding an ROI: * burned in to the dataset, with a value that may or may not be outside the normal range of normally occurring values * as separate purely graphic information, such as with vector or bitmap (rasterized) drawing elements, perhaps with some accompanying plain (unstructured) text annotation * as separate structured semantic information (such as coded value types) with a set of spatial and/or temporal coordinates (WIkiPedia)
in a time-volume (4D dataset), the outline of an object at or during a particular time interval
in a volume (3D dataset), the contours or surfaces outlining an object
In neuroimaging, usually a cortical or subcortical area if defined anatomically, but it may be defined anatomically or functionally.
on a waveform (1D dataset), a time or frequency interval
on an image (2D dataset), the boundaries of an object
Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM. The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG (http://www.fil.ion.ucl.ac.uk/spm/).
a type of quantitative value for a specific point in a multidimensional data set.
a type of spatial value for a specific point in a 2D data set.
a type of spatial value for a specific point in a 3D data set.
Wide-field fluorescence imaging protocol
A Positron emission tomography scanner is a device used in a nuclear medicine to observe metabolic processes in the body.
Single-photon emission computed tomography scanner
A Single-photon emission computed tomography scanner is a device used in nuclear medicine tomographic imaging to measure perfusion in the body using gamma rays.
A Magnetoencephalography machine is a device used in functional neuroimaging for mapping brain activity by recording magnetic fields produced by electrical currents occurring naturally in the brain, using very sensitive magnetometers..
A Electroencephalography machine is a device used in electrophysiology to record electrical activity of the brain..
An anatomical MRI protocol is a structural MRI protocol that can be used to delineate the anatomy, for example by the way of a segmentation or parcellation.
A measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically.
An assay by which an antigen is precipitated from solution using an antibody.
OBI has immunoprecipitation under "process"; we insert "assay" in between process and immunoprecipitation. Not sure what to do here.
An assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
Serial block face scanning electron microscopic imaging assay
serial block face scanning electron microscopy
Scanning electron microscopy assay that combines automated block-face imaging with serial sectioning inside the chamber of a scanning electron microscope and uses backscattering contrast to visualize the heavy-metal staining of tissue (adapted from Denk and Horstmann, PLoS Biol. 2004 Nov;2(11):e329, 2004).
Denk W & Horstmann H (2004) Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol 2: e329
Scanning electron microscopic imaging assay
Electron microscopic imaging assay where the image is formed by scanning an electron beam across a sample in a scanning electron microscope, and collecting scattered electrons to form an image. The signals result from interactions of the electron beam with atoms at or near the surface of the sample. In the most common or standard detection mode, secondary electron imaging or SEI, the SEM can produce very high-resolution images of a sample surface, revealing details about less than 1 to 5 nm in size. Due to the very narrow electron beam, SEM micrographs have a large depth of field yielding a characteristic three-dimensional appearance useful for understanding the surface structure of a sample. (adapted from Wikipedia; http://en.wikipedia.org/wiki/Scanning_electron_microscopy)
Includes the use of various techniques to either directly or indirectly image the structure, function/pharmacology of the brain. It is a relatively new discipline within medicine and neuroscience/psychology. - definition adapted from Wikipedia
Methods for visualizing REGIONAL BLOOD FLOW, metabolic, electrical, or other physiological activities in the CENTRAL NERVOUS SYSTEM using various imaging modalities. (MeSH)
A resource that provides an application or program that is used to rapidly display a sequence of images of 2-D or 3-D artwork or model positions in order to create an illusion of movement.
A resource that provides an application or program that is middleware for distributed systems to standardize a data-centric publish-subscribe programming model.
A resource that provides an application or program that is used to obtain a permanent holding place for digital data, until purposely erased.
A resource that provides an application or program that is used to transfer data from point-to-point often represented as an electro-magnetic signal over a physical point-to-point or point-to-multipoint communication channel. An example of such channels are wireless communication channels.
A portal where either the aggregated resources are restricted to those describing or associated with the community or access to the portal is limited to the members of the community.
A resource that provides an application or program that is used to generate an image from a model, where the model describes three-dimensional objects in a strictly defined language or data structure. In the graphics pipeline, it is the last major step, giving the final appearance to the models and animation.
A resource that provides a collection of subroutines or classes used to develop software. Software libraries contain code and data that provide services to independent programs. This allows code and data to be shared and changed in a modular fashion.
Inside the spinal canal (the canal in successive vertebrae through which the spinal cord passes-Wordnet definition) . For example, intrathecal immunoglobulin production means production of this substance in the spinal cord; intrathecal injection is an injection into the the spinal canal (intrathecal space surrounding the spinal cord), as in a spinal anaesthesia or in chemotherapy or pain management applications.
A magnetic resonance imaging (MRI) method that produces in vivo images of biological tissues weighted with the local microstructural characteristics of water diffusion. The field of diffusion MRI can be understood in terms of two distinct classes of application – Diffusion Weighted MRI and Diffusion Tensor MRI. (Adapted from wikipedia: http://en.wikipedia.org/wiki/Diffusion_MRI)
functional magnetic resonance imaging assay
Diffusion weighted magnetic resonance imaging assay
High angular resolution diffusion imaging
Tuch DS, Reese TG, Wiegell MR, et al (2002). "High angular resolution diffusion imaging reveals intravoxel white matter fiber heterogeneity". Magn. Res. Med. 48: 577–582
Magnetoencephalography is an imaging technique used to measure the magnetic fields produced by electrical activity in the brain via extremely sensitive devices such as superconducting quantum interference devices (SQUIDs). These measurements are commonly used in both research and clinical settings. There are many uses for the MEG, including assisting surgeons in localizing a pathology, assisting researchers in determining the function of various parts of the brain, neurofeedback, and others. - definition adapted from Wikipedia
An assay in which a tracer is injected into a region of the nervous system or one of its targets that is taken up by cells, axons or axon terminals in order to determine axonal projections to or from that region.
A molecule that is used to trace axonal projections either to or from a part of the nervous system or one of its targets.
Role of a substance that is used for tract tracing studies in the nervous system that is taken up by cell bodies and transported towards the axon terminals.
Role of a tracer that can be used to trace connections in post-mortem tissue.
Role of a substance that is used for tract tracing studies in the nervous system that is taken up by the axon terminals and transported towards the cell soma.
Role of a tracer where the tracer can pass from neuron to neuron through synaptic connections
A longitudinal study is a correlational research study that involves repeated observations of the same items over long periods of time. (Adapted from Wikipedia)
The strengthening (or potentiation) of the connection between two nerve cells which lasts for an extended period of time (minutes to hours in vitro and hours to days and months in vivo). LTP can be induced experimentally by applying a sequence of short, high-frequency stimulations to nerve cell synapses.
Gene Ontology Biological Process lists Long Term Potentiation etc. I think we should probably just use the GO for now and extend it for neuroscience.
A behavioral protocol in which response times are assessed.
A behavioral paradigm in which the subject rests quietly.
A behavioral paradigm in which subjects are asked to press a button each time a checkerboard display flashes. In this blocked design, a flashing checkerboard was displayed for 12 seconds and alternated with 12 second blocks of a fixation cross.
A gradient-recalled echo pulse sequence that is used to map the geometric distortions caused by static magnetic field inhomogeneities.
The educational process of instructing (research subjects). (MSH); educational process of instructing (research subjects). (CSP)
A localizer scan is one used to determine where the imaging slices should be placed to image the anatomical structures of interest.
MRI Imaging protocol in which data may or may not be collected but are not included in later analyses.
A parameter for an MRI imaging protocol. The value is usually set at the time of scanning/data collection.
Magnitude image from a B0 field mapping protocol
The magnitude images created by a B0 field mapping scan.
Phase image from a B0 field mapping protocol
The phase images created by a B0 field mapping scan.
A localizer scan which has a sagittal orientation.
In parallel MRI, the scan time is reduced by increasing the distance in k-space between each phase encoding line by a factor, R, called the acceleration factor.
An MR acquisition parameter that defines the range of frequencies that the MR acquisition is sensitive to.
The type of head and or body coil used for the transmission and reception of radio frequency data in Magnetic Resonance (MR) scanners.
The total extent of an image along a spatial dimension (Huettel, Song, McCarthy, 2004)
The strength of the main magnetic field generated by a magnetic resonance scanner.
The change in the precession angle of the net magnetization following excitation (Huettel, Song, McCarthy, 2004).
The amount of space between slices of excitation, collected during magnetic resonance scanning.
The company who manufactures and distributes the magnetic resonance scanner.
The maximum magnetic field gradient strength attainable by a set of gradient coils in a magnetic resonance scanner.
The manner in which an image is displayed. When applied to magnetic resonance images, it can be in reference to an anatomical landmark (e.g., parallel to the anterior and posterior commissures) or in reference to inferior-superior, anterior-posterior, or left-right dimensions.sagittal, axial or coronal directions.
The path taken through k-space by a given pulse sequence. Different pulse sequences adopt different k-space traversals or trajectories; e.g. 'spiral', 'rectilinear' (Huettel, Song, McCarthy, 2004, modified kgh).
The dimensions of the array in computer memory used to store the data acquired during a pulse sequence. Related to the number of phase-encoding steps, frequency-encoding points and number of slices.
The number of images collected at the beginning of a functional run that are discarded, usually without examination. This is done because the change in net magnetization following excitation has not yet reached a steady state. (Huettel, Song, & McCarthy, 2004)
The number of slices collected during an MRI experiment. A slice is a single slab of an imaging volume. (Huettel, Song, McCarthy, 2004).
The number of fMRI images collected at different points in time. Usually used in reference to a single run of an experiment. Each time point is equal to a single TR (repetition time) interval.
The direction in which phase is encoded. Typically discussed in conjunction with frequency encoding. The combination of the two allow for spatial localization within a slice.
The direction in which the frequency encoding gradient is applied. Also called the 'readout' direction.
The name given to a certain magnetic resonance scanner hardware configuration. For example, one GE model is the 3.0T Signa Excite HD.
The version of software that controls the operation of a computer and directs the processing of programs (as by assigning storage space in memory and controlling input and output functions) on a magnetic resonance scanner. (adapted from www.m-w.com)
The maximum rate of change of signal; usually refers to the current supplied to the magnetic field gradient coils.
The order in which slices, slabs of an imaging volume are acquired. Two typical methods are sequential and interleaved. Sequential collection involves collecting slices in adjacent order, or in adjacent order with a small gap between slices (e.g., 1,2,3,4,5,6). Interleaved collection involves collecting every other slice, and then taking a second pass to collect the others (e.g., 1,3,5,2,4,6). Slices can be collected along any of the planes (e.g., inferior to superior, left to right, posterior to anterior).
The thickness of the slabs of an imaging volume. Typically measured in units of millimeters. A single slice is defined by the the strength of the gradient and the bandwidth of the electromagnetic pulse used to select it. (Huettel, Song, & McCarthy, 2004).
Refers to the usage of a pulse sequence, applied before any other data is acquired, that registers the subsequent imaging volume to an imaging volume acquired at an earlier time.
A protocol is a rule which guides how an activity should be performed; a set of formal rules used to specify the format of an exchange of data. (NCI)
Image description and standard sequence name
Non-manufacturer specific name for an imaging protocol, e.g. 'echo-planar imaging' rather than 'ep2d'.
A T1 Weighted scan which is acquired as a volume rather than slice by slice.
This refers to a T1 image that has undergone a post-processing technique to remove identifiable facial features.
Common or vendor name and number of diffusion-weighted directions (i.e., Jones30, Siemens default 30, …)
The number of b=0 volumes plus the number of b NE 0 volumes.
The list of diffusion-weighting gradient amplitude vectors
A magnetic resonance imaging protocol that is sensitive to the diffusion of water molecules.
Vector quantities obtained by diagonalizing the diffusion tensor
Scalar quantity used to characterize diffusional anisotropy
scalar quantities obtained by diagonalizing the diffusion tensor
A periodical or magazine, esp. one published for a special group, learned society, or profession: the Journal of Neuroscience.
Data transformation where different sets of images are aligned to a single coordinate system.
I looked at OBI and could not tell from their current classes where this set of entities should go. So I'm putting it here temporarily. (Maryann Martone)
An electronic lab notebook is a software program designed to replace paper laboratory notebooks (adapted from Wikipedia).
Benchmarking is the process of comparing the cost, cycle time, productivity, or quality of a specific process or method to another that is widely considered to be an industry standard or best practice.
A type of study that examines genetic variation across a given genome, designed to identify genetic associations with observable traits. In human studies, this might include traits such as blood pressure or weight, or why some people get a disease or condition. (Adapted from Wikipedia)
Electromyography surface recording protocol
A macro-electrode recording technique for recording the activation signal of muscles through the use of surface electrode. EMG may also be performed intramuscularly by inserting a needle into the muscle (intramuscular EMG)
Classical conditioning paradigm where a painful or otherwise aversive stimulus is paired with a neutral stimulus leading to the neutral stimulus provoking a state of fear.
A substance giving origin to a coloring matter that is detectable by eye in a chemical reaction.
A type of energy transfer between two fluorophores whereby a donor fluorophore, intially in its electronic excited state, may transfer energy to an acceptor fluorophore (in close proximity, typically <10 nm) through nonradiative dipole-dipole coupling. (adapted from Wikipedia)
Compound that serves to sense changes in calcium levels, usually through a change in fluorescence properties upon binding to calcium.
Definition::A device for the detection of an analyte that combines a biological component with a physicochemical detector component. 1) the sensitive biological element (biological material (eg. tissue, microorganisms, organelles, cell receptors, enzymes, antibodies, nucleic acids, etc), a biologically derived material or biomimic) The sensitive elements can be created by biological engineering. 2) the transducer or the detector element (works in a physicochemical way; optical, piezoelectric, electrochemical, etc.) that transforms the signal resulting from the interaction of the analyte with the biological element into another signal (i.e., transducers) that can be more easily measured and quantified; 3) associated electronics or signal processors that is primarily responsible for the display of the results in a user-friendly way.[2] The most widespread example of a commercial biosensor is the blood glucose biosensor, which uses the enzyme glucose oxidase to break blood glucose down. In doing so it first oxidizes glucose and uses two electrons to reduce the FAD (a component of the enzyme) to FADH2. This in turn is oxidized by the electrode (accepting two electrons from the electrode) in a number of steps. The resulting current is a measure of the concentration of glucose. In this case, the electrode is the transducer and the enzyme is the biologically active component. (from Wikipedia
High-pressure liquid chromotography protocol
Immunolabeling protocol application that involves localizing proteins in a tissue section through exploiting the principle of antibodies binding specifically to antigens in biological tissues. It takes its name from the roots "immuno," in reference to antibodies used in the procedure, and "histo," meaning tissue (compare to immunocytochemistry). (from wikipedia)
National Institute of Alcohol Abuse & Alcoholism
National Institute of Allergy and Infectious Diseases
National Institute of Arthritis and Musculoskeletal and Skin Diseases
National Institute of Biomedical Imaging and Bioengineering
Center for Disease Control and Prevention
National Institutes of Health Clinical Center
National Institute of Child Health and Human Development
National Institute of Deafness and Other Communication Disorder
National Institute of Dental and Cranialfacial Research
National Institute of Diabetes and Digestive and Kidney Diseases
Office of the Director of the National Institutes of Health
National Institute of Environmental Health Sciences
National Institute of General Medical Sciences
Agency for Healthcare Research and Quality
Agency for Toxic Substances and Disease Registry
Health Resources and Services Administration
National Heart, Lung and Blood Institute
National Human Genome Research Institute
John E. Fogarty International Center For Advanced Study in the Health Sciences
National Center on Minority Health and Health Disparities
National Institute of Neurological Disorders and Stroke
National Center for Complementary and Alternative Medicine
Substance Abuse and Mental Health Services Administration
National Institutes of Health Center for Information Technology
Cognitive Atlas Ontology did not have any label or definition for this class. The label is given only for the purpose of grouping the terms. (December 2012)