Resources With Definitions
From NeuroLex
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| Definition | Synonym | Comment | |
|---|---|---|---|
| 1D Time-series analysis software | |||
| 2D Time-series analysis software | |||
| 2D spatial image | |||
| 3D Time-series analysis software | 4D analysis software | ||
| 3D spatial image | An image that has an x, y and z dimension | Volume | |
| 3D visualization software | |||
| 4D visualization software | |||
| AFNI | |||
| Abstract | |||
| Accession number | Accession | ||
| Action observation paradigm | A behavioral paradigm in which subjects view images of moving body parts (Brain Map). | Action Observation | |
| Acupuncture paradigm | A behavioral paradigm where subjects are stimulated with Chinese acupuncture, a procedure in which thin needles are passed through the skin to specific points. | ||
| Affective neuroscience | Branch of neuroscience involving the study of the neural mechanisms of emotion. This interdisciplinary field combines neuroscience with the psychological study of personality, emotion, and mood. - definition adapted from Wikipedia | ||
| Algorithm | an algorithm is a plan which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. | ||
| Alternative title | alt title secondary title |
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| Amperometric electrode recording protocol | |||
| Analysis service resource | A resource that provides a service, which transforms any input into data, such as producing gene expression profiles of a sample of tissue, or interpretation of EEG data. For example, the NIH blueprint core facility (La Jolla Core facility) can run certain types of experiments for researchers who do not wish to purchase equipment or develop expertise in the field. Viewing this as an input/output relationship the input would be a physical entity such as a mouse and the output would be the data. | ||
| Anatomical atlas data set | Atlas | ||
| Anatomical data set | |||
| Anatomical pathology | Branch of pathology. | ||
| Anatomy | branch of biology and Medicine that studies primarily the internal structure and design of the structure of living things.
It is a general term that includes human anatomy, animal anatomy (zootomy) and plant anatomy (phytotomy). Anatomy is divided into various sub specialties in some of its facets anatomy is closely related to Embryology, Histology, comparative anatomy and comparative embryology, through common roots in evolution. Anatomy is subdivided into gross anatomy (or macroscopic anatomy) and microscopic anatomy. Gross anatomy (also called topographical anatomy, regional anatomy, or anthropotomy) is the study of anatomical structures that can be seen by unaided vision with the naked eye. Microscopic anatomy is the study of minute anatomical structures assisted with microscopes, which includes histology (the study of the organization of tissues), and cytology (the study of cells). The history of anatomy has been characterized, over time, by a continually developing understanding of the functions of organs and structures in the body including the clinical understanding of how damage to these structures effects other functions in the body. Methods have also advanced dramatically, advancing from examination of animals through dissection of cadavers (dead human bodies) to technologically complex techniques developed in the 20th century including X-ray technology, Sonogram and MRI technology. Anatomy should not be confused with anatomical pathology (also called morbid anatomy or histopathology), which is the study of the gross and microscopic appearances of diseased organs. - definition adapted from Wikipedia |
Anatomist | |
| Animal physiology | Branch of physiology concerned with animals. | ||
| Animation software | 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. | ||
| Anti saccade paradigm | 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) | Anti-saccades paradigm | |
| Antibody supplier | |||
| Apache License | |||
| Application programming interface | |||
| Assessment test provider | A material resource that provides scientific data assessment instruments, for example, the Behavioral Scale assessments at CERAD (Consortium to Establish a Registry for Alzheimer\\\\u2019s Disease). | evaluation instrument provider assessment tool provider assessment instrument provider |
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| Atlas | A resource that provides a type of anatomical data set containing a collection of spatially indexed anatomical maps. | ||
| Audio track | A resource that provides an audio recording, such as multichannel spike recordings from a central pattern generator circuit. | audio | |
| Auditory oddball paradigm | An oddball discrimination paradigm that involves responding to auditory stimuli that are dissimilar to the majority of auditory stimuli presented. | ||
| Author | |||
| Author affiliation | author adress | ||
| Author set | |||
| Autoradiography protocol | A technique that uses X- ray film to locate radioactively labeled molecules or fragments of molecules by recording on a photographic plate or emulsion the radiation emitted by radioactive material within the object. (adapted from NCI) | ||
| BSD License | BSD licenses represent a family of permissive free software licenses. The original was used for the Berkeley Software Distribution (BSD), a Unix-like operating system for which the license is named. The first version of the license was revised, and the resulting licenses are more properly called modified BSD licenses. Permissive licenses, sometimes with important differences pertaining to license compatibility, are referred to as "BSD-style licenses". Several BSD-like licenses, including the New BSD license, have been vetted by the Open Source Initiative as meeting their definition of open source. The licenses have few restrictions compared to other free software licenses such as the GNU General Public License or even the default restrictions provided by copyright, putting it relatively closer to the public domain. | ||
| BSD license resource | A resource that provides any of the family of permissive free software licenses. The original was used for the Berkeley Software Distribution (BSD), a Unix-like operating system for which the license is named. The first version of the license was revised, and the resulting licenses are more properly called modified BSD licenses. Permissive licenses, sometimes with important differences pertaining to license compatibility, are referred to as \\\\u201cBSD-style licenses\\\\u201d. Several BSD-like licenses, including the New BSD license, have been vetted by the Open Source Initiative as meeting their definition of open source. The licenses have few restrictions compared to other free software licenses such as the GNU General Public License or even the default restrictions provided by copyright, putting it relatively closer to the public domain. | BSD license | |
| Behavioral analysis service | A resource that provides data from whole behaving animals, which are either provided to the service provider or purchased by the service provider specifically for the experiment which the provider was contracted to perform. Viewing this as an input/output relationship the input would be an animal and the output would be data such as an excel sheet of 'times of escape' from the Morris water maze. | ||
| Behavioral conditioning paradigm | |||
| Behavioral neuroendocrinology | the study of hormonal processes and neuroendocrine systems that regulate behavior. | Behavioral neuroendocrinologist Behavioural neuroendocrinology Behavioural neuroendocrinologist |
|
| Behavioral neuropharmacology | Branch of neuropharmacology dealing with behavior. | ||
| Behavioral paradigm | 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. | ||
| Behavioral science | From BRO: Behavioural science (or Behavioral science) is a term that encompasses all the disciplines that explore the activities of and interactions among organisms in the natural world. It involves the systematic analysis and investigation of human and animal behaviour through controlled and naturalistic experimental observations and rigorous formulations. (E. D. Klemke, R. Hollinger, and A. D. Kline, (ed) (1980)) - definition adapted from Wikipedia | Behavior Behaviour Behavioural science Behavioural scientist Behavioral scientist |
|
| Bibliographic database | |||
| Bibliographic resource | A narrative resource that provides published scientific works or licensing. | Consider removing the word 'published' from the definition to allow the inclusion non-published works. | |
| Bibliography | A resource that provides access to published scientific works or licensing. | ||
| Binary executable | Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) | Software application software program program |
I think we should make "software application" as the preferred label rather than "binary executable" |
| Biochemical specimen preparation protocol | |||
| Biochemistry | |||
| Bioinformatics | From BRO: Bioinformatics is the application of information technology to the field of molecular biology. The term bioinformatics was coined by Paulien Hogeweg in 1978 for the study of informatic processes in biotic systems. Bioinformatics now entails the creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data. - definition adapted from wikipedia | Informatics Neuroinformatics Neurotechnology Technology development IT |
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| Biology | Branch of science concerned with studying living organisms. | ||
| Biomaterial analysis service | A resource that provides data from any biomaterial sample that was given to the service provider. This can also be a service which performs an experiment such as electrophysiological examination of LTP in a transgenic mouse. Viewing this as an input/output relationship the input would be a tissue or an animal and the output would be data. | ||
| Biomaterial manufacture | A resource that produces a product that is of organismal origin. An example of a biomaterial service is the production of a knockout mouse or cell culture. Note, for simplicity of definitions all molecules including antibodies and toxins are considered reagents even though some may have an organismal origin. | ||
| Biomaterial supply resource | A material resource that provides physical materials like tissue samples, cell lines or organisms. For example, the Jackson Laboratory supplies knockout transgenic mice. Note, for the sake of simplicity we have excluded molecules of organismal origin from this category as these can be manufactured chemically and have included them under the reagent category (e.g., antibodies, toxins). | Biomaterial supply Biomaterial supplies |
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| Biophysics | is an interdisciplinary science that employs and develops theories and methods of the physical sciences for the investigation of biological systems. Studies included under the umbrella of biophysics span all levels of biological organization, from the molecular scale to whole organisms and ecosystems. Biophysical research shares significant overlap with biochemistry, nanotechnology, bioengineering, agrophysics and systems biology.
Molecular biophysics typically addresses biological questions that are similar to those in biochemistry and molecular biology, but the questions are approached quantitatively. Scientists in this field conduct research concerned with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis, as well as how these interactions are regulated. A great variety of techniques are used to answer these questions. Fluorescent imaging techniques, as well as electron microscopy, x-ray crystallography, NMR spectroscopy and atomic force microscopy (AFM) are often used to visualize structures of biological significance. Conformational changes in structure can be measured using techniques such as dual polarisation interferometry and circular dichroism. Direct manipulation of molecules using optical tweezers or AFM can also be used to monitor biological events where forces and distances are at the nanoscale. Molecular biophysicists often consider complex biological events as systems of interacting units which can be understood through statistical mechanics, thermodynamics and chemical kinetics. By drawing knowledge and experimental techniques from a wide variety of disciplines, biophysicists are often able to directly observe, model or even manipulate the structures and interactions of individual molecules or complexes of molecules. In addition to traditional (i.e. molecular and cellular) biophysical topics like structural biology or enzyme kinetics, modern biophysics encompasses an extraordinarily broad range of research. It is becoming increasingly common for biophysicists to apply the models and experimental techniques derived from physics, as well as mathematics and statistics, to larger systems such as tissues, organs, populations and ecosystems. |
Biological Physics Physics Psychophysics |
|
| Biostatistics | From BRO: (a combination of the words biology and statistics; sometimes referred to as biometry or biometrics) is the application of statistics to a wide range of topics in biology. The science of biostatistics encompasses the design of biological experiments, especially in medicine and agriculture; the collection, summarization, and analysis of data from those experiments; and the interpretation of, and inference from, the results. - definition adapted from Wikipedia | ||
| Biotengineering | The application of engineering principles to address challenges in the fields of biology and medicine. | Neurotechnology Neural Engineering Bioengineering Neuroengineering Technology development Robotics |
|
| Block design | Box_car_design | ||
| Blog | |||
| Blood Oxygenation Level Dependent signal | BOLD | ||
| Body system model | |||
| Book | A written or printed work of fiction or nonfiction, usually on sheets of paper fastened or bound together within covers. | ||
| Book resource | A bibliographic resource that provides a written or printed work of fiction or nonfiction, usually on sheets of paper fastened or bound together within covers. | Book | |
| Book series volume | |||
| Botany | branch of biology concerned with plants. | ||
| Brain bank | |||
| Breathhold paradigm | A behavioral paradigm that requires subjects to hold their breath one or more times. | ||
| Bright-field imaging protocol | |||
| Cardinality value | |||
| Cell biology | Branch of biology concerned with the study of cells and cellular processes.
(formerly cytology, from the Greek kytos, "container") is an academic discipline that studies cells – their physiological properties, their structure, the organelles they contain, interactions with their environment, their life cycle, division and death. This is done both on a microscopic and molecular level. Cell biology research encompasses both the great diversity of single-celled organisms like bacteria and protozoa, as well as the many specialized cells in multicellular organisms like humans. Knowing the components of cells and how cells work is fundamental to all biological sciences. Appreciating the similarities and differences between cell types is particularly important to the fields of cell and molecular biology as well as to biomedical fields such as cancer research and developmental biology. These fundamental similarities and differences provide a unifying theme, sometimes allowing the principles learned from studying one cell type to be extrapolated and generalized to other cell types. Hence, research in cell biology is closely related to genetics, biochemistry, molecular biology and developmental biology. - definition adapted from Wikipedia |
Cytology | |
| Cell repository | A resource providing cell lines or isolated cells as opposed to intact tissue samples | Cell bank | |
| Cell-attached single-channel recording protocol | |||
| Cell-detached inside-out single-channel recording protocol | |||
| Cell-detached inside-out single-channel recording protocol (birnlex 2285) | |||
| Cell-detached single-channel recording protocol | |||
| Certificate program | |||
| Chemical supplier | A reagent resource that provides chemicals, e.g., drugs, toxins, buffers | ||
| Chemistry | Branch of science concerned with properties of matter.
(from Egyptian kēme (chem), meaning "earth") is the science concerned with the composition, structure, and properties of matter, as well as the changes it undergoes during chemical reactions. It is a physical science for studies of various atoms, molecules, crystals and other aggregates of matter whether in isolation or combination, which incorporates the concepts of energy and entropy in relation to the spontaneity of chemical processes. Modern chemistry evolved out of alchemy following the chemical revolution (1773). Scientific_disciplines within chemistry are traditionally grouped by the type of matter being studied or the kind of study. These include inorganic chemistry, the study of inorganic matter; organic chemistry, the study of organic matter; biochemistry, the study of substances found in biological organisms; physical chemistry, the energy related studies of chemical systems at macro, molecular and submolecular scales; analytical chemistry, the analysis of material samples to gain an understanding of their chemical composition and structure. Many more specialized disciplines have emerged in recent years, e.g. neurochemistry the chemical study of the nervous system (see subdisciplines). - definition adapted from Wikipedia |
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| Chronic drug administration paradigm | A drug administration paradigm where a drug is given regularly over the course of the experiment, to mimic the effects of chronic drug administration | chronic drug | |
| Citation record | |||
| Citation record element | Those elements defined as a part of the PubMed DTD and used by many literature citation databases | ||
| Classical conditioning paradigm | 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. | ||
| Client program | software client | ||
| Clinical finding | |||
| Clinical pathology | Branch of pathology dealing with clinical aspects of pathological examination of excisions and postmortem analysis. | ||
| Clinical studies | Branch of medicine which is concerned with human clinical trials. From BRO: studies or resources that help investigators do clinical studies or trials, including, epidemiology, outcome development, physiological human studies, interventional trials, etc | ||
| Closed-source license | Any non open source license with restrictions on the source code. | ||
| Code profiler | 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. | ||
| Code testing framework | 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. | ||
| Cognitive psychology | Branch of psychology concerned with the study of cognition | ||
| Comment | Note | ||
| Commercial license | |||
| Community building portal | 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. | ||
| Community building portal resource | A resource that is a gateway site that functions as a point of access to information on the World Wide Web where 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. | Community building portal | |
| Compiler | 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. | ||
| Computational biology | From BRO: is an interdisciplinary field that applies the techniques of computer science, applied mathematics and statistics to address biological problems. The main focus lays on developing mathematical modeling and computational simulation techniques. By these means it addresses scientific reaserch topics with their theoretical and experimental questions without a laboratory. - definition adapted from Wikipedia Note: this class may need to be collapsed with bioinformatics -AB | ||
| Computational hosting | |||
| Computational model | |||
| Computer Axial Tomography imaging protocol | CAT scan CT scan CAT imaging protocol CT Imaging protocol |
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| Conditioned place preference paradigm | A behavioral conditioning paradigm where the animal is presented with a positive stimulus (e.g., food or the effects of a drug of abuse) paired with placement in a distinct environment containing various cues (e.g., tactile, visual, and/or olfactory). When later tested in the normal state, measures of the preference for the compartments previously associated with the positive stimulus, e.g., approaches or amount of time spent in the compartment, serves as an indicator of preference and a measure of reward learning. This paradigm is commonly used in animal studies to evaluate preferences for environmental stimuli that have been associated with a positive or negative reward. The technique is often used to determine the addiction potential of drugs. (adapted from Wikipedia) | environmental place conditioning | |
| Conditioning paradigm | |||
| Conference proceeding | |||
| Confocal imaging protocol | confocal imaging confocal microscopy |
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| Continuing medical education | |||
| Convolution | |||
| Covert braille reading paradigm | A behavioral paradigm in which a subject reads aloud with fingers. | ||
| Covert visual reading paradigm | |||
| Cross-sectional nuclear imaging protocol | |||
| Cuff-electrode recording protocol | Suction electrode recording protocol | ||
| Current clamp voltage recording protocol | |||
| Dark-field imaging protocol | |||
| Data access protocol | |||
| Data acquisition software | 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. | ||
| Data analysis service | A resource that provides data computation service, such as interpreting EEG data. Note, this may include human and/or computer expertise, so that a software tool may be included as a data computational service. | ||
| Data analysis software | 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. | ||
| Data compression software | |||
| Data distribution software | A resource that provides an application or program that is middleware for distributed systems to standardize a data-centric publish-subscribe programming model. | ||
| Data object | Datum | ||
| Data operations software | A resource that provides an application that performs a specific set of operations on acquired data; for example, acquiring the data, processing the data or visualizing the data. | ||
| Data processing software | A resource that provides an application or program that is used to convert or manipulate data into information or knowledge. | ||
| Data processing software resource | Data processing software | please delete, this should be Data processing software, which already exists. | |
| Data resource | A resource that provides data which may be in different forms, e.g., databases vs. datum, and of different types, e.g., images. | ||
| Data set | |||
| Data storage repository | A resource that provides data storage and maintenance of primary data sets, such as a database which accepts submissions of similar data for storage and use. For example, the Cell Centered Database (CCDB) encourages submissions of anatomical images that will increase its holdings. | ||
| Data storage software | A resource that provides an application or program that is used to obtain a permanent holding place for digital data, until purposely erased. | ||
| Data transfer software | 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. | ||
| Data visualization software | 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. | ||
| Database | A data resource that delivers its' data by way of a 'database', which involves a structured data store and interrogation methods for data selection. | ||
| Deductive reasoning paradigm | A behavioral paradigm in which subjects are required to utilize problem-solving skills and logic to determine the correct solution; feedback is sometimes given. | ||
| Degree granting program | |||
| Delayed matching to sample paradigm | 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. | ||
| Delayed response paradigm | |||
| Department portal | 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. | ||
| Developmental biology | Branch of biology concerned with the study of development. | ||
| Developmental psychology | Branch of psychology that deals with development. | ||
| Difference | |||
| Differential interference contrast imaging protocol | Differential interference contrast microscopy Nomarski optical imaging protocol |
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| Diffusion magnetic resonance imaging protocol | |||
| Diffusion tensor imaging protocol | Diffusion tensor imaging DTI |
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| Digital aggregate entity | |||
| Digital entity | A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. | OBI has this as a child of "non realizable information entity"; we may need to update the entire hierarchy (MEM) | |
| Discussion | 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). | ||
| Disease-related portal | A portal where the aggregated resources are restricted to those describing or related to a particular disease. | ||
| Divided auditory attention paradigm | 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. | ||
| Documentation generation software | 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. | ||
| Downloadable database | |||
| Drawing paradigm | A behavioral paradigm in which the subject is asked to draw lines, circles or more complex figures using a pen or stylus. | ||
| Drug administration paradigm | A paradigm in which a drug is administered to a subject through a specific route of administration, over an interval of time and/or at specific intervals, e.g., chronic cocaine paradigm | ||
| Drug withdrawal paradigm | An experimental paradigm where the subject is withdrawn from a drug or other compound | withdrawal | |
| Dublin Core | |||
| Duration (birnlex 2052) | |||
| Dynamic HTML document | |||
| Dynamic causal modeling | |||
| EM imaging protocol | Electron microscopy imaging protocol | ||
| Eating paradigm | Behavioral paradigm in which the subject ingests food. | ||
| Echo planar imaging protocol | EPI | ||
| Electrical recording protocol | Electrophysiology | ||
| Electrocardiography recording protocol | |||
| Electroencephalography recording protocol | |||
| 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) | Electromyography | |
| Electron Energy Loss Spectroscopy imaging protocol | Electron Energy Loss Spectroscopy | ||
| Electron tomography imaging protocol | Electron microscopy imaging protocol in which the specimen is imaged as it is tilted along one or more axes. | ||
| Electron tomography software | |||
| Electronic laboratory notebook | Electronic lab notebook | ||
| Electrophysiology | is the study of the electrical properties of biological cells and tissues. It involves measurements of voltage change or electric current on a wide variety of scales from single ion channel proteins to whole organs like the heart. In neuroscience, it includes measurements of the electrical activity of neurons, and particularly action potential activity. - definition adapted from Wikipedia | ||
| Encoding paradigm | A behavioral paradigm in which a subject views stimuli (words, pictures, letters) and are instructed to memorize them. | ||
| End page | |||
| Endocrinology | is a branch of medicine dealing with disorder of the endocrine system and its specific secretions called hormones. - definition adapted from Wikipedia | ||
| Episodic recall paradigm | A behavioral paradigm in which subjects recall items from episodic memory (autobiographical history, long-term event memories). | ||
| Event-related design | |||
| Experimental paradigm | I'm wondering if this should be a sibling of protocol and not a child? | ||
| Experimental protocol | A resource that provides detailed plans for a scientific experiment, medical trial, or other piece of research. | Protocol | |
| Experimental psychology | Experimental psychologists regard psychology as a natural science; research is conducted with the help of experimental methods. The concern of experimental psychology is discovering the processes underlying behavior and cognition. Experimental psychology is a methodological approach rather than a subject and encompasses varied fields within psychology. Experimental psychologists have traditionally conducted research, published articles, and taught classes on neuroscience, developmental psychology, sensation, perception, attention, consciousness, learning, memory, thinking, and language. Recently, however, the experimental approach has extended to motivation, emotion, and social psychology. - definition adapted from Wikipedia | ||
| Extracellular electrode recording protocol | |||
| Eye Saccade paradigm | A behavioral paradigm in which a subject makes a rapid eye movement relative to an initial target (JB). | ||
| FMRI beta | BETA | ||
| FMRIB software library | |||
| Fear conditioning paradigm | 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. | I am assuming that this is a classical conditioning paradigm, but it needs to be reiewed by behavioral experts | |
| Field electrode recording protocol | Surface electrode recording protocol | ||
| Filtered R-weighted back projection | |||
| Fixation protocol | |||
| Fluorescence labeling protocol | This class should probably be deleted as it is not orthogonal to the axis of classification. | ||
| Fluorescence resonance energy transfer imaging protocol | FRET protocol | ||
| Franklin and Paxinos (2008) | |||
| Functional MRI protocol | |||
| Funding resource | A resource that provides funding opportunities in the form of grants or contracts. | ||
| GNU General Public License | 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. | ||
| GNU Lesser General Public License | |||
| GNU general public license resource | A resource that provides any of the widely used free software licenses, 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. | GPL GNU GPL GNU general public license |
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| GRID computing software | |||
| Gaussian Random Field | 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) | ||
| Gene regulatory network model | Gene network model | ||
| General Linear Model | 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) | ||
| Genetics | |||
| Genome-wide association study | 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) | genetic association study | Not sure whether this is a type of protocol; consider this graph position temporary |
| Genomics | From BRO: The study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. In contrast, the investigation of the roles and functions of single genes is a primary focus of molecular biology and is a common topic of modern medical and biological research. Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome's networks. Adapted from Wikipedia | ||
| Golgi staining protocol | |||
| Government publication | |||
| Graduate program resource | A resource that provides information about educational programs in neuroscience appropriate for graduate students, such as departments of neuroscience that accept graduate students for masters PhD programs. A good example is the directory of graduate training programs in neuroscience. | ||
| Grant number | |||
| Grant sponsor | |||
| Graphical pipeline construction software | |||
| Grid electrode recording protocol | |||
| Group author | collaborative author | ||
| High-pressure liquid chromotography protocol | HPLC protocol | ||
| Histochemical protocol | Histochemistry | ||
| Human subject report | patient report | ||
| Hydrophobicity model | 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. | hydrophobicity analysis hydrophobicity plot |
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| Image | A picture or likeness of somebody or something. | ||
| Image acquisition software | |||
| Image analysis software | image analysis tool image analysis tools |
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| Image processing software | 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. | ||
| Image reconstruction algorithm | Algorithm used to compute a reconstruction from a set of images, e.g., R-weighted back projection. | ||
| Image reconstruction software | |||
| Imaging protocol | Imaging | ||
| Immunocytochemistry protocol | immunocytochemistry | ||
| Immunohistochemical 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) | ||
| Immunolabeling protocol | A means of localizing particular antigens within cells or tissue where the localization depends on the interaction of the binding region of an antibody with a specific epitope. The antibody itself may carry a detectable tag, e.g., a fluorophore, or the tag may be applied through additional steps. | ||
| Immunology | Branch of medicine that concerns itself with the study of the immune system. | ||
| Immunoprecipitation protocol | A protocol employing immunoprecipitation to separate an antigen from a solution based on antibody binding | ||
| In vivo Immunolabeling protocol | An immunolabeling protocol in which the primary antibody is applied to living cells or tissues. | ||
| In-situ hybridization protocol | |||
| Indentifying value | |||
| Independent Components Analysis | 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). | ||
| Informatics | Informatics is a field of study focusing on development and application of information technology. | ||
| Information content entity | |||
| Information entity | |||
| Information portal | 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. Examples of portals are NIF, BIRN, and SfN. Aside from the search engine standard, web portals may offer other services such as news, upcoming events, important resources 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. | ||
| Information portal resource | A resource that is a gateway site that functions as a point of access to information on the World Wide Web. Information portals present information from diverse sources in a unified way. Aside from the search engine standard, information portals may offer other services such as news, upcoming events, important resources 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. Examples include Neuroscience Information Framework, Biomedical Informatics Research Network, and the Society for Neuroscience. | Information portal portal |
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| Institutional portal | A portal where either the aggregated resources are restricted to those describing or associated with the institution or access to the portal is limited to the members of the institution. | ||
| Institutional portal resource | A resource that is a gateway site that functions as a point of access to information on the World Wide Web where the aggregated resources are restricted to those describing or associated with the institution or access to the portal is limited to the members of the institution. | Institutional portal Institutional website |
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| Instrument manufacture | A resource that produces neuroscience related tools, equipment, or devices. An example is producing a made to order microarray chip. | ||
| Instrument supplier | A resource that provides scientific instruments such as microscopes, amplifiers or dissection tools. For example, Grass Instruments is a site that sells amplifiers and other equipment useful for electrophysiology. | ||
| International Standard Book Number | |||
| International Standard Serial Number | |||
| International standard specification | consortium standard specification | ||
| Intracellular electrode recording protocol | |||
| Intracellular injection protocol | |||
| Intrinsic emission imaging protocol | Intrinsic emission microscopy | ||
| Investigation design | |||
| Investigation record | |||
| Ion channel recording protocol | |||
| Ion-sensitive electrode recording protocol | |||
| Ionic current model | Membrane current model | ||
| Issue | |||
| Item recognition paradigm | 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. | ||
| Job resource | A resource that provides listing or employment opportunities. | ||
| Journal | A periodical or magazine, esp. one published for a special group, learned society, or profession: the Journal of Neuroscience. | ||
| Journal article | A written composition, usually nonfiction, on a specific topic, forming an independent part of a journal or other publication. | ||
| Journal article resource | A bibliographic resource that provides a written composition, usually nonfiction, on a specific topic, forming an independent part of a journal or other publication. | Journal article | |
| Journal resource | A bibliographic resource that provides a periodical or magazine, esp. one published for a special group, learned society, or profession; e.g., The Journal of Neuroscience. | Journal | |
| K-12 program resource | A resource that provides informational about educational programs in neuroscience appropriate for young people, such as educational outreach programs. | ||
| Knowledge environment resource | An information resource that facilitates collaborative knowledge building, decision making, inference or discovery, depending on the epistemological premises and goals of the community. | ||
| Laboratory portal | 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. | ||
| Laser scanning confocal imaging protocol | |||
| Lexical processing algorithm | 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. | Text-mining algorithm | |
| License | Official permission to do something, either from a government or under a law or regulation. | ||
| License resource | A resource that provides official permission to do something, either from a government or under a law or regulation. Note: this is not to be confused with a resource that is covered by a license, which is an attribute. | License | |
| Life Science Indenfier | |||
| Light emitting optical imaging protocol | fluorescence/chemiluminescence/phosphorescence optical imaging protocol | ||
| Light transmission optical imaging protocol | |||
| Link aggregation site | A web site containing a curated set of links typically focussed on a particular topic or set of related topics. Link classification site Link clustering site |
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| List | Listserv or discussion group (as an entity, as opposed to a single discussion thread which uses the value "discussion") (NLM). | ||
| Listserv | Listserv of discussion group (as an entity, as opposed to a single discussion thread which uses the value "discussion"). | ||
| Literature corpus | literature | ||
| Longitudinal magnetization | |||
| Longitudinal relaxation time | |||
| Longitudinal study design | A longitudinal study is a correlational research study that involves repeated observations of the same items over long periods of time , A longitudinal study is a correlational research study that involves repeated observations of the same items over long periods of time, A longitudinal study is a correlational research study that involves repeated observations of the same items over long periods of time | ||
| MIT License | |||
| MNI Atlas | |||
| MRI 2D image | |||
| MRI 3D image | |||
| MRI protocol | A protocol that employs magnetic resonance imaging | MRI protocol | |
| Macro-electrode recording protocol | |||
| Macroscopic anatomical structure model | anatomical model | ||
| Material analysis service | A resource that provides data from any material sample that was given to the service provider. This can also be a service which performs an experiment such as electrophysiological examination of LTP magnitude in the presence of a drug given to the service provider. Viewing this as an input/output relationship the input would involve a drug and the ouput would be data such as a dose response curve. | ||
| Material resource | A resource that provides access to physical materials like reagents, tissue samples or organisms. | ||
| Material service resource | A resource that provides a service the output of which is a material object. That material object might be an instrument, a chemical, or an animal. | ||
| Material storage repository | A resource that provides material storage, maintenance and retrieval, such as the Harvard brain tissue bank. | Material storage repository | |
| Mathematics | The study of numbers. | ||
| Medical school program resource | A resource that provides information about educational programs in neuroscience appropriate for medical students, such as departments of neuroscience or neurology in medical schools. A good example is the Stanford Department of Neurology and Neurological Sciences. | ||
| Medicine | |||
| Meeting resource | A resource that provides information about professional meetings, such as SFN's Neuroscience meeting. | ||
| Metabolomics | |||
| Meyer et al 1989 | |||
| Micro-electrode recording protocol | |||
| Microbiology | |||
| Microscopy contrast enhancement protocol | I would change the label of this class to "Contrast enhancement protocol" because these techniques can be used without microscopy | ||
| Mismatch negativity paradigm | behavioral paradigm that assesses a response to non-attended stimuli which are dissimilar to the majority of stimuli presented. | ||
| Molecular biology | is the study of biology at a molecular level. The field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis as well as learning how these interactions are regulated.
Writing in Nature, William Astbury described molecular biology as: "(...)not so much a technique as an approach, an approach from the viewpoint of the so-called basic sciences with the leading idea of searching below the large-scale manifestations of classical biology for the corresponding molecular plan. It is concerned particularly with the forms of biological molecules and(...) is predominantly three-dimensional and structural—which does not mean, however, that it is merely a refinement of morphology. It must at the same time inquire into genesis and function." - definition adapted from Wikipedia |
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| Molecular neuropharmacology | Branch of neuropharmacology dealing with molecular interactions. | ||
| Molecular neuroscience | is the study of the central nervous system at a molecular level. | ||
| Mozilla Public License | |||
| Multi-cell model | tissue model | ||
| Multiphoton imaging protocol | An imaging protocol that produces images using a microscopy in multiphoton mode | Multiphoton microscopy Multiphoton imaging |
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| Multiple electrode extracellular recording protocol | |||
| Multiple-electrode voltage clamp recording protocol | |||
| Myelin staining protocol | |||
| Narrative object | |||
| Narrative resource | An information resource that provides a literary work, book, story or account of events, experiences, or the like, whether true or fictitious. | ||
| National standard specification | government standard specification | ||
| Natural language processing algorithm | 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. | ||
| Natural science | Branch of science that usually includes: Biology, Medicine, Botany, Zoology, and Pathology. | ||
| Nerve cell functional model | computational neuronal model neuronal physiological model |
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| Nerve cell structural model | neuronal structure model | ||
| Network analysis software | pathway analysis software | ||
| Network graph visualization software | |||
| Network interaction model | |||
| Neural circuit model | neural network model circuit model nerve cell circuit model |
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| Neuroanatomy | Branch of anatomy concerned with the nervous system. | ||
| Neurobiology | Field of biology that is concerned with the study of the nervous system. | ||
| Neurochemistry | Branch of science concerned with properties of matter that resides in the central nervous system. | ||
| Neuroeconomics | Branch of economics that is concerned with neuroscience. | ||
| Neuroendocrinology | is a branch of medicine dealing with disorder of the endocrine system and its specific secretions called hormones, which effect the nervous system. | ||
| Neuroethology | Branch of ethology which uses an evolutionary and comparative approach to the study of animal behavior and its underlying mechanistic control by the nervous system. | Ethology | |
| Neurogenetics | Studies the role of genetics in the development and function of the nervous system. - adapted from Wikipedia | ||
| Neuroimmunology | Branch of immunology concerned with the connection of the nervous system and the immune system. | ||
| Neurology | Medical specialty dealing with disorders of the nervous system. | ||
| Neuropathology | Subfield of pathology dealing with excised or postmortem examination of the nervous system tissues. | Psychopathology | |
| Neuropharmacology | Subdiscipline in pharmacology concerned with drug-induced changes in the functioning of cells in the nervous system. | Psychopharmacology | |
| Neurophysiology | A discipline which utilizes physiological techniques to study the nervous system. | Psychophysiology | |
| Neuropsychology | Branch of psychology that studies the structure and function of the brain related to specific psychological processes and overt behaviors. | ||
| Neuroscience | Branch of science that deals with the study of the nervous system. | ||
| Neurosurgery | The surgical discipline focused on treating nervous system disease. | Neurosurgeon | |
| Neurovirology | The study of viruses and virus-like agents and how these effect the central nervous system. | ||
| Nissl staining protocol | |||
| Non-realizable information entity | |||
| Nuclear medicine imaging protocol | NMR | ||
| Number of b NE 0 volumes | number of diffusion-weighted directions multiplied by the number of non-zero b-values | ||
| Number of b values | number of distinct b-values used | ||
| Number of diffusion-weighted directions | the number of gradient amplitude vectors used in each complete set of diffusion-weighted data | ||
| Nursing | From BRO: medical profession focused on patient care. | ||
| Oddball discrimination paradigm | A behavioral paradigm that assesses a response to non-attended stimuli which are dissimilar to the majority of stimuli presented | ||
| Oncology | is the branch of medicine dealing with tumors (cancer). A medical professional who practices oncology is an oncologist. | ||
| Ontology | 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 | ||
| Open source license resource | A resource that provides 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). | Open source license | |
| Open-source license | 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). | ||
| Ophthalmology | Branch of medicine which deals with the diseases and surgery of the visual pathways, including the eye, brain, and areas surrounding the eye, such as the lacrimal system and eyelids. | ||
| Optical imaging protocol | Light microscopy imaging protocol | ||
| Organism supplier | A resource that provides organisms such as transgenic mice; e.g., the Jackson Laboratory. | ||
| Organization portal | 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. | Institution portal | |
| Outreach program | |||
| PET 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) | Positron Emission Tomography imaging protocol | |
| PH-sensitive electrode recording protocol | |||
| Part-of-speech tagging algorithm | 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. | ||
| Patent | |||
| Pathology | From BRO: (from Greek πάθος, pathos, "fate, harm"; and -λογία, -logia) is the study and diagnosis of disease through examination of organs, tissues, bodily fluids, and whole bodies (autopsies). The term also encompasses the related scientific study of disease processes, called General pathology. Medical pathology is divided in two main branches, Anatomical pathology and Clinical pathology. Veterinary pathology is concerned with animal disease whereas Phytopathology is the study of plant diseases. - definition adapted from Wikipedia | General pathology | |
| Pathway model | signaling pathway model regulatory network model enzyme network model |
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| Patient-support portal | A portal where the aggregated resources are restricted to those describing or related to a particular disease and are specifically targetted to provided information to the community of patients and the families of patients diagnosed with that disease. | Patient-advocate portal | |
| Paxinos, Huang and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999) | |||
| Pediatric neuropsychology | Medical and psychology specialty concerned with the study of brain-behavior relationships in children with known or suspected brain injury, neurodevelopmental disorders, learning disorders or other congenital disorders. | ||
| Pediatrics | From BRO: Branch medicine that deals with the medical care of infants, children, and adolescents. | Paediatrics | |
| People resource | A resource that provides access to individual people based, for example, on expertise or affiliation. | ||
| Personal communication | Informal communication | ||
| Pharmacokinetics pharmacodynamics | From BRO: (in Greek: “pharmacon” meaning drug and “kinetikos” meaning putting in motion, the study of time dependency; sometimes abbreviated as “PK”) is a branch of pharmacology dedicated to the determination of the fate of substances administered externally to a living organism. In practice, this discipline is applied mainly to drug substances, though in principle it concerns itself with all manner of compounds ingested or otherwise delivered externally to an organism, such as nutrients, metabolites, hormones, toxins, etc. Pharmacokinetics is often studied in conjunction with pharmacodynamics. Pharmacodynamics explores what a drug does to the body, whereas pharmacokinetics explores what the body does to the drug. Pharmacokinetics includes the study of the mechanisms of absorption and distribution of an administered drug, the rate at which a drug action begins and the duration of the effect, the chemical changes of the substance in the body (e.g. by enzymes) and the effects and routes of excretion of the metabolites of the drug. - definition adapted from Wikipedia | ||
| Pharmacology | is concerned with drug-induced changes in the functioning of cells. | Neuropharmacology Psychopharmacology |
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| Phase contrast imaging protocol | Phase contrast microscopy | ||
| Philosophy | is the study of general and fundamental problems concerning matters such as existence, knowledge, truth, beauty, law, justice, validity, mind, and language. Philosophy is distinguished from other ways of addressing these questions (such as mysticism or mythology) by its critical, generally systematic approach and its reliance on reasoned argument. The word is of Greek origin: φιλοσοφία, philosophía, "love of wisdom". - adapted from Wikipedia | ||
| Phoenetics | Branch of linguistics that comprises the study of the sounds of human speech. It is concerned with the physical properties of speech sounds (phones), and the processes of their physiological production, auditory reception, and neurophysiological perception. - definition adapted from Wikipedia | ||
| Physical science | Branch of science that usually includes: Physics, Chemistry and Engineering. | ||
| Physiological model | A mathematical description of the complex physical and temporal dependencies between a set of related biological entities and their immediated environment. | Physiological system model | |
| Physiology | From BRO: Branch of biology dealing with the study of the mechanical, physical, and biochemical functions of living organisms.
Physiology has traditionally been divided between plant physiology and animal and all living things physiology but the principles of physiology are universal, no matter what particular organism is being studied. For example, what is learned about the physiology of yeast cells may also apply to human cells. The field of animal physiology extends the tools and methods of human physiology to non-human animal species. Plant physiology also borrows techniques from both fields. Its scope of subjects is at least as diverse as the tree of life itself. Due to this diversity of subjects, research in animal physiology tends to concentrate on understanding how physiological traits changed throughout the evolutionary history of animals. Other major branches of scientific study that have grown out of physiology research include biochemistry, biophysics, paleobiology, biomechanics, and pharmacology. - definition adapted from Wikipedia |
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| Pipeline processing software | workflow processing software | ||
| Pixel | |||
| Planar imaging protocol | |||
| Plant physiology | Branch of physiology concerned with the study of plants. | ||
| Polarization contrast imaging protocol | Polarization microscopy | ||
| Polynomial coefficient | scaling coefficient proportionality coefficient |
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| Population genetics | Branch of genetics concerned with genetic variability in a given species. | ||
| Portal | 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. | ||
| Portlet component | |||
| Postdoctoral program resource | A resource that provides information about training fellowship programs in neuroscience, for example the Case Western fellowship information site. | ||
| Primary key | |||
| Primatology | is the study of primates. It is a diverse discipline and primatologists can be found in departments of biology, anthropology, psychology and many others. It is a branch of Physical anthropology, which, in itself, studies the genus Homo, especially Homo sapiens. The fields cross over in the study of the hominids, which include all ape-like ancestors of man and the other great apes (for a list of common ancestors with other living species see The Ancestor's Tale). Modern primatology is an extremely diverse science. It ranges from anatomical studies of primate ancestors and field studies of primates in their natural habitat, to experiments in animal psychology and ape language. It has cast an immense amount of light on basic human behaviors and ancient ancestry of these behaviors. - adapted from Wikipedia | ||
| Production service resource | Any resource that provides a service whose intent is to produce a physical object or data, including as a custom micro-array chip, a made to order antibody, or a behavioral dataset. | ||
| Protein folding model | |||
| Protein structure classification | 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. | protein classification | |
| Protocol | |||
| Psychiatry | Medical specialty officially devoted to the treatment, study and prevention of mental disorders. | ||
| Psycholinguistics | Part of psychology concerned with the study of language.
The study of the processes through which learners acquire language. By itself, language acquisition refers to first language acquisition, which studies infants' acquisition of their native language, whereas second language acquisition deals with acquisition of additional languages in both children and adults. One hotly debated issue is whether biology contributes capacities specific to language acquisition, often referred to as universal grammar, or the language acquisition device (LAD). For fifty years, some linguists, notably Noam Chomsky and the late Eric Lenneberg, have argued for the hypothesis that children have innate, language-specific abilities that facilitate and constrain language learning. Other researchers, including Elizabeth Bates, Catherine Snow, Brian MacWhinney, and Michael Tomasello, have hypothesized that language learning results from general cognitive abilities and the interaction between learners and their surrounding communities. Recent work by William O'Grady proposes that complex syntactic phenomena result from an efficiency-driven, linear computational system. O'Grady describes his work as "nativism without Universal Grammar." One of the most important advances in the study of language acquisition was the creation of the CHILDES database by Brian MacWhinney and Catherine Snow. - definition adapted from Wikipedia |
Language acquisition Linguistics Psycholinguist |
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| Psychology | Branch of science concerned with the study of human mental functions and behavior.
(Greek: Ψυχολογία, lit. "study of the mind", from ψυχή psykhē "breath, spirit, soul"; and -λογία, -logia "study of") is an academic and applied discipline involving the systematic, and often scientific, study of human mental functions and behavior. Occasionally, in addition or opposition to employing the scientific method, it also relies on symbolic interpretation and critical analysis, although it often does so less prominently than other social sciences such as sociology. Psychologists study such phenomena as perception, cognition, emotion, personality, behavior and interpersonal relationships. Some, especially depth psychologists, also study the unconscious mind. Psychological knowledge is applied to various spheres of human activity, including issues related to everyday life—such as family, education and employment—and to the treatment of mental health problems. Psychologists attempt to understand the role of mental functions in individual and social behavior, while also exploring the underlying physiological and neurological processes. Psychology includes many sub-fields of study and applications concerned with such areas as human development, sports, health, industry, media and law. Psychology incorporates research from the natural sciences, social sciences and humanities. A professional theorist or practitioner of psychology is called a psychologist. - definition adapted from Wikipedia |
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| Psychometrics | From BRO: is the field of study concerned with the theory and technique of educational and psychological measurement, which includes the measurement of knowledge, abilities, attitudes, and personality traits. The field is primarily concerned with the study of measurement instruments such as questionnaires and tests. It involves two major research tasks, namely: (i) the construction of instruments and procedures for measurement; and (ii) the development and refinement of theoretical approaches to measurement. - definition adapted from Wikipedia | ||
| Quantitative value | |||
| R-weighted back projection | 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. | ||
| Radiographic imaging protocol | |||
| Radiolabeling protocol | |||
| Reading paradigm | A behavioral paradigm in which a subject is asked to read either silently (covert) or aloud (overt) | ||
| Reagent manufacture | A resource that produces a product whose role is that of a reagent. Examples include producing antibodies to a particular antigen (Charles River custom antibody service) or designing drugs which fit a receptor. Note, for simplicity of definitions all molecules including antibodies and toxins are considered reagents even though some may have an organismal origin. | NOTE for ontologists: This will probably be an inferred class. | |
| Reagent supplier | A material resource that provides access to reagents, such as antibodies or drugs. Included in this definition are sites designed to work with individual service providers of reagents such as ExactAntigen who do not sell antibodies directly, but provide a catalog with pricing information for most commercial and noncommercial antibody providers. | ||
| Reconstituted bilayer electrical recording protocol | |||
| Reconstituted bilayer single-channel patch recording protocol | |||
| Reference atlas | |||
| Region of Interest | 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) | ||
| Registration software | |||
| Relational database | 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? | ||
| Relaxation time | |||
| Rendering software | 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. | ||
| Report | |||
| Residency | |||
| Resource Descriptor | Resource | Please change the preferred label to "Resource" | |
| Restricted license resource | A resource that provides any license with restrictions on the source code above those of an open source license. | Restricted license | |
| SEM imaging protocol | Scanning electron microscopy imaging protocol | ||
| SPECT 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) | Single Photon Emission Computed Tomography imaging protocol | |
| STEM imaging protocol | Scanning transmission electron microscopy imaging protocol | ||
| Scientific discipline | a branch of scientific knowledge. | Academic discipline Area of research Area of study |
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| Segmentation software | A tool or resource that comprises computer software functionality, including self-contained executable, software development support or libraries that are invoked by the user on local machines or remote servers (NITRC). | ||
| Semi structured knowledge resource | |||
| Sensorimotor paradigm | A behavioral paradigm that requires the subject respond to stimuli that are dissimilar to the majority of stimuli presented | ||
| Sequence analysis software | 1D correlative analysis software sequence pattern analysis software |
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| Sequence homology model | A mathematical description of the phylogenetic relatedness of a set of nucleic acid sequences based on a correlative comparison of linear sequence. | homology model | |
| Sequence-based model | 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. | ||
| Serial item recognition paradigm | 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). | ||
| Serial number | number | ||
| Serial publication element | |||
| Serial title | Journal title | ||
| Service resource | A resource that provides a service such as producing a reagent, performing computational on a cluster or preparing tissue specimens. | ||
| Short course | |||
| Signal processing algorithm | 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. | DSP algorithm Digital signal processing algorithm |
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| Signal processing software | |||
| Simple saccade paradigm | 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) | ||
| Simulation software | 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. | Simulator | |
| Single electrode extracellular recording protocol | |||
| Single tilt electron tomography imaging protocol | Electron tomography protocol where the specimen is imaged at intervals as it is rotated along a single axis | ||
| Single-electrode voltage clamp recording protocol | |||
| Slice preparation protocol | Slice preparation | ||
| Slide | A resource that provides a slide or a slide set, such as power point slides created for an introductory neurobiology course. | Slides | |
| Social psychology | Branch of psychology concerned with the study of social interactions. | Social neuroscience | |
| Social science | Branch of science that usually includes: Psychology, Sociology, Anthropology | ||
| Software application | A resource that provides any tool that functions and is operated by means of a computer, with the purpose of supporting or improving the software user\\\\u2019s work. In other words, it is the subclass of computer software that employs the capabilities of a computer directly and thoroughly to a task that the user wishes to perform. This should be contrasted with system software (infrastructure) or middleware (computer services/ processes integrators) which is involved in integrating a computer\\\\u2019s various capabilities, but typically does not directly apply them in the performance of tasks that benefit the user. In this context the term application refers to both the application software and its implementation. Example: L-Measure. | Application | |
| 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. | ||
| Software development tool | |||
| Software library | 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. | ||
| Software resource | A resource that provides access to software or software functionality, including self-contained executable, software development support or libraries that are invoked by the user on local machines or remote servers. | software tools tool |
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| Software toolkit | 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). | ||
| Source code | A source code module is an information content entity that specifies, using a programming language, some algorithm. | We need to have this in there somewhere, but it looks like OBI has something equivalent "source code module"; they have it classified as an information content entity, so I placed it here . | |
| Spatial value | |||
| Spatially referenced dataset | |||
| Specimen preparation protocol | |||
| Spectroscopic imaging protocol | Spectroscopic microscopy | ||
| Staining protocol | |||
| Standard specification | standard spec standards document |
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| Start page | |||
| Static HTML document | |||
| Statistical Parametric Mapping | 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/). | ||
| Statistics | Branch of mathematics dealing with statistical phenomena. | ||
| 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). | delayed match-to-sample paradigm | |
| Storage service resource | A resource that provides storage of an access to data or specimens. | ||
| Structural MRI protocol | MRI | ||
| Structural model | A coordinate-based mathematical description of a collection of biological structures. | ||
| Structured knowledge resource | |||
| Subject report | |||
| Systems interoperability 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 \\u201cthe 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\\u201d. | ||
| Systems neuroscience | is a subdiscipline of neuroscience which studies the function of neural circuits and systems, most commonly in awake, behaving intact organisms. It is an umbrella term, encompassing a number of areas of study concerned with how nerve cells behave when connected together to form neural networks: vision, for example, or voluntary movement. At this level of analysis, neuroscientists study how different neural circuits analyze sensory information, form perceptions of the external worlds, make decisions, and execute movements. Researchers concerned with systems neuroscience focus on the vast space that exists between molecular and cellular approaches to the brain and the study of high-level mental functions such as language, memory, and self-awareness (which are the purview of behavioral and cognitive neuroscience). Systems neuroscientists typically employ techniques for understanding networks of neurons while they function in vivo (e.g. electrophysiology (single or multi-electrode recording), in vivo imaging, fMRI, PET). The term is commonly used in an educational framework: a common sequence of graduate school neuroscience courses consists of cellular/molecular neuroscience for the first semester, then systems neuroscience for the second semester. It is also sometimes used to distinguish a subdivision within a neuroscience department at an academic institution. - definition adapted from Wikipedia | Systems | |
| T1 relaxation time | |||
| T1 weighted 2D image | |||
| T1 weighted protocol | |||
| T2 relaxation time | transverse relaxation time | ||
| T2 weighted 2D image | |||
| T2 weighted protocol | |||
| T2* relaxation time | T-two-star | ||
| TA | MRI acquitision time | ||
| TE | MRI echo time | ||
| TEM imaging protocol | Transmission electron microscopy imaging protocol | ||
| TR | MRI repetition time | ||
| Talairach-Tournoux Atlas | |||
| Temporal characteristic value | |||
| Text-mining software | |||
| Theology | |||
| Thesis | |||
| Time-series analysis software | |||
| Tissue Bank | A resource that provides tissue samples such as brain samples taken from persons suffering from Alzheimer\\u2019s disease. | ||
| Title | primary title | ||
| Title set | |||
| Topical portal | A portal where the aggregated resources are restricted to those describing or related to a particular topic. | ||
| Topical portal resource | A resource that is a gateway site that functions as a point of access to information on the World Wide Web where the aggregated resources are restricted to those describing or related to a particular topic. | Topical portal Topical website |
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| Total internal reflection imaging protocol | Total internal reflection microscopy | ||
| Toxicology | From BRO: Branch of science which studies the adverse effects of chemicals on living organisms. | ||
| Training resource | A resource that provides access to educational materials or events, such as courses, workshops or graduate programs. | ||
| Training service resource | A resource that provides training to people. | ||
| Transverse magnetization | |||
| Ultrasonographic imaging protocol | * 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) | Echography Ultrasonography Ultrasonic imaging protocol Sonography Ultrasound imaging protocol Ultrasound imaging procedure |
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| Undergraduate program resource | A resource that provides information about educational programs in neuroscience appropriate for undergraduates, such as departments of neuroscience at colleges and universities with an undergraduate major, minor or a psychology department with a focus in neuroscience. For example, the Association of Neuroscience Departments and Programs or individual neuroscience department websites are resources that are targeted for undergraduates interested in neuroscience programs. | ||
| Unfiltered R-weighted back projection | |||
| Unstructured knowledge resource | |||
| Value | |||
| Vector | |||
| Version source control system | 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. | Revision control Version control (system) (source) code management Source control |
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| Video | A resource that provides a video or movie, such as the Michigan State University Brain Biodiversity Bank's MRI movies. | Movie Videos Movies |
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| Virology | The study of viruses and virus-like agents: their structure, classification and evolution, their ways to infect and exploit cells for virus reproduction, the diseases they cause, the techniques to isolate and culture them, and their use in research and therapy. Virology is often considered a part of microbiology or of pathology. - adapted from Wikipedia | ||
| Visual oddball paradigm | An oddball discrimination paradigm where subjects view letters or objects and indicate when they see a target stimulus. | ||
| Voltage clamp current recording protocol | |||
| Volume (birnlex 2391) | |||
| Voxel | |||
| Web accessible database | |||
| Web service | 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. | ||
| Website | A connected group of pages on the World Wide Web regarded as a single entity, usually maintained by one person or organization and devoted to a single topic or several closely related topics. | ||
| Website resource | A resource that is a connected group of pages on the World Wide Web regarded as a single entity, usually maintained by one person or organization and devoted to a single topic or several closely related topics. | Website | |
| Western blot protocol | A protocol that uses a Western blot assay to identify and quantify a binder protein interaction. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane. (Adapted from the Protein Affinity Reagent ontology) | ||
| Whole-cell voltage clamp recording protocol | |||
| Wide-field fluorescence imaging protocol | |||
| Wiki | |||
| Workflow software | A resource that provides an application or program which automates, at least to some degree, a process or processes that requires a series of steps. Workflow are created to quicken processes, help manage relationships, and define the series of requirements. Workflow software works in the background allowing the user to do something simultaneously. | ||
| Zoology | Branch of biology that focuses on the structure, function, behavior, and evolution of animals. The correct pronunciation of "zoology" is /zoʊˈɑləʤɪ/. | zoölogy |

