NeuroLex is a lexicon of neuroscience concepts supported by the Neuroscience Information Framework project, which is funded by the NIH Blueprint for Neuroscience Research.[1] It is the lexical part of the NIF knowledge base, and NeuroLex is intended to make literature review easier and ensure consistent terminology and usage across researchers for the topics of experimental, clinical, and transnational neuroscience, and for genetic and genomic resources.[2] It is structured as a semantic wiki, using Semantic MediaWiki.
NIF provides access to resources that are relevant to neuroscience, search strategies tailored to the field, and access to content that is traditionally "hidden" from web search engines. The Framework is an inventory of neuroscience databases, annotated and integrated with a unified system of biomedical terminology (i.e., NeuroLex). NIF supports concept-based queries across multiple scales of biological structure and multiple levels of biological function.
As part of the NIF, a search interface to many different sources of neuroscience information and data is provided. To make this search more effective, the NIF is constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g. stating that a neuron is a cell. This will allow users to perform more effective searches and to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that are used to describe data.
Content
The initial entries in NeuroLex were built from the NIFSTD ontologies, which subsumed an earlier vocabulary, BIRNLex. It currently contains concepts that span gross anatomy, cells of the nervous system, subcellular structures, diseases, functions, and techniques. NIF relies on community input to add more content and correct the current information.
Computational neuroscience is a branch of neuroscience which employs mathematics, computer science, theoretical analysis and abstractions of the brain to understand the principles that govern the development, structure, physiology and cognitive abilities of the nervous system.
The epithalamus is a posterior (dorsal) segment of the diencephalon. The epithalamus includes the habenular nuclei, the stria medullaris, the anterior and posterior paraventricular nuclei, the posterior commissure, and the pineal gland.
The Society for Neuroscience (SfN) is a professional society, headquartered in Washington, D.C., for basic scientists and physicians around the world whose research is focused on the study of the brain and nervous system. It is especially well known for its annual meeting, consistently one of the largest scientific conferences in the world.
Betz cells are giant pyramidal cells (neurons) located within the fifth layer of the grey matter in the primary motor cortex. These neurons are the largest in the central nervous system, sometimes reaching 100 μm in diameter.
In neuroscience, Golgi cells are the most abundant inhibitory interneurons found within the granular layer of the cerebellum. Golgi cells can be found in the granular layer at various layers. The Golgi cell is essential for controlling the activity of the granular layer. They were first identified as inhibitory in 1964. It was also the first example of an inhibitory feedback network in which the inhibitory interneuron was identified anatomically. Golgi cells produce a wide lateral inhibition that reaches beyond the afferent synaptic field and inhibit granule cells via feedforward and feedback inhibitory loops. These cells synapse onto the dendrite of granule cells and unipolar brush cells. They receive excitatory input from mossy fibres, also synapsing on granule cells, and parallel fibers, which are long granule cell axons. Thereby this circuitry allows for feed-forward and feed-back inhibition of granule cells.
Neuroinformatics is the emergent field that combines informatics and neuroscience. Neuroinformatics is related with neuroscience data and information processing by artificial neural networks. There are three main directions where neuroinformatics has to be applied:
The Blue Brain Project is a Swiss brain research initiative that aims to create a digital reconstruction of the mouse brain. The project was founded in May 2005 by the Brain Mind Institute of École Polytechnique Fédérale de Lausanne (EPFL) in Switzerland. Its mission is to use biologically-detailed digital reconstructions and simulations of the mammalian brain to identify the fundamental principles of brain structure and function.
NeuroNames is an integrated nomenclature for structures in the brain and spinal cord of the four species most studied by neuroscientists: human, macaque, rat and mouse. It offers a standard, controlled vocabulary of common names for structures, which is suitable for unambiguous neuroanatomical indexing of information in digital databases. Terms in the standard vocabulary have been selected for ease of pronunciation, mnemonic value, and frequency of use in recent neuroscientific publications. Structures and their relations to each other are defined in terms of the standard vocabulary. Currently NeuroNames contains standard names, synonyms and definitions of some 2,500 neuroanatomical entities.
The anterior hypothalamic nucleus is a nucleus of the hypothalamus.
The International Neuroinformatics Coordinating Facility is an international non-profit organization with the mission to develop, evaluate, and endorse standards and best practices that embrace the principles of Open, FAIR, and Citable neuroscience. INCF also provides training on how standards and best practices facilitate reproducibility and enables the publishing of the entirety of research output, including data and code. INCF was established in 2005 by recommendations of the Global Science Forum working group of the OECD. The INCF is hosted by the Karolinska Institutet in Stockholm, Sweden. The INCF network comprises institutions, organizations, companies, and individuals active in neuroinformatics, neuroscience, data science, technology, and science policy and publishing. The Network is organized in governing bodies and working groups which coordinate various categories of global neuroinformatics activities that guide and oversee the development and endorsement of standards and best practices, as well as provide training on how standards and best practices facilitate reproducibility and enables the publishing of the entirety of research output, including data and code. The current Directors are Mathew Abrams and Helena Ledmyr, and the Governing Board Chair is Maryann Martone
The Neuroscience Information Framework is a repository of global neuroscience web resources, including experimental, clinical, and translational neuroscience databases, knowledge bases, atlases, and genetic/genomic resources and provides many authoritative links throughout the neuroscience portal of Wikipedia.
MUSIC is software developed and released by the INCF and Royal Institute of Technology (KTH) School of Computer Science and Communication in Stockholm, Sweden. MUSIC is designed for interconnecting large scale neuronal network simulators, either with each other or with other tools. It allows spike events and continuous time series to be communicated between such applications in a cluster computer. The typical usage cases are connecting models developed for different simulators and connecting a parallel simulator to a post-processing tool.
NeuroML is an XML based model description language that aims to provide a common data format for defining and exchanging models in computational neuroscience. The focus of NeuroML is on models which are based on the biophysical and anatomical properties of real neurons.
NEST is a simulation software for spiking neural network models, including large-scale neuronal networks. NEST was initially developed by Markus Diesmann and Marc-Oliver Gewaltig and is now developed and maintained by the NEST Initiative.
Neuronal tracing, or neuron reconstruction is a technique used in neuroscience to determine the pathway of the neurites or neuronal processes, the axons and dendrites, of a neuron. From a sample preparation point of view, it may refer to some of the following as well as other genetic neuron labeling techniques,
The cerebellar glomerulus is a small, intertwined mass of nerve fiber terminals in the granular layer of the cerebellar cortex. It consists of post-synaptic granule cell dendrites and pre-synaptic terminals of mossy fibers.
SciCrunch is a collaboratively edited knowledge base about scientific resources. It is a community portal for researchers and a content management system for data and databases. It is intended to provide a common source of data to the research community and the data about Research Resource Identifiers (RRIDs), which can be used in scientific publications. After starting as a pilot of two journals in 2014, by 2022 over 1,000 journals have been using them and over half a million RRIDs have been quoted in the scientific literature. In some respect, it is for science and scholarly publishing, similar to what Wikidata is for Wikimedia Foundation projects. Hosted by the University of California, San Diego, SciCrunch was also designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas
Upinder Singh Bhalla is an Indian computational neuroscientist, academic and a professor at National Centre for Biological Sciences of the Tata Institute of Fundamental Research. He is known for his studies on neuronal and synaptic signalling in memory and olfactory coding using computational and experimental methods and is an elected fellow of the Indian Academy of Sciences and the Indian National Science Academy. The Council of Scientific and Industrial Research, the apex agency of the Government of India for scientific research, awarded him the Shanti Swarup Bhatnagar Prize for Science and Technology, one of the highest Indian science awards, in 2007, for his contributions to biological sciences. The Infosys Science Foundation awarded him the Infosys Prize 2017 in Life Sciences for his pioneering contributions to the understanding of the brain's computational machinery.
Hierarchical Event Descriptors (HED) is a conceptual and software framework that includes a family of controlled vocabularies for annotating experimental metadata and experienced events on the timeline of neuroimaging and behavioral experiments. The goal of HED is to standardize annotations and the mechanisms for handling these annotations to enable searching, comparing, and extracting data of interest for analysis. HED is the event annotation mechanism used by the Brain Imaging Data Structure (BIDS) standard for describing events.
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