Neuroscience Information Framework
Encyclopedia
The Neuroscience Information Framework is a repository of global neuroscience
web resources, including experiment
al, clinical, and translational neuroscience database
s, knowledge bases, atlases, and genetic
/genomic
resources.
.
Development of the NIF started in 2008, when the University of California, San Diego
School of Medicine obtained an NIH contract to create and maintain "a dynamic inventory of web-based neurosciences data, resources, and tools that scientists and students can access via any computer connected to the Internet". The project is headed by Maryann Martone, co-director of the National Center for Microscopy and Imaging Research (NCMIR), part of the multi-disciplinary Center for Research in Biological Systems (CRBS), headquartered at UC San Diego. Together with co-principal investigators Jeffrey S. Grethe and Amarnath Gupta, Martone will lead a national collaboration that includes researchers at Yale University
, the California Institute of Technology
, George Mason University
, and Washington University
.
s, NIF provides deeper access to a more focused set of resources that are relevant to neuroscience, search strategies tailored to neuroscience, and access to content that is traditionally “hidden” from web search engine
s. The NIF is a dynamic 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, making it easier to search for and understand the results. NIF will also provide a registry through which resources providers can disclose availability of resources relevant to neuroscience research. NIF is not intended to be a warehouse or repository itself, but a means for disclosing and locating resources elsewhere available via the web
.
A listing of current resources can be found at www.neuinfo.org/registry
Neuroscience
Neuroscience is the scientific study of the nervous system. Traditionally, neuroscience has been seen as a branch of biology. However, it is currently an interdisciplinary science that collaborates with other fields such as chemistry, computer science, engineering, linguistics, mathematics,...
web resources, including experiment
Experiment
An experiment is a methodical procedure carried out with the goal of verifying, falsifying, or establishing the validity of a hypothesis. Experiments vary greatly in their goal and scale, but always rely on repeatable procedure and logical analysis of the results...
al, clinical, and translational neuroscience database
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
s, knowledge bases, atlases, and genetic
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
/genomic
Genomics
Genomics is a discipline in genetics concerning 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,...
resources.
Description
The Neuroscience Information Framework (NIF) is an initiative of the NIH Blueprint for Neuroscience Research, which was established in 2004 by the National Institutes of HealthNational Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
.
Development of the NIF started in 2008, when the University of California, San Diego
University of California, San Diego
The University of California, San Diego, commonly known as UCSD or UC San Diego, is a public research university located in the La Jolla neighborhood of San Diego, California, United States...
School of Medicine obtained an NIH contract to create and maintain "a dynamic inventory of web-based neurosciences data, resources, and tools that scientists and students can access via any computer connected to the Internet". The project is headed by Maryann Martone, co-director of the National Center for Microscopy and Imaging Research (NCMIR), part of the multi-disciplinary Center for Research in Biological Systems (CRBS), headquartered at UC San Diego. Together with co-principal investigators Jeffrey S. Grethe and Amarnath Gupta, Martone will lead a national collaboration that includes researchers at Yale University
Yale University
Yale University is a private, Ivy League university located in New Haven, Connecticut, United States. Founded in 1701 in the Colony of Connecticut, the university is the third-oldest institution of higher education in the United States...
, the California Institute of Technology
California Institute of Technology
The California Institute of Technology is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering...
, George Mason University
George Mason University
George Mason University is a public university based in unincorporated Fairfax County, Virginia, United States, south of and adjacent to the city of Fairfax. Additional campuses are located nearby in Arlington County, Prince William County, and Loudoun County...
, and Washington University
Washington University in St. Louis
Washington University in St. Louis is a private research university located in suburban St. Louis, Missouri. Founded in 1853, and named for George Washington, the university has students and faculty from all fifty U.S. states and more than 110 nations...
.
Goals
Unlike general search engineSearch engine
A search engine is an information retrieval system designed to help find information stored on a computer system. The search results are usually presented in a list and are commonly called hits. Search engines help to minimize the time required to find information and the amount of information...
s, NIF provides deeper access to a more focused set of resources that are relevant to neuroscience, search strategies tailored to neuroscience, and access to content that is traditionally “hidden” from web search engine
Web search engine
A web search engine is designed to search for information on the World Wide Web and FTP servers. The search results are generally presented in a list of results often referred to as SERPS, or "search engine results pages". The information may consist of web pages, images, information and other...
s. The NIF is a dynamic inventory of neuroscience databases, annotated and integrated with a unified system of biomedical terminology] (i.e. NeuroLex
NeuroLex
NeuroLex is a dynamic lexicon of neuroscience concepts. It is a structured as a semantic wiki, using Semantic MediaWiki. NeuroLex is supported by the Neuroscience Information Framework project.- Overview :...
). NIF supports concept-based queries across multiple scales of biological structure and multiple levels of biological function, making it easier to search for and understand the results. NIF will also provide a registry through which resources providers can disclose availability of resources relevant to neuroscience research. NIF is not intended to be a warehouse or repository itself, but a means for disclosing and locating resources elsewhere available via the web
World Wide Web
The World Wide Web is a system of interlinked hypertext documents accessed via the Internet...
.
Content
NIF content can be thought of as a Catalog (NIF Registry) and deep database search (NIF Data Federation)- The NIF Catalog has the largest listing of NIH-funded, neuroscience-relevant resources, including scientific databases, software tools, experimental reagents and tools, knowledge bases and portals, and other entities identified by the neuroscience research community.
A listing of current resources can be found at www.neuinfo.org/registry
- The NIF Data Federation searches deep database content of over 100 databases including: various NCBI databases (PubMed, Gensat, Entrez Gene, Homologene, GEO) as well as many large and small databases that have something to do with neuroscience including Gemma (microarray data from the nervous system), CCDB & CIL (images of neurons and astrocytes, mainly), GeneNetwork, AgingGenesDB, XNAT, 1000 Functional Connectomes and many more.
- In addition many databases that have very similar types of data have been integrated into 'virtual databases', which combine many databases into one table. For example, the AntibodyRegistry combines data from 200+ vendors, the BrainGeneExpression combines gene expression data from Gensat, Alan Brain, and Mouse Genome Informatics, the Connectivity view combines six databases that have statements about nervous system connectivity, the Integrated Animal view combines data about experimental animal catalogs available to researchers from worms, zebrafish, mice and rats. We add more of these as data are registered, so check back to this page to see the current contents.
- For an exhaustive and up to date list of Databases and Datasets registered to NIF please check this page www.neurolex.org.