Content | |
---|---|
Description | Web-based neuroscience resources: data, materials, and tools |
Data types captured | Neuroscience |
Contact | |
Authors | Martone, M.E. |
Release date | 2008 |
Access | |
Data format | html, xml, json, csv |
Website | http://www.neuinfo.org/ |
Web service URL | http://neuinfo.org/developers |
Sparql endpoint | http://neurolex.org/ query sparql end point |
Miscellaneous | |
License | Creative Commons Attribution 3.0 |
Versioning | 6.2 |
Data release frequency | weekly |
Curation policy | continuous human and machine |
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.
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 Health. [1]
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". [2] [3] 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 leads a national collaboration that includes researchers at Yale University, the California Institute of Technology, George Mason University, Harvard, and Washington University.
Unlike general search engines, NIF provides much deeper access to a 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 engines. 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.
The NIFSTD, or NIF Standard Ontology contains many of the terms, synonyms and abbreviations useful for neuroscience, as well as dynamic categories such as defined cell classes based on various properties like neuron by neurotransmitter or by circuit role or drugs of abuse according to the National Institutes on Drug Abuse. Any term (with associated synonyms) or dynamic category (all terms with their synonyms) can be used to simultaneously query all of the data that NIF currently indexes, please find several examples below:
NIF content can be thought of as a Catalog (NIF Registry) and deep database search (NIF Data Federation)
A listing of current resources can be found at www.neuinfo.org/registry
Dataset or Database Name | Type |
---|---|
ZFIN | Database, Data repository, Image collection |
Zebrafish International Resource Center | Biomaterial supply resource, Antibody supplier, Biomaterial analysis service, Organism supplier, Material storage repository |
XNAT Central | Database, Image collection, Data repository |
WormBase | Database, Data repository, Data analysis service, Software resource |
Wired Science Blogs | Blog, Narrative resource |
Wired Science | Blog |
WikiPathways | Wiki |
VMD | Database, Data analysis service |
Visiome Platform | Database, Video resource, Topical portal, Software repository, Data repository, Image |
UniProtKB | Database, Data repository |
UCSF Laboratory for Visual Neuroscience | Laboratory portal, Image, Video resource |
UCLA Multimodal Connectivity Database | Data repository, Data analysis service, Database |
This Week In Science | Podcast |
TheScienceJobs.com | Job resource, Meeting resource, Workshop |
The Guardian: Science Weekly | Podcast |
The Guardian: Science Videos | Video resource |
The Guardian: Science | Blog, Narrative resource |
The Daily Scan | Narrative resource, Blog |
The Cell: An Image Library | Video resource, Image, Data repository |
Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat | Database |
TAIR | Database, Data repository, Data analysis service, Experimental protocol |
T3DB | Database |
Synapse Web | Atlas, Image collection, Training material |
SumsDB (Surface Management System Database) and WebCaret Online Visualization | Atlas, Database, Data repository, Data analysis service |
Simtk.org | Topical portal, Software resource, Data set, Software repository |
SGN | Database, Data repository, Data analysis service, Source code |
SGD | Database, Data repository, Standard specification, Data analysis service |
SfN Brain Briefings | Narrative resource |
SFARI Gene: AutDB | Database, Data repository |
SciLogs | Blog |
Scientific American Observations | Blog |
Scientific American Guest Blog | Blog |
Scientific American Cross-Check | Blog |
Scientific American Bering in Mind | Blog |
ScienceNOW | Narrative resource |
ScienceBlogs: Medicine and Health | Blog |
ScienceBlogs: Life Science | Blog |
ScienceBlogs: Brain and Behavior | Blog |
Science Talk | Podcast |
Science Podcast | Podcast, Narrative resource |
Science Careers | Job resource, Narrative resource |
Sciblogs | Blog |
Royal College of Psychiatrists Podcasts | Podcast |
RGD | Data repository, Web accessible database, Database, Data analysis service, Organism supplier |
RetractionWatch.com | Blog |
Retina Project | Spatially referenced dataset, Image collection |
ResearchCrossroads | Funding resource, Data repository |
Research Blogging | Blog, Database, Data repository |
Reactome | Database, Data analysis service, Web service, Book |
QUEST | Narrative resource, Community building portal, Podcast, Outreach program, Training material, Training resource, Video resource |
PubMed Health | Database |
PubChem | Web accessible database, Database, Service resource, Data repository, 3D spatial image |
Psychoactive Drug Screening Program Ki Database | Database, Data repository |
Pseudomonas Genome Database | Database, Data analysis service |
Protocol Online - Your labs reference book | Experimental protocol |
PomBase | Database, Data repository |
PolygenicBlog | Blog |
PLoS Blogs | Blog |
Physiobank | Database |
PharmGKB | Web accessible database, Database, Data repository, Web service, Data set |
PDB | Database, 3D spatial image, Web service, Data analysis service, Data repository |
Oxford Science Blog | Blog |
Open Access Series of Imaging Studies | Atlas, Database |
One Mind Biospecimen Bank Listing | Tissue bank, Cell repository, Brain bank, Data repository |
OMIM | Database |
Olfactory Receptor DataBase | Database, Data analysis service, Data repository |
Olfactory Bulb Odor Map DataBase (OdorMapDB) | Atlas, Database |
Now at NEJM | Blog |
Novus Biologicals | Antibody supplier, Biomaterial manufacture, Material resource, Service resource |
NITRC-IR | Image collection, Data repository |
NITRC | Community building portal, Software repository |
NIMH Chemical Synthesis and Drug Supply Program | Reagent manufacture, Reagent supplier |
NIH VideoCasting | Video resource, Podcast, Data repository |
NIH Neuroscience Microarray Consortium | Data analysis service, Database, Data repository |
NIGMS Human Genetic Cell Repository | Cell repository, Biospecimen repository |
NIF Registry Automated Crawl Data | Data set |
NIF Registry | Database |
NIF Integrated Video View | Video resource |
NIF Integrated Software View | Software resource |
NIF Integrated Podcasts View | Podcast |
NIF Integrated Nervous System Connectivity View | Database |
NIF Integrated Manually Extracted Annotation | Data set |
NIF Integrated Jobs | Job resource |
NIF Integrated Gene-Disease Interaction | Database |
NIF Integrated Disease View | Database |
NIF Integrated Clinical Trials | Database |
NIF Integrated Brain Gene Expression View | Database |
NIF Integrated Blogs | Blog, Narrative resource |
NIF Integrated Auto-Extracted Annotation | Data set |
NIF Integrated Animal View | Organism supplier |
New York Times - Well | Blog |
New Scientist Jobs | Job resource, Postdoctoral program resource |
Neuroskeptic | Blog |
NeuroPod | Podcast |
NeuronDB | Database, Data analysis service |
NeuroMorpho.Org | Data repository, Database, Image collection |
NeuroMab | Antibody supplier |
Neurology Podcast | Podcast |
Neurofed | People resource |
neuroelectro | Database |
Neurodatabase.org | Database, Data repository |
NCBI Protein | Database |
NCBI Gene | Web accessible database, Database |
NCBI | Data repository, Data analysis software |
Naturejobs | Job resource, Narrative resource |
Nature Podcast | Podcast |
Nature Network Blogs | Blog |
Naturally Selected | Blog |
National Institutes of Health Stem Cell Tables | Data set |
National Institutes of Health Research Portfolio Online Reporting Tool | Database |
National Academy of Sciences Podcasts | Podcast |
MPO | Ontology |
Mouse Genome Informatics Transgenes | Semi structured knowledge |
Monster | Job resource |
ModelDB | Simulation software, Database, Data repository, Source code |
MNI Podcasts | Podcast |
Mind Hacks | Blog, Book |
MGI | Database, Data repository |
LabSpaces | Narrative resource, Blog, Community building portal, Experimental protocol |
Kawasaki Disease Dataset2 | Data set |
Kawasaki Disease Dataset1 | Data set |
Journal of Visualized Experiments | Journal, Video resource, Experimental protocol |
Journal of Comparative Neurology Antibody database | Database |
jobs.ac.uk | Job resource |
JCVI CMR | Database, Data analysis service |
IXI dataset | Data set, Image collection |
It Takes 30 | Blog, Job resource |
Internet Brain Volume Database | Database, Web service, Data analysis service |
International Mouse Strain Resource | Organism supplier, Data repository |
Indeed | Job resource |
Immune Epitope Database and Analysis Resource | Database, Data analysis service, Web service |
Human Brain Atlas | Atlas, Video resource, Training resource |
HomoloGene | Web accessible database, Database, Service resource |
Health.Data.gov | Database, Software resource, Structured knowledge |
Hays | Job resource, Service resource |
H2SO4Hurts | Blog |
Gray Matters | Podcast, Narrative resource |
Grants.gov | Funding resource |
Gramene | Database, Web service, Data analysis service |
goCognitive | Training material, Video resource, Assessment test provider |
GO | Ontology, International standard specification, Database, Data repository |
Glomerular Activity Response Archive | Database, Image collection, Data analysis service |
GENSAT - Gene Expression Nervous System Atlas | Atlas, Organism supplier, Biomaterial manufacture, Biomaterial supply resource |
Genomes Unzipped | Blog, Data set, Source code |
Genetic Analysis Software | Data set, Software resource, Software repository |
GeneNetwork | Database, Data repository |
GeneDB Tbrucei | Database, Data analysis service |
GeneDB Pfalciparum | Database |
GeneDB Lmajor | Database, Data analysis service |
Gene Weaver | Web accessible database, Data analysis service, Data repository |
Gene Ontology Tools | Data set, Software repository, Registry |
Gene Expression Omnibus | Database, Data repository, Service resource, Data set |
Gemma | Database, Data processing software, Data repository |
Gait in Parkinsons Disease | Database |
Gait Dynamics in Neuro-Degenerative Disease Data Base | Database, Web accessible database |
FLYBASE | Database, Data repository, Organism-related portal, Data analysis service |
F1000 Posters | Storage service resource, Narrative resource, Analysis service resource |
Expression Atlas of the Marmoset | Data set, Expression atlas |
EU Clinical Trials Register | Database |
EEGbase | Data repository, Database |
EcoCyc | Database |
DrugBank | Database |
Drug Related Gene Database | Database, Data repository |
Disorders index from the National Institute of Neurological Disorders and Stroke (NINDS) | Data set |
Discover Magazine | Narrative resource, Blog, Podcast, Image collection |
DISCO | Software resource, Service resource |
DictyBase | Database, Biospecimen repository |
Daring Nucleic Adventures - genegeek | Blog |
CRCNS | Data set, Data repository, Funding resource |
Comparative Toxicogenomics Database | Database, Data analysis service |
CoCoMac (Collations of Connectivity Data on the Macaque Brain) | Database, Data visualization software, Data repository, Bibliography |
Clinicaltrials.gov: A Service Of The National Institutes Of Health | Database, Data repository |
Clinical Trials Network (CTN) Data Share | Data set |
ChEMBLdb | Web accessible database, Database |
CHEBI | Database, Ontology |
Cerebellar Platform | Database, Software repository, Data repository, Data analysis software |
CENtral Science | Blog |
Cell Centered Database | Database, Data repository, Image collection |
Cassandras Tears | Blog |
Candida Genome Database | Database, Data repository, Data analysis service |
Caenorhabditis Genetics Center | Organism supplier, Biospecimen repository, Standard specification, Cell repository |
Brede Database | Database, Data analysis service |
BrainSpan: RNA-Seq exons summarized to genes | Expression atlas |
BrainSpan: RNA-Seq exons | Expression atlas |
BrainSpan: Exon microarray summarized to probe sets | Expression atlas |
BrainSpan: Exon microarray summarized to genes | Expression atlas |
BrainPod | Podcast |
BrainMaps.org: High Resolution Brain Atlases | Atlas, Data analysis service |
BrainInfo | Atlas, Database, Topical portal, Standard specification |
Brain Science Podcast | Podcast, Narrative resource |
Brain Architecture Management System | Database, Ontology, Data repository |
BMI (Brain Machine Interface) Platform | Data repository, Database, Bibliography, Software repository |
Bloomington Drosophila Stock Center | Organism supplier, Material storage repository |
BioPortfolio | Narrative resource, Blog, Job resource, Database, Portal |
BioNOT | Database |
Biointeractive | Training resource, Video resource, Podcast, Training material |
BioGRID | Database, Web service, Software resource, Data repository |
Biocompare | Database, Antibody supplier |
Beta Cell Biology Consortium | Database, Reagent supplier |
BAMS Nested Regions | Database |
BAMS Connectivity | Database |
BAMS Cells | Database |
Avian Brain Circuitry Database | Spatially referenced dataset, Data repository, Image |
ASPGD | Database, Data repository, Data analysis service |
ASAP | Database, Data repository, Data analysis service |
Antibody Registry | Database |
AmiGO | Software application, Database, Data analysis service |
American Journal of Psychiatry Podcasts | Podcast |
Allen Mouse Brain Connectivity Atlas | Spatially referenced dataset |
Allen Mouse Brain Atlas | Atlas, Database |
All In The Mind | Podcast |
Aging Genes and Interventions Database | Database, Data repository |
Addgene | Topical portal, Biospecimen repository, Biomaterial supply resource |
Access-ScienceJobs.co.uk | Job resource, Narrative resource |
A Lady Scientist | Blog |
60-Second Mind | Podcast |
The idea of NIF is that while scientific databases do have a plethora of interfaces, some quite complex, there should be a uniform way of looking at them and searching though them. This uniform search idea has been extended to services so that developers can take advantage of the work done at NIF to enhance their own applications by gaining access to all of the data available through the NIF interface.
When data is made public via NIF, it also becomes immediately available via web services. These RESTful web services can be thought of as programming functions that can be built into other applications. Currently, the data can be queried and pulled as an XML feed and several other sites are now pulling NIF data via services, including DOMEO and Eagle i. Developers can learn how to access data by viewing the WADL file available at http://neuinfo.org/developers
Below are some public RESTful services that can be accessed by students or used in building applications:
* http://nif-services.neuinfo.org/servicesv1/v1/annotate?content=The%20cerebellum%20is%20a%20wonderful%20thing&longestOnly=true
The url contains the text you want to annotate, the input, which is "The cerebellum is a wonderful thing". To change this you can try to use any other text. The output from the service will return the sentence with a SPAN tag denoting that it recognized the term cerebellum and it is a type of anatomical_structure. The terms that are not recognized are returned without span tags. Note, the longestOnly=true parameter is optional it means that only the longest set of terms will be recognized an in this example it makes no difference, but in terms like hippocampal neuron it will only return one response.
Developers can use the span tags to bring back information about the recognized term because the identifier is unique and linked to definitions, synonyms, other brain regions and in some cases images: For a human readable version see
* http://neurolex.org/wiki/Birnlex_1489
For a machine readable version see
* http://nif-services.neuinfo.org/ontoquest/concepts/Birnlex_1489?get_super=true
* http://nif-services.neuinfo.org/servicesv1/v1/vocabulary?prefix=hippocampu
The above example shows the term completion for "hippocampu", but you can try to type on the url any other set of letters. The return of the service is a set of terms that matches this string including: Hippocampus and many hippocampal cells.
* http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nlx_144509-1?q=miame
The NIF Registry is a data source and this service will return all items in the registry that match the particular search term. In this case the term is miame, as in the miame standard. To use this data retrieving function you can type query terms into the end of this url in addition to or instead of the term miame. This will work the same way as typing your terms into the search box here:
* https://neuinfo.org/mynif/search.php?q=hippocampus&t=registry
Note, make sure to check the terms and conditions for any source of data, terms and conditions are available as a courtesy in NIF, but you may also check with the individual sources that you wish to incorporate in your applications, all of the above described data is owned by NIF and is covered under the Creative Commons Attribution license, so it can be freely distributed and shared.
A brain is an organ that serves as the center of the nervous system in all vertebrate and most invertebrate animals. It is located in the head, usually close to the sensory organs for senses such as vision. It is the most complex organ in a vertebrate's body. In a human, the cerebral cortex contains approximately 14–16 billion neurons, and the estimated number of neurons in the cerebellum is 55–70 billion. Each neuron is connected by synapses to several thousand other neurons. These neurons communicate with one another by means of long protoplasmic fibers called axons, which carry trains of signal pulses called action potentials to distant parts of the brain or body targeting specific recipient cells.
A neuron, neurone or nerve cell, is an electrically excitable cell that communicates with other cells via specialized connections called synapses. It is the main component of nervous tissue in all animals except sponges and placozoa. Plants and fungi do not have nerve cells.
Neuroscience is the scientific study of the nervous system. It is a multidisciplinary branch of biology that combines physiology, anatomy, molecular biology, developmental biology, cytology, mathematical modeling, and psychology to understand the fundamental and emergent properties of neurons and neural circuits. The understanding of the biological basis of learning, memory, behavior, perception, and consciousness has been described by Eric Kandel as the "ultimate challenge" of the biological sciences.
The striatum, or corpus striatum, is a nucleus in the subcortical basal ganglia of the forebrain. The striatum is a critical component of the motor and reward systems; receives glutamatergic and dopaminergic inputs from different sources; and serves as the primary input to the rest of the basal ganglia.
Spike-timing-dependent plasticity (STDP) is a biological process that adjusts the strength of connections between neurons in the brain. The process adjusts the connection strengths based on the relative timing of a particular neuron's output and input action potentials. The STDP process partially explains the activity-dependent development of nervous systems, especially with regard to long-term potentiation and long-term depression.
An engram is a unit of cognitive information inside the brain, theorized to be the means by which memories are stored as biophysical or biochemical changes in the brain in response to external stimuli.
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.
Basket cells are inhibitory GABAergic interneurons of the brain, found throughout different regions of the cortex and cerebellum.
Purkinje cells, or Purkinje neurons, are a class of GABAergic neurons located in the cerebellum. They are named after their discoverer, Czech anatomist Jan Evangelista Purkyně, who characterized the cells in 1839.
The spinocerebellar tract is a nerve tract originating in the spinal cord and terminating in the same side (ipsilateral) of the cerebellum.
The globose nucleus is one of the deep cerebellar nuclei. It is located medial to the emboliform nucleus and lateral to the fastigial nucleus. This nucleus contains primarily large and small multipolar neurons.
The fastigial nucleus is located in the cerebellum. It is one of the four deep cerebellar nuclei, and is grey matter embedded in the white matter of the cerebellum.
Neuroinformatics is a research field concerned with the organization of neuroscience data by the application of computational models and analytical tools. These areas of research are important for the integration and analysis of increasingly large-volume, high-dimensional, and fine-grain experimental data. Neuroinformaticians provide computational tools, mathematical models, and create interoperable databases for clinicians and research scientists. Neuroscience is a heterogeneous field, consisting of many and various sub-disciplines. In order for our understanding of the brain to continue to deepen, it is necessary that these sub-disciplines are able to share data and findings in a meaningful way; Neuroinformaticians facilitate this.
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.
FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae. For the most extensively studied species and model organism, Drosophila melanogaster, a wide range of data are presented in different formats.
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.
The following outline is provided as an overview of and topical guide to brain mapping:
The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) is a neuroimaging informatics knowledge environment for MR, PET/SPECT, CT, EEG/MEG, optical imaging, clinical neuroinformatics, imaging genomics, and computational neuroscience tools and resources.
SciCrunch is a collaboratively edited knowledge base about scientific resources, 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. In some respect, it is for science and scholarly publishing, 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