Neuroscience Information Framework

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Neuroscience Information Framework
NIF Screen shot 2014-02-02.png
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
Tools
Miscellaneous
License CC-BY icon.svg
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.

Description[edit]

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.

Goals[edit]

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 neurotrasmitter 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:


Content[edit]

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 150 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. The 'complete' list (as of April 2013) can be found in the table below. An updated list can be found on the Data Federation page.
  • 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 NIF Integrated 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 transgenic or inbred 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. The table below was updated April 9th, 2013.
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
ExactAntigen / Labome Database, Reagent supplier, Service resource
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

Data Via Web Services[edit]

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:

  • Annotate any text by using this url:
  * 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 


  • Retrieve neuroscience auto-complete suggestions, e.g.,
  * 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.

  • Retrieve the registry items that match a search term:
  * 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.

Notes and references[edit]

  1. ^ The NIH Blueprint for Neuroscience Research supports the development of new tools, training opportunities, and other resources to assist neuroscientists in both basic and clinical research.
  2. ^ Under contract HHSN271200577531C from the NIH administered by NIDA
  3. ^ University of California Press Release

See also[edit]

External links[edit]