Neuroscience Information Framework

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.

Neuroscience Information Framework
Content
DescriptionWeb-based neuroscience resources: data, materials, and tools
Data types
captured
Neuroscience
Contact
AuthorsMartone, M.E.
Release date2008
Access
Data formathtml, xml, json, csv
Websitehttp://www.neuinfo.org/
Web service URLhttp://neuinfo.org/developers
Sparql endpointhttp://neurolex.org/ query sparql end point
Miscellaneous
License
Creative Commons Attribution 3.0
Versioning6.2
Data release
frequency
weekly
Curation policycontinuous human and machine

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 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

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:

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 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 9, 2013.
Dataset or Database NameType
ZFINDatabase, Data repository, Image collection
Zebrafish International Resource CenterBiomaterial supply resource, Antibody supplier, Biomaterial analysis service, Organism supplier, Material storage repository
XNAT CentralDatabase, Image collection, Data repository
WormBaseDatabase, Data repository, Data analysis service, Software resource
Wired Science BlogsBlog, Narrative resource
Wired ScienceBlog
WikiPathwaysWiki
VMDDatabase, Data analysis service
Visiome PlatformDatabase, Video resource, Topical portal, Software repository, Data repository, Image
UniProtKBDatabase, Data repository
UCSF Laboratory for Visual NeuroscienceLaboratory portal, Image, Video resource
UCLA Multimodal Connectivity DatabaseData repository, Data analysis service, Database
This Week In SciencePodcast
TheScienceJobs.comJob resource, Meeting resource, Workshop
The Guardian: Science WeeklyPodcast
The Guardian: Science VideosVideo resource
The Guardian: ScienceBlog, Narrative resource
The Daily ScanNarrative resource, Blog
The Cell: An Image LibraryVideo resource, Image, Data repository
Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the RatDatabase
TAIRDatabase, Data repository, Data analysis service, Experimental protocol
T3DBDatabase
Synapse WebAtlas, Image collection, Training material
SumsDB (Surface Management System Database) and WebCaret Online VisualizationAtlas, Database, Data repository, Data analysis service
Simtk.orgTopical portal, Software resource, Data set, Software repository
SGNDatabase, Data repository, Data analysis service, Source code
SGDDatabase, Data repository, Standard specification, Data analysis service
SfN Brain BriefingsNarrative resource
SFARI Gene: AutDBDatabase, Data repository
SciLogsBlog
Scientific American ObservationsBlog
Scientific American Guest BlogBlog
Scientific American Cross-CheckBlog
Scientific American Bering in MindBlog
ScienceNOWNarrative resource
ScienceBlogs: Medicine and HealthBlog
ScienceBlogs: Life ScienceBlog
ScienceBlogs: Brain and BehaviorBlog
Science TalkPodcast
Science PodcastPodcast, Narrative resource
Science CareersJob resource, Narrative resource
SciblogsBlog
Royal College of Psychiatrists PodcastsPodcast
RGDData repository, Web accessible database, Database, Data analysis service, Organism supplier
RetractionWatch.comBlog
Retina ProjectSpatially referenced dataset, Image collection
ResearchCrossroadsFunding resource, Data repository
Research BloggingBlog, Database, Data repository
ReactomeDatabase, Data analysis service, Web service, Book
QUESTNarrative resource, Community building portal, Podcast, Outreach program, Training material, Training resource, Video resource
PubMed HealthDatabase
PubChemWeb accessible database, Database, Service resource, Data repository, 3D spatial image
Psychoactive Drug Screening Program Ki DatabaseDatabase, Data repository
Pseudomonas Genome DatabaseDatabase, Data analysis service
Protocol Online - Your labs reference bookExperimental protocol
PomBaseDatabase, Data repository
PolygenicBlogBlog
PLoS BlogsBlog
PhysiobankDatabase
PharmGKBWeb accessible database, Database, Data repository, Web service, Data set
PDBDatabase, 3D spatial image, Web service, Data analysis service, Data repository
Oxford Science BlogBlog
Open Access Series of Imaging StudiesAtlas, Database
One Mind Biospecimen Bank ListingTissue bank, Cell repository, Brain bank, Data repository
OMIMDatabase
Olfactory Receptor DataBaseDatabase, Data analysis service, Data repository
Olfactory Bulb Odor Map DataBase (OdorMapDB)Atlas, Database
Now at NEJMBlog
Novus BiologicalsAntibody supplier, Biomaterial manufacture, Material resource, Service resource
NITRC-IRImage collection, Data repository
NITRCCommunity building portal, Software repository
NIMH Chemical Synthesis and Drug Supply ProgramReagent manufacture, Reagent supplier
NIH VideoCastingVideo resource, Podcast, Data repository
NIH Neuroscience Microarray ConsortiumData analysis service, Database, Data repository
NIGMS Human Genetic Cell RepositoryCell repository, Biospecimen repository
NIF Registry Automated Crawl DataData set
NIF RegistryDatabase
NIF Integrated Video ViewVideo resource
NIF Integrated Software ViewSoftware resource
NIF Integrated Podcasts ViewPodcast
NIF Integrated Nervous System Connectivity ViewDatabase
NIF Integrated Manually Extracted AnnotationData set
NIF Integrated JobsJob resource
NIF Integrated Gene-Disease InteractionDatabase
NIF Integrated Disease ViewDatabase
NIF Integrated Clinical TrialsDatabase
NIF Integrated Brain Gene Expression ViewDatabase
NIF Integrated BlogsBlog, Narrative resource
NIF Integrated Auto-Extracted AnnotationData set
NIF Integrated Animal ViewOrganism supplier
New York Times - WellBlog
New Scientist JobsJob resource, Postdoctoral program resource
NeuroskepticBlog
NeuroPodPodcast
NeuronDBDatabase, Data analysis service
NeuroMorpho.OrgData repository, Database, Image collection
NeuroMabAntibody supplier
Neurology PodcastPodcast
NeurofedPeople resource
neuroelectroDatabase
Neurodatabase.orgDatabase, Data repository
NCBI ProteinDatabase
NCBI GeneWeb accessible database, Database
NCBIData repository, Data analysis software
NaturejobsJob resource, Narrative resource
Nature PodcastPodcast
Nature Network BlogsBlog
Naturally SelectedBlog
National Institutes of Health Stem Cell TablesData set
National Institutes of Health Research Portfolio Online Reporting ToolDatabase
National Academy of Sciences PodcastsPodcast
MPOOntology
Mouse Genome Informatics TransgenesSemi structured knowledge
MonsterJob resource
ModelDBSimulation software, Database, Data repository, Source code
MNI PodcastsPodcast
Mind HacksBlog, Book
MGIDatabase, Data repository
LabSpacesNarrative resource, Blog, Community building portal, Experimental protocol
Kawasaki Disease Dataset2Data set
Kawasaki Disease Dataset1Data set
Journal of Visualized ExperimentsJournal, Video resource, Experimental protocol
Journal of Comparative Neurology Antibody databaseDatabase
jobs.ac.ukJob resource
JCVI CMRDatabase, Data analysis service
IXI datasetData set, Image collection
It Takes 30Blog, Job resource
Internet Brain Volume DatabaseDatabase, Web service, Data analysis service
International Mouse Strain ResourceOrganism supplier, Data repository
IndeedJob resource
Immune Epitope Database and Analysis ResourceDatabase, Data analysis service, Web service
Human Brain AtlasAtlas, Video resource, Training resource
HomoloGeneWeb accessible database, Database, Service resource
Health.Data.govDatabase, Software resource, Structured knowledge
HaysJob resource, Service resource
H2SO4HurtsBlog
Gray MattersPodcast, Narrative resource
Grants.govFunding resource
GrameneDatabase, Web service, Data analysis service
goCognitiveTraining material, Video resource, Assessment test provider
GOOntology, International standard specification, Database, Data repository
Glomerular Activity Response ArchiveDatabase, Image collection, Data analysis service
GENSAT - Gene Expression Nervous System AtlasAtlas, Organism supplier, Biomaterial manufacture, Biomaterial supply resource
Genomes UnzippedBlog, Data set, Source code
Genetic Analysis SoftwareData set, Software resource, Software repository
GeneNetworkDatabase, Data repository
GeneDB TbruceiDatabase, Data analysis service
GeneDB PfalciparumDatabase
GeneDB LmajorDatabase, Data analysis service
Gene WeaverWeb accessible database, Data analysis service, Data repository
Gene Ontology ToolsData set, Software repository, Registry
Gene Expression OmnibusDatabase, Data repository, Service resource, Data set
GemmaDatabase, Data processing software, Data repository
Gait in Parkinsons DiseaseDatabase
Gait Dynamics in Neuro-Degenerative Disease Data BaseDatabase, Web accessible database
FLYBASEDatabase, Data repository, Organism-related portal, Data analysis service
F1000 PostersStorage service resource, Narrative resource, Analysis service resource
Expression Atlas of the MarmosetData set, Expression atlas
EU Clinical Trials RegisterDatabase
EEGbaseData repository, Database
EcoCycDatabase
DrugBankDatabase
Drug Related Gene DatabaseDatabase, Data repository
Disorders index from the National Institute of Neurological Disorders and Stroke (NINDS)Data set
Discover MagazineNarrative resource, Blog, Podcast, Image collection
DISCOSoftware resource, Service resource
DictyBaseDatabase, Biospecimen repository
Daring Nucleic Adventures - genegeekBlog
CRCNSData set, Data repository, Funding resource
Comparative Toxicogenomics DatabaseDatabase, 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 HealthDatabase, Data repository
Clinical Trials Network (CTN) Data ShareData set
ChEMBLdbWeb accessible database, Database
CHEBIDatabase, Ontology
Cerebellar PlatformDatabase, Software repository, Data repository, Data analysis software
CENtral ScienceBlog
Cell Centered DatabaseDatabase, Data repository, Image collection
Cassandras TearsBlog
Candida Genome DatabaseDatabase, Data repository, Data analysis service
Caenorhabditis Genetics CenterOrganism supplier, Biospecimen repository, Standard specification, Cell repository
Brede DatabaseDatabase, Data analysis service
BrainSpan: RNA-Seq exons summarized to genesExpression atlas
BrainSpan: RNA-Seq exonsExpression atlas
BrainSpan: Exon microarray summarized to probe setsExpression atlas
BrainSpan: Exon microarray summarized to genesExpression atlas
BrainPodPodcast
BrainMaps.org: High Resolution Brain AtlasesAtlas, Data analysis service
BrainInfoAtlas, Database, Topical portal, Standard specification
Brain Science PodcastPodcast, Narrative resource
Brain Architecture Management SystemDatabase, Ontology, Data repository
BMI (Brain Machine Interface) PlatformData repository, Database, Bibliography, Software repository
Bloomington Drosophila Stock CenterOrganism supplier, Material storage repository
BioPortfolioNarrative resource, Blog, Job resource, Database, Portal
BioNOTDatabase
BiointeractiveTraining resource, Video resource, Podcast, Training material
BioGRIDDatabase, Web service, Software resource, Data repository
BiocompareDatabase, Antibody supplier
Beta Cell Biology ConsortiumDatabase, Reagent supplier
BAMS Nested RegionsDatabase
BAMS ConnectivityDatabase
BAMS CellsDatabase
Avian Brain Circuitry DatabaseSpatially referenced dataset, Data repository, Image
ASPGDDatabase, Data repository, Data analysis service
ASAPDatabase, Data repository, Data analysis service
Antibody RegistryDatabase
AmiGOSoftware application, Database, Data analysis service
American Journal of Psychiatry PodcastsPodcast
Allen Mouse Brain Connectivity AtlasSpatially referenced dataset
Allen Mouse Brain AtlasAtlas, Database
All In The MindPodcast
Aging Genes and Interventions DatabaseDatabase, Data repository
AddgeneTopical portal, Biospecimen repository, Biomaterial supply resource
Access-ScienceJobs.co.ukJob resource, Narrative resource
A Lady ScientistBlog
60-Second MindPodcast

Data Via Web Services

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

  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

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