Neuroscience Information Framework
 | |
| 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.
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 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:
- available data about the hippocampus including synonyms
- data about parkinson's disease including archaic synonyms like paralysis agitans
- neocortical neuron a dynamic category includes all neurons that have cell soma in any part of the neocortex
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 9, 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 |
| 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]- ^ The NIH Blueprint for Neuroscience Research Archived 2009-01-30 at the Wayback Machine supports the development of new tools, training opportunities, and other resources to assist neuroscientists in both basic and clinical research.
- ^ Under contract HHSN271200577531C from the NIH administered by NIDA
- ^ University of California Press Release