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Neuroscience Information Framework

Search for Neuroscience Resources

Advanced Search · Search Tips · What is this? (example searches: cerebellum, "pulvinar nucleus", gene:snca)

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What is NIF?

A dynamic inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected to the Internet.

An initiative of the NIH Blueprint for Neuroscience Research, the Neuroscience Information Framework advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.

See what else NIF Offers >>

News & Events

NIH Meeting on Informatics for Data and Resource Discovery in Addiction Research
July 2nd, 2010 12:10 PM
The NIH Meeting on Informatics for Data and Resource Discovery in Addiction Research will be held from July 8 – 9, 2010. It will ... read more »
CCDB adds beautiful data set
June 25th, 2010 04:36 PM
The CCDB just released 3 beautiful large scale brain mosaics detailing the distribution of plasma membrane calcium-dependent ATPases ... read more »
NIF Webinar – June 15, 2010 / Topic: URLs and URIs
June 8th, 2010 10:00 AM
The Neuroscience Information Framework (NIF) hosts Webinar series on topics focused on collaborating with NIF, getting involved in ... read more »
Live Session with NIF – June 4, 2010 / Topic: Introduction to NIF
June 2nd, 2010 05:00 PM
An informative session and demonstration on the usage of NIF will be held this Friday,  June 4th, 2010. Please join us to learn ... read more »
The Bioimage Informatics 2010
June 1st, 2010 10:00 AM
The Bioimage Informatics 2010 will be held from September 17 to19 at the new Gates and Hillman Centers of the School of Computer ... read more »

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Current Release Ver. 2.6

Release Notes

Data Federation : 58
NIF Registry : 2,959
Web Index : 1,184,261
NIF Vocabulary : 53,023

Blog

By Anita Bandrowski, Ph.D. Humanity began writing on stone and clay tablets, and then moved to papyrus, paper, and now we write with electrons.  Does it seem that our media for information storage is becoming more flimsy or is it better to search through piles of electrons than card catalogs?  How can we save the wonderful work [...] read more »

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NIF Tools


NIF searches concurrently across multiple resource types, including many that are invisible to traditional search engines.

read more about NIF Tools »

Current resource types include:

  • The NIF Registry
  • NIF Web
  • NIF Data Federation
  • NIF Literature
  • NIF Vocabularies
  • NIF DISCO
  • NIF LinkOut Broker (Beta)
  • MyNIF (Beta)
  • Resource Registration Tools
  • Genetics of Drug Addiction Database

We continue to add new resources to the NIF. Are we missing a resource? Recommend a Resource to us.

NIF Tools

NIF Vocabularies


NIF has developed a comprehensive vocabulary for annotating and searching neuroscience resources. The vocabularies are available for download as an OWL file and also through the NCBO BioPortal.

Please see our Wiki page for help in understanding the structure of the NIF ontologies and loading them into Protege.

A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology that can be used to describe and retrieve neuroscience-relevant resources. With the advent of the World Wide Web—an ever-evolving, easy-to-access, shared information systems--the need for a shared semantic framework for neuroscience has become critically important, all the more so if individual researchers and automated search agents are to access and utilize the most up-to-date information. To address this need, NIF has created NeuroLex, a comprehensive lexicon of common neuroscience terminology woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data.

NeuroLex is built from our core OWL ontology, NIFSTD, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction. NeuroLex also includes detailed concepts for describing experimental techniques and instruments typically employed to carry out neuroscientific studies, as well as concepts for describing digital resources being created throughout the neuroscience community.

Efforts that have used NIFSTD include:

  • NeuroPsyGrid: http://www.neuropsygrid.org
  • NDAR: http://ndar.nih.gov
  • Disease Phenotype Ontology: http://openccdb.org/wiki/index.php/Disease_Ontology

Browse some of the NIF hierarchies on the NeuroLex Wiki:

  • Behavioral Activity
  • Behavioral Paradigms
  • Brain Regions
  • Diseases
  • Molecules
  • Nervous System Function
  • Neuron
  • Subcellular Components
  • Information Resources
  • Qualities

Following best practices established by the Open Biological Ontology (OBO) community, NeuroLex reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources as necessary. Each concept is accompanied by a human readable definition to facilitate the application of NeuroLex to data. Each distinct domain module is represented using the Web Ontology Language (OWL) (Bug et al Neuroinformatics 2008 Sep; 6(3):175-94). NIF is actively looking to expand the content of the NeuroLex and will be working with neuroscientists and others who have created terminology resources for neuroscience to incorporate them into the NIF. We are developing community tools for comment and extension, such as the NeuroLex Wiki. If you have a terminology that covers a domain not currently represented in NIF, please consider working with the NIF to make your vocabulary available. For questions about NeuroLex or making your vocabulary available to NIF, please contact Maryann Martoneat maryann@ncmir.ucsd.edu. Visit our Wiki for the latest developments.
Download the NIFSTD OWL file
Visit NeuroLex
Visit NIF Wiki

NeuroLex
Webinar Archive

NIF Webinars


Upcoming Events


Topic: Bio2RDF
Date: August 24th, 2010
Presenter: Michel Dumontier
URL: http://connect.neuinfo.org/webinar
Dial-In
(toll-free):
866-740-1260
Access Code: 8220739
Description:

Web-based knowledge discoveris ia painful process, one that requires extensive digging through the syntactic web structure. Portals like Pubmed and NCBI can provide us with structured information, but we need to be able to expose the so-called "deep web" to searching. Join us as we discuss the strategies used to integrate the available databases.


Community News Archive

Community News


NHGRI Pledges $25.5M for Electronic Medical Records (EMR) Program
July 19, 2010

Over the next four years the National Human Genome Research Institute plans to move into the next phase of its electronic medical records research program. NHGRI plans to give out around $25.5 million in grants to fund investigators involved starting a coordinating center for research support. the Electronic Medical Records and Genomics network (eMERGE) that was founded in 2007 will continue to play an important part in the combining of electronic medical recods with DNA biorepositories for use in large-scale, high-throughput genomics research projects.

Read more at the Vanderbildt University homepage for the eMERGE project.

Gonzo Labs Presents The "Dance your PhD" Contest
July 10, 2010

From the Gonzo Labs website - The dreaded question. “So, what’s your Ph.D. research about?” You take a deep breath and launch into the explanation. People’s eyes begin to glaze over… At times like these, don’t you wish you could just turn to the nearest computer and show people an online video of your Ph.D. thesis interpreted in dance form? Now you can. And while you’re at it, you can win $1000, achieve immortal geek fame on the Internet, and be recognized by Science for your effort.

Read more at the contest website.

INCF Image Competition - share your best neuroinformatics images and win prizes sponsored by Olympus and Frontiers
July 6, 2010

The INCF recently launched its first Image Competition on the subject of neuroinformatics! Sharing your best neuroinformatics images with the world could win you one of the prizes sponsored by Olympus and Fronteirs. The INCF Olympus Prize is sponsored by Olympus and has a ¥200 000 (about $2130 USD) prize, awarded to the best neuroinformatics image. The images will be judged based on the criteria of originality, informational content, visual impact, educational value and relevance to INCF Programs, activities and objectives. The INCF Frontiers Prize, awarded to the image best fitting the theme "Brain and Art". The short list for this prize will be picked by the Specialty Chief Editors of Frontiers in Neuroscience, and the final image will be selected by a panel of 5 top-class artists. The winning image will be featured on the cover of the "Brain and Art" e-book from Frontiers in Neuroscience. Submit your image by August 1! Winners will be announced at Neuroinformatics 2010 at the end of August.

Read more at the INCF website.

1000 Genomes Project Releases Data From Pilot Projects on Path to Providing Database For 2,500 Human Genomes
June 30, 2010

The 1000 Genomes Project was launched in 2008 with the goal of creating the most complete and detailed map of human variation to date and has reached completion on three pilot projects. The first three completed projects focused on creating a catalogue of genetic variants present in 1% or more of European, African, and East Asian populations that were chosen for the studies. Further development of the catalogue over the next two years will allow researchers to apply the genetic information within to the study of the genetic variation of illness. The data available on the 1000 Genome website and through Amazon Web Services (AWS) includes a catalogue of single nucleotide polymorphisms (SNPs), small insertions and deletions (indels), and large changes in chromosme structure and copy number (copy number variations).

Read Article at the Sanger Institute website.

View further information about the 1000 Genomes project.

ISB, Gladstone Institute Launch Collaboration Focused on Huntington's Disease
June 16, 2010

From GenomeWeb Daily News – The Taube-Koret Center for Huntington’s Disease Research, a subdivision of the Gladstone Institute of Neurological Disease (GIND), is working with the Institute for Systems Biology (ISB) to catalogue the genes and drug targets that are related to the onset and progression of Huntington’s disease by studying the sequences of whole genomes. This is the largest comparative whole-genome study to-date, and is a methodology that can hiopefully be applied to the study of more common and more complex neurodegenerative diseases.

Read Article at GenomeWeb [Premium subscription required]

Drugmakers to Share Data to Speed Brain Research
June 11, 2010

From Reuters - A collaboration between major drug-makers will share data from Alzheimer and Parkinson’s disease clinical trials. The partnership is coordinated by the Coalition Against Major Diseases and will catalogue the data collected from more 4,000 patients with neurodegenerative diseases, allowing researchers access to a more varied and complete body of information than what is available from individual clinical trials. The database aims to reduce the amount of time that clinical trials will take from beginning to end by increasing efficiency through information availability.

Read Article at the Reuters website.

To request access to the database, click here.

Fed-funded Research Impact Tracker in the Works
June 9, 2010

GenomeWeb Daily News, by Matt Jones - A partnership between NIH and FDP (Federal Demonstration Partnership) ha been launched, with the goal of revamping the reporting practices for federally funded research programs. The program, called STAR METRICS (Science and Technology for America's Reinvestment: Measuring the Effect of Research on Innovation), seeks to ease reporting practices for researchers and make them more transparent for reviewers, ultimately creating a system which better allows for the review of government funding allocations. FDP seeks to achieve this in three ways: the standardizing of reporting practices, collaboration with principal investigators, and a push to demonstrate the impact of scientific investments on a "wide range of outcomes." NIH and FDP hope to create an easy to understand system that will give a clearer picture of how the 3.2 billion dollar budget of the NIH is allocated each year, along with what tangible benefits that allocation of these funds provides.

Read Article [ Premium subscription required. ]

View further information about the STAR METRICS project.

NIH Seek Licensee or Collaborators for Drug Discovery Software
June 4, 2010

From Bioform -The National Institutes of Health is seeking licensees or collaborative partners to work on a software package developed by the National Institute on Aging for analyzing "extremely large experimental data sets in a simple yet multidimensional manner." The software, called Omnimorph, nables users to find "extremely subtle" correlated differences between experimental datasets in order to identify "far more drug- or disease-specific factors than other analytical methods currently used. It has already been used to discover novel G protein-independent receptor-based pharmacotherapeutics, which also makes it "a simple and unbiased tool to detect novel and unexpected modes of GPCR-based drug actions. Omnimorph was developed by Stuart Maudsley, a senior investigator at NIA.

Read Article [ Premium subscription required. ]

View further information about the Omnimorph sofware.

Ariadne and Quertle Partnership to Improve Search Results
June 2, 2010

Quertle, LLC and Ariadne announced a technology partnership that will enhance search results from Quertle's search engine for biomedical literature. Ariadne, which designs and develops software and knowledge integration solutions for pharmaceutical and life science researchers and is a leader in the field, will provide proprietary technology and technical resources to Quertle, packaging it as an appliance solution for the pharmaceutical and agricultural industry.

Quertle is a biomedical search engine focused on delivering informative results to biomedical researchers using advanced linguistic technologies, along with an in-depth understanding of the biomedical field. It will be the first biomedical search engine to focus on meaningful relationships.

read more »

Developers Tools


NIF is dedicated to providing open access to data and tools for the community. For Web users, there is a Web portal for searching neurosciences resources and information using simple yet very powerful concept-based searching user interface. For developers, we have published data access and tools using open standards-based application programming interfaces that can be accessed and used programmatically.

NIF provides access to data stored in online neuroscience databases, Web pages, carefully picked and humanly curated catalog of resources, ontologies, and RDF data to the community. The following links provide more information about NIF developers tools:

  • NIF Services

  • SPARQL Endpoint

  • RDF Data:
    NIF is also working on making RDF (Resource Description Framework) version of the data available to the user. RDF is a World Wide Web Consortium’s standard for encoding knowledge in to data. More information about RDF and currently available data in RDF format visit https://confluence.crbs.ucsd.edu/display/NIF/RDF+datasets+on+NIF

  • DISCO

  • NIF LinkOut Broker

Related Links

NIF Wiki
NeuroLex Wiki

Last updated: Friday, 30-Jul-2010 22:03:21 PDT

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Principal Investigators:
Maryann Martone
maryann@ncmir.ucsd.edu

Amarnath Gupta
gupta@sdsc.edu


Jeffrey S. Grethe
jgrethe@ncmir.ucsd.edu

Project Manager:
Ashraf Memon
amemon@sdsc.edu
Curation:
Anita Bandrowski
abandrowski@ucsd.edu
External Relations/Web Support:
Lee G. Hornbrook
lee@ncmir.ucsd.edu