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The Neuroscience information framework The Neuroscience information framework

The Neuroscience information framework - PowerPoint Presentation

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The Neuroscience information framework - PPT Presentation

A Users Guide NIF Team UCSD Yale Washington U Cal Tech George Mason University SFN Neuroinformatics Committee International Neuroinformatics Coordinating Facility Introduction to the NIF ID: 598019

search nif tools neuroscience nif search neuroscience tools vocabularies disease information resource resources synonyms cerebellum data neurodegenerative registry literature

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Slide1

The Neuroscience information framework

A User’s GuideSlide2

NIF Team

UCSD

Yale

Washington U

Cal Tech

George Mason University

SFN

Neuroinformatics

Committee

International

Neuroinformatics

Coordinating FacilitySlide3

Introduction to the NIF

What is NIF for?

Who is NIF for?

What tools does NIF have?

How do I search for resources using NIF?

How do I register a resource to NIF?

The Neuroscience Information Framework (NIF) is a dynamic inventory of web-based neurosciences data, resources, and tools that scientists and students can access via any computer connected to the Internet. An initiative of the NIH Blueprint for Neuroscience Research, the NIF will advance neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.Slide4

Where do I find…

Data

Software tools

Materials

Services

Training

Jobs

Funding opportunitiesSlide5

Where is this information?

Websites

Databases

Catalogs

Literature

Supplementary materialInformation portals

Search engines like Google do a very good job for some sources, e.g., websites, but not so well for othersSlide6

NIF offers…

Simultaneous search across different types of information sources

Catalog of neuroscience resources (NIF Registry)

Web

Databases

Literature

NIF provides tools for “concept-based search”

“Neurodegenerative disease” = Parkinson’s disease, Huntington’s disease, Alzheimer’s disease…Slide7

Who is NIF for

Our main target is neuroscience researchers, but NIF is for everyone interested in neuroscience

We provide a range of search options and tools, from simple to advanced, that can be used to find and understand informationSlide8

Why is NIF for neuroscientists?

NIF focuses on neuroscience –relevant resources

NIF Registry: Catalog of neuroscience resources assembled by human curators and annotated with a controlled vocabulary

NIF Web: A custom web index built from the NIF Registry

Allows the ability to customize rankings according to neuroscience criteria

NIF Literature: A set of tools for extracting information from the literature tuned for neuroscience

NIF vocabularies: Vocabularies that cover the major domains of neuroscience, contributed to by neuroscientistsSlide9

Training topics

The NIF search features

NIF Tools

NIF Registry

NIF Web

NIF DatabasesNIF Literature

Viewing and building the NIF vocabularies

Registering a resource to NIFSlide10

Searching the NIF

NIF supports multiple types of search:

Simple keyword

e.g., Cerebellum

Boolean queries

Cerebellum AND alpha synuclein

Search tip: To search for compound terms, put the term in “”’

s

.

Cerebellum and “alpha

synuclein

“Concept-based” queries

Synonyms

Categories

Related termsSlide11

Simple search through NIFSlide12

Advanced Search

NIF search can take advantage of the NIF vocabularies for refining or expanding search

Search 1: Searching for synonyms

Search for Parkinson’s disease

Select a term from the NIF vocabularies; NIF automatically searches for synonyms

Search for the alpha synuclein gene

Typing

gene:Snca

into the NIF search box will search for all synonyms of alpha synuclein from Entrez geneSlide13

Search tip: Using synonyms

NIF searches for synonyms, acronyms and abbreviations

Search tip: Watch the acronyms!

Abbreviations like “PD” (Parkinson’s disease) can be non-specific and cause unexpected search results. Sometimes it’s better to remove these from the search box Slide14

Advanced search: Searching for categories

Search 2: Neurodegenerative disease

What I mean is “Types of neurodegenerative disease”

Use the NIF vocabulary expansion to search for subtypes of neurodegenerative disease, e.g., Parkinson’s disease, Huntington’s disease, etc.Slide15

Other relationships

Search Cerebellum

What I mean is cerebellum and parts of cerebellum

The NIF vocabularies also have other relationships, e.g., “part of” that are available for expanding searchSlide16

Combining queries

Gene:Snca

and “Neurodegenerative disease”Slide17

The NIF vocabularies

Molecules

Diseases

Anatomy

Cells

Parts of cells

Techniques

ProtocolsSlide18

How do we build them?

We import existing terminologies/ontologies where they are available

We extend them for neuroscience where necessarySlide19

You’re missing something!

How can we contribute content to the NIF vocabularies?

Answer:

The NeuroLex Wiki!Slide20
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Slide28

How do I register a resource to NIF?

We work with resource providers to integrate their resources into the NIF in a variety of ways

Create a description in the NIF Registry

NIF Resource descriptors provide a controlled vocabulary for annotating resources

Register your database or data with the NIF

NIF has a variety of tools that lets NIF search the deep content of your data resource by creating wrappers that let NIF talk to your resource

Annotating your data with the NIF vocabularies lets us search more effectivelySlide29

Where do I find NIF?

http://neuinfo.org

NIF2.0 is scheduled for release in Sept.

Use the NIF search plug in

Available for FirefoxSlide30

How do I get help using the NIF?

Video training materials are

available