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
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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!Slide20Slide21Slide22Slide23Slide24Slide25Slide26Slide27Slide28
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