The Neuroscience information
framework
A User’s Guide
NIF Team
•
•
•
•
•
UCSD
Yale
Washington U
Cal Tech
George Mason University
• SFN Neuroinformatics Committee
• International Neuroinformatics Coordinating
Facility
Introduction to the 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.
•
•
•
•
•
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?
Where do I find…
•
•
•
•
•
•
•
Data
Software tools
Materials
Services
Training
Jobs
Funding opportunities
Where is this information?
•
•
•
•
•
•
Websites
Databases
Catalogs
Literature
Supplementary material
Information portals
– Search engines like Google do a very good job
for some sources, e.g., websites, but not so well
for others
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…
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 information
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
neuroscientists
Training topics
• The NIF search features
• NIF Tools
– NIF Registry
– NIF Web
– NIF Databases
– NIF Literature
• Viewing and building the NIF vocabularies
• Registering a resource to NIF
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 terms
Simple search through NIF
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 gene
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
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.
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 search
Combining queries
• Gene:Snca and “Neurodegenerative disease”
The NIF vocabularies
•
•
•
•
•
•
•
Molecules
Diseases
Anatomy
Cells
Parts of cells
Techniques
Protocols
How do we build them?
• We import existing
terminologies/ontologies where they are
available
• We extend them for neuroscience where
necessary
You’re missing something!
• How can we contribute content to the
NIF vocabularies?
– Answer: The NeuroLex Wiki!
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 effectively
Where do I find NIF?
• http://neuinfo.org
– NIF2.0 is scheduled for release in Sept.
• Use the NIF search plug in
– Available for Firefox
How do I get help using the
NIF?
• Video training materials are available