The Neuroscience information frameworkA 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

• 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.

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