Neuroscience Information Framework: Increasing Access to Neuroscience

Resources on the Web

Maryann E.Martone, Ph. D.

University of California, San Diego

Neuroscience Information Framework

• Catalog of Neuroscience Resources, annotated with controlled vocabulary

• Annotated archive of Neuroscience literature with tools for mining

• Means to query “hidden” web content in databases

• Interface for searching across multiple types of resources

• Tools for creating discoverable resources• Strong foundation for data integration

http://nif.nih.govhttp://nif.nih.gov

NIF Collaborators

Amarnath Gupta, UCSD, Co Investigator

Jeff Grethe, UCSD, Co Investigator

Gordon Shepherd, Yale University

Perry Miller

Luis Marenco

David Van Essen, Washington University

Erin Reid

Paul Sternberg, Cal Tech

Arun Rangarajan

Hans Michael Muller

Giorgio Ascoli, George Mason University

Sridevi Polavarum

Integrated Search• NIF Registry

~400 web resources annotated by humans with NIF vocabularies

• NIF Neuroscience WebCustom web index built using

open source web tools (Nutch) from the NIF registry

• Neuroscience literature~70,000 articles, full text

indexed using Textpresso tool

• NIF Data FederationWeb accessible databases

registered to NIF mediator for deep content query

Limited number proof of concept

• Other portalsExisting web resources that

are themselves portals to resources

Science.gov

Registering a Resource to NIF

Level 1NIF Registry: high level descriptions from NIF vocabularies supplied by human curators

Level 2Access to deeper content; mechanisms for query and discovery

Level 3Direct query of web accessible databaseAutomated registrationMapping of database content to NIF vocabulary by human

Comprehensive Ontology

• Underlying the NIF is a rich ontology of neuroscience concepts, created from existing community resources

• Built as separate modules covering domains such as anatomy, function, dysfunction, with minimum cross domain properties

• Includes synonyms, lexical variants, UMLS mappings

NIFSTDNIFSTD

MacroscopicAnatomy

MacroscopicAnatomyOrganismOrganism NS

DysfunctionNS

Dysfunction

NS FunctionNS Function

QualityQuality

MoleculeMolecule InvestigationInvestigationSubcellular Anatomy

Subcellular Anatomy

MacromoleculeMacromolecule GeneGene

Molecule DescriptorsMolecule Descriptors

TechniquesTechniques

ReagentReagent ProtocolsProtocols

CellCell

ResourceResource InstrumentsInstruments

• NIF Basic: • Daniel Gardner held a series of workshops with

neuroscientists to obtain sets of terms that are useful for neuroscientists

• NIFSTD (NIF Standardized) (http://purl.org/nif/ontology/nif.owl)• Bill Bug built a set of expanded vocabularies using the

structure of the BIRNLex and the import of existing terminological resources

• Built from existing resources when possible• S

tandardized to same upper ontology

• Provides enhanced coverage of domains in NIF Basic• Provides coverage of domains not included in NIF but covered by existing resources, e.g., molecules

• Encoded in OWL/RDF• Provides mapping to source terminologies, including NIF Basic• Provides synonyms, lexical variants, abbreviations

Building the NIF Vocabularies

Makes use of relations in the NIF ontology to broaden search

Makes use of relations in the NIF ontology to broaden search

Supports “AND” and “OR” searchesSupports “AND” and “OR” searches

Moving Forward

•NIF is redesigning the initial registry to provide better support for level 1, 2 and 3•Population of resources•Services to access resources•Expanding the ontologies•Exploring new interfaces and new ways of query

Anatomy Cell TypeCellular

ComponentSmall

Molecule

Neuro-transmitter

TransmembraneReceptor

GABA GABA-R

TransmitterVesicle

Terminal AxonBouton

Presynapticdensity

PurkinjeCell

Neuron

Dentate NucleusNeuron

CNS

Cpllection of Deep Cerebellar

Nuclei

PurkinjeCell Layer

DentateNucleus

CytoarchitecturalPart of

Cerebellar Cortex

Expressed in

Located in

NIFLex Wiki