1. University of California, San Diego
Neuroscience Information Framework: Increasing Access to Neuroscience Resources on the Web
Maryann E.Martone, Ph. D.
University of California, San Diego

2. 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

3. 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

4. Integrated Search NIF Registry NIF Neuroscience Web
~400 web resources annotated by humans with NIF vocabularies
NIF Neuroscience Web
Custom 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 Federation
Web accessible databases registered to NIF mediator for deep content query
Limited number proof of concept
Other portals
Existing web resources that are themselves portals to resources
Science.gov

5. Registering a Resource to NIF
Level 1
NIF Registry: high level descriptions from NIF vocabularies supplied by human curators
Level 2
Access to deeper content; mechanisms for query and discovery
Level 3
Direct query of web accessible database
Automated registration
Mapping of database content to NIF vocabulary by human

6. Comprehensive Ontology
NIFSTD
Organism
Macroscopic
Anatomy
Cell
NS Dysfunction
Quality
Molecule
Subcellular Anatomy
NS Function
Investigation
Macromolecule
Gene
Techniques
Resource
Instruments
Molecule Descriptors
Reagent
Protocols
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

7. Building the NIF Vocabularies
NIF Basic:
Daniel Gardner held a series of workshops with neuroscientists to obtain sets of terms that are useful for neuroscientists
NIFSTD (NIF Standardized) (
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
Standardized 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

8. Makes use of relations in the NIF ontology to broaden search
Supports “AND” and “OR” searches

9. 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

10. Anatomy Cell Type Neuron CNS Cellular Component Small Molecule Neuro-
transmitter
Transmembrane
Receptor
GABA
GABA-R
Transmitter
Vesicle
Terminal Axon
Bouton
Presynaptic
density
Purkinje
Cell
Neuron
Dentate
Nucleus
CNS
Cpllection of
Deep Cerebellar
Nuclei
Cell Layer
Cytoarchitectural
Part of
Cerebellar Cortex
Expressed in
Located in

11. NIFLex Wiki