Transcript Neuroscience Information Framework: Increasing Access to Neuroscience Resources on the Web Maryann E.Martone, Ph.

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.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 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
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
Comprehensive Ontology
NIFSTD
Macroscopic
Anatomy
Organism
Subcellular
Anatomy
Molecule
Macromolecule
Molecule Descriptors
•
•
•
NS
Dysfunction
Cell
Gene
NS Function
Techniques
Resource
Reagent
Quality
Investigation
Instruments
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
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) (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
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
Makes use of relations in the NIF ontology
to broaden search
Supports “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 Type
CNS
Neuron
Cellular
Component
Small
Molecule
Neurotransmitter
Transmembrane
Receptor
Purkinje
Cell
Cytoarchitectural
Part of
Cerebellar Cortex
Purkinje
Cell Layer
Dentate
Nucleus
Neuron
Cpllection of
Deep Cerebellar
Nuclei
Expressed in
GABA
Presynaptic
density
Terminal Axon
Bouton
Dentate
Nucleus
Transmitter
Vesicle
Located in
GABA-R
NIFLex Wiki