Neuroscience Information Framework: Increasing Access to Neuroscience Resources on the Web

1
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

http//nif.nih.gov
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
• 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
Macroscopic Anatomy
Organism
NS Dysfunction
Quality
Cell
NS Function
Molecule
Investigation
Subcellular Anatomy
Gene
Techniques
Resource
Instruments
Macromolecule
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) (http//purl.org/nif/ont
  ology/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

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
(No Transcript)
11
NIFLex Wiki