Neuroscience Information Framework:  Increasing Access to Neuroscience Resources on the Web
This presentation is the property of its rightful owner.
Sponsored Links
1 / 11

Neuroscience Information Framework: Increasing Access to Neuroscience Resources on the Web PowerPoint PPT Presentation


  • 70 Views
  • Uploaded on
  • Presentation posted in: General

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

Download Presentation

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

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Neuroscience information framework increasing access to neuroscience resources on the web

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

Maryann E.Martone, Ph. D.

University of California, San Diego


Neuroscience information framework

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


Neuroscience information framework increasing access to neuroscience resources on the web

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

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


Neuroscience information framework increasing access to neuroscience resources on the web

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

Comprehensive Ontology

NIFSTD

  • 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

Organism

Macroscopic

Anatomy

Cell

NS Dysfunction

Quality

Molecule

Subcellular Anatomy

NS Function

Investigation

Gene

Techniques

Resource

Instruments

Macromolecule

Molecule Descriptors

Reagent

Protocols


Neuroscience information framework increasing access to neuroscience resources on the web

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


Neuroscience information framework increasing access to neuroscience resources on the web

Makes use of relations in the NIF ontology to broaden search

Supports “AND” and “OR” searches


Moving forward

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


Neuroscience information framework increasing access to neuroscience resources on the web

Cellular

Component

Small

Molecule

Anatomy

Cell Type

CNS

Neuron

Neuro-

transmitter

Transmembrane

Receptor

Purkinje

Cell

Dentate

Nucleus

Neuron

Expressed in

GABA

GABA-R

Cytoarchitectural

Part of

Cerebellar Cortex

Cpllection of

Deep Cerebellar

Nuclei

Presynaptic

density

Terminal Axon

Bouton

Dentate

Nucleus

Purkinje

Cell Layer

Transmitter

Vesicle

Located in


Niflex wiki

NIFLex Wiki


  • Login