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Integrating Neuronal Information in WormBase

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~ Raymond Lee ~. Integrating Neuronal Information in WormBase. Database of Caenorhabditis elegans and related nematodes. Why Caenorhabditis elegans. Small free-living round worm, easy to breed and study in the lab. Simple nervous system, 302 or 381 neurons.

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why caenorhabditis elegans
WhyCaenorhabditis elegans
  • Small free-living round worm, easy to breed and study in the lab.
  • Simple nervous system, 302 or 381 neurons.
  • Fully sequenced 100Mb genome, 30% genes have human orthologs. (http://inparanoid.cgb.ki.se/)
challenges we face
Challenges We Face

information

KNOWLEDGE

information

information

information

goals to achieve
Goals To Achieve
  • Comprehensive
  • Integrated
  • Accessible
  • Standardized
slide6

Cells

C. elegans Literature

Physiology

Genes

comprehensive information
Comprehensive Information
  • Gene expression.
  • Neuronal anatomy (schematics, also see WormAtlas).
  • Neuronal connection (incomplete).
  • Neuronal cell function (starting).
integrated data
Integrated Data
  • Low-level integration: data type connections specified in models of an object-oriented database.
  • High-level integration: collated WWW views of major aspects, such as Gene, Sequence, Cell and Function.
standardization
Standardization
  • Allows inter-operability
  • Allows better knowledge transfer.
standardization in wormbase
Standardization in WormBase
  • Shared software tools, familiar interface: GMOD
  • Shared vocabulary: Gene Ontology, Sequence Ontology, Anatomy Ontology(WB-specific so far).
why ontology
Why Ontology?
  • Controlled vocabulary and Semantics
  • A hierarchical classification scheme that helps data acquisition and searching
slide15

Anatomy Ontology: Goals

  • Organize cell and anatomy knowledge such that the knowledge is more accessible and computer-friendly.
  • Use it to annotate cell- and anatomy-based experimental results.
query utilizing ontology
Query Utilizing Ontology
  • What genes are expressed in the left but not in the right amphid neurons?
  • What genes are found in amphid but not other neurons?
easy access
Easy Access
  • Web-based, user-friendly interface.
  • Multiple query tools.
  • Downloadable data sets.
  • Package for local installation.
  • Open-source, open-access software.
literature search tool textpresso
Literature Search Tool: Textpresso
  • Full text search.
  • Category search.
categories
Categories

Locus

let-7

lsy-6

LIN-41

PATHWAY

precursor

upstream cascade

descendants

GENE

Neuron

EMS

HSN AB

ASE

REGULATION

CELL

repress

enhanced up-regulate

inhibition

q what genes are expressed in the asel neuron
Q: What genes are expressed in the ASEL neuron?
  • Keyword search – there is no good query
  • Category search is better:

“gene” + “ASEL”

q what genes are expressed in the asel neuron1
Q: What genes are expressed in the ASEL neuron?
  • Keyword search – there is no good query
  • Category search is better:

“gene” + “ASEL” + “express*”

Even Better!

www wormbase org
www.wormbase.org
  • Comprehensive
  • Integrated
  • Accessible
  • Standardized
wormbasers
WormBasers

Jack Chen Todd Harris Lincoln Stein

Payan CanaranIgor Antoshechkin Carol Bastiani

Juancarlos Chan Wen Chen Eimear Kenny Ranjana Kishore Raymond Lee Hans-Michael Muller

Cecilia Nakamura Andrei Petcherski Erich Schwarz   Paul Sternberg Kimberly Van Auken Daniel Wang

Tamberlyn Bieri Darin Blasiar John Spieth

Keith Bradnam Chao-Kung Chen  Paul Davis

Richard Durbin  Dan Lawson Phil Ozersky  

Anthony Rogers

Jonathan  Hodgkin (CGC) Theresa Stiernagle (CGC)

Funded by US-NIH and British MRC

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