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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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Raymond lee

~ Raymond Lee ~

Integrating Neuronal Information in WormBase


Database of caenorhabditis elegans and related nematodes
Database of Caenorhabditis elegans and related nematodes


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


Integrating neuronal information in wormbase

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


Integrating neuronal information in wormbase

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