building a c elegans cell and anatomy ontology
Download
Skip this Video
Download Presentation
Building a C. elegans Cell and Anatomy Ontology

Loading in 2 Seconds...

play fullscreen
1 / 18

Building a C. elegans Cell and Anatomy Ontology - PowerPoint PPT Presentation


  • 87 Views
  • Uploaded on

Building a C. elegans Cell and Anatomy Ontology. What is it good for? What knowledge is there? What are the practical issues? Progress and future plans. Raymond Lee. November 2002. A Nobel Prize for Worms!. Sydney Brenner. John E. Sulston. H. Robert Horvitz. Cells.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Building a C. elegans Cell and Anatomy Ontology' - lee-humphrey


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
building a c elegans cell and anatomy ontology
Building a C. elegans Cell and Anatomy Ontology
  • What is it good for?
  • What knowledge is there?
  • What are the practical issues?
  • Progress and future plans.

Raymond Lee

November 2002

slide2

A Nobel Prize for Worms!

Sydney Brenner

John E. Sulston

H. Robert Horvitz

slide3

Cells

C. elegans Research

Genes

Behavior

goals
Goals
  • Organize cell and anatomy knowledge into an ontology so that the knowledge is more accessible and computer-friendly.
  • Use the ontology to annotate cell- and anatomy-based experimental results.
building a c elegans cell and anatomy ontology1
Building a C. elegans Cell and Anatomy Ontology
  • What is it good for?
  • What knowledge is there?
  • What are the practical issues?
  • Progress and future plans.

Raymond Lee

November 2002

anatomy
Anatomy

Pictures from WormAtlas.org

neural anatomy
Neural Anatomy

Schematic of nerve bundles in the head

Neural Circuit

[White et al., 1986; WormAtlas.org]

cells and nuclei
Cells and Nuclei

[Leon Avery]

[Albertson and Thomson, 1975]

[Ron Ellis]

development and cell lineage

AB.alaaaa

l

r

r

l

l

r

AB.alaaaalal; AINL

AB.alaaaalpp; ILshL

AB.alaaaarlp; RMEL

AB.alaaaarrp; RMER

Development and Cell Lineage

Time

[Drawing from Nick Rhind]

building a c elegans cell and anatomy ontology2
Building a C. elegans Cell and Anatomy Ontology
  • What is it good for?
  • What knowledge is there?
  • What are the practical issues?
  • Progress and future plans.

Raymond Lee

November 2002

adopt a directed acyclic graph structure

LINEAGE

ORGAN

AB.plpaappaa

Amphid Sensilla

TYPE

POSITION

Neuron

Left Lateral Ganglion

FUNCTION

Sense Noxious Stimuli

Adopt a Directed Acyclic Graph Structure

ASHL

slide13

MS.paapaaa

Lineage

P0

P1’

EMS

MS

MS.p

P

P

P

P

P

P

P

MS.pa

MS.paa

MS.paap

MS.paapa

MS.paapaa

MS.paapaaa

Organ

pharynx

terminal bulb

M1

MS.paapaaa

Cell Type

neuron

motor neuron

M1

MS.paapaaa

MS.paapaaa

i

i

i

i

i

terminal

bulb

corpus

isthmus

a few tricks
A Few Tricks
  • Treat cell lineage as a relationship of nuclei.
  • A nucleus is PART_OF a cell; Two or more nuclei are PART_OF a syncytium.
  • Sexual dimorphism is coded in relation types: DESC_HERM and DESC_MALE.
  • Indeterminacy is represented by indeterminate-state nodes.
slide15

i

i

i

i

Z4.aaa(5L)

D

D

AC nucleus

Cell

P

Z1.ap

Z4.aaa

Z4.apa

Z4.aap

Z4.app

anchor cell

P

Z1.ppp

AC nucleus

Lineage

P

Z1.paa

Z1.ppa

Z1.pap

Z4.pa

Z1.p

Z1.pp

5R

Z1.ppp

H

Z1.ppp(5R)

D

D

AC nucleus

Z4.a

Z4.aa

Z4.aaa

H

anchor cell

Z1.ppx/Z4.aax

Z1.ppx/Z4.aax (5L)

D

Z4.aaa(5L)

D

D

AC nucleus

Z1.ppx/Z4.aax (5R)

D

Z1.ppp(5R)

5L

D

D

AC nucleus

Z4.apa

Z1.ap

Z4.app

Z4.aap

Z4.aaa

Z1.paa

Z1.ppa

Z1.pap

Z4.pa

Z1.ppp

[Kimble and Hirsh, 1979]

progress and plans
Progress and Plans
  • 5000+ nodes and relationships, expect 15,000 to call it ‘complete’.
  • Focus on cell group terms that are of immediate utility in WormBase (e.g. for gene expression annotation).
  • Collaborate with WormAtlas and GMODs to develop high-level terms for comparative anatomy.
  • Integration with life stage ontology.
  • Include information on other nematodes.
building a c elegans cell and anatomy ontology3
Building a C. elegans Cell and Anatomy Ontology
  • What is it good for?
  • What knowledge is there?
  • What are the practical issues?
  • Progress and future plans.

Raymond Lee

November 2002

acknowledgements
Acknowledgements
  • WormBase ConsortiumDrs. Sylvia Martinelli, Paul Sternberg
  • GeneOntology Consortium
  • WormAtlas Group
  • The Worm Research Community
ad