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

Sydney Brenner

H. Robert Horvitz John E. Sulston

A Nobel Prize for Worms!

Cells

BehaviorGenes

C. elegans Research

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 Ontology

• What is it good for?

• What knowledge is there?• What are the practical issues?

• Progress and future plans.

Raymond Lee

November 2002

Anatomy

Pictures from WormAtlas.org

Neural Anatomy

Schematic of nerve bundles in the head

Neural Circuit

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

Cells and Nuclei

[Albertson and Thomson, 1975][Ron Ellis]

[Leon Avery]

Follow Cells With Green Fluorescent Proteins in a Live Animal

[WormAtlas.org]

Development and Cell Lineage

Time

[Drawing from Nick Rhind]

AB

.alaaaarlp; R

ME

L

AB.alaaaa

l r

l r

AB

.alaaaalal; AIN

L

rl

AB

.alaaaalpp

; ILsh

L

AB

.alaaaarrp; R

ME

R

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

Sense Noxious Stimuli

AB.plpaappaa Amphid Sensilla

Left Lateral Ganglion

Neuron

P1’

LineageP0

EMSMS

MS.pMS.pa

MS.paaMS.paap

MS.paapaMS.paapaa

MS.paapaaa

Organ

Cell Type

pharynxterminal bulb

M1MS.paapaaa

neuronmotor neuron

M1MS.paapaaa

corpus isthmus terminalbulb

MS.paapaaa

MS.paapaaa

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.

5R

5L

LineageZ1.pZ1.pp

Z1.pppZ1.ppp(5R)

Z4.aZ4.aa

Z4.aaa

Z1.ppx/Z4.aax

Cell

Z4.aaa(5L)

Z1.ppx/Z4.aax (5L)Z4.aaa(5L)

Z1.ppx/Z4.aax (5R)Z1.ppp(5R)

[Kimble and Hirsh, 1979]

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 Ontology

• What is it good for?

• What knowledge is there?

• What are the practical issues?

• Progress and future plans.

Raymond Lee

November 2002

Acknowledgements

• WormBase ConsortiumDrs. Sylvia Martinelli, Paul Sternberg

• GeneOntology Consortium

• WormAtlas Group

• The Worm Research Community