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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

Building a C. elegans Cell and Anatomy Ontology

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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. - PowerPoint PPT Presentation

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Page 1: 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

Page 2: Building a  C. elegans  Cell and Anatomy Ontology

Sydney Brenner

H. Robert Horvitz John E. Sulston

A Nobel Prize for Worms!

Page 3: Building a  C. elegans  Cell and Anatomy Ontology

Cells

BehaviorGenes

C. elegans Research

Page 4: Building a  C. elegans  Cell and Anatomy Ontology

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.

Page 5: 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

Page 6: Building a  C. elegans  Cell and Anatomy Ontology

Anatomy

Pictures from WormAtlas.org

Page 7: Building a  C. elegans  Cell and Anatomy Ontology

Neural Anatomy

Schematic of nerve bundles in the head

Neural Circuit

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

Page 8: Building a  C. elegans  Cell and Anatomy Ontology

Cells and Nuclei

[Albertson and Thomson, 1975][Ron Ellis]

[Leon Avery]

Page 9: Building a  C. elegans  Cell and Anatomy Ontology

Follow Cells With Green Fluorescent Proteins in a Live Animal

[WormAtlas.org]

Page 10: Building a  C. elegans  Cell and Anatomy Ontology

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

Page 11: 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

Page 12: Building a  C. elegans  Cell and Anatomy Ontology

Adopt a Directed Acyclic Graph Structure

Sense Noxious Stimuli

AB.plpaappaa Amphid Sensilla

Left Lateral Ganglion

Neuron

Page 13: Building a  C. elegans  Cell and Anatomy Ontology

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

Page 14: Building a  C. elegans  Cell and Anatomy Ontology

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.

Page 15: Building a  C. elegans  Cell and Anatomy Ontology

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]

Page 16: Building a  C. elegans  Cell and Anatomy Ontology

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.

Page 17: 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

Page 18: Building a  C. elegans  Cell and Anatomy Ontology

Acknowledgements

• WormBase ConsortiumDrs. Sylvia Martinelli, Paul Sternberg

• GeneOntology Consortium

• WormAtlas Group

• The Worm Research Community