Building a C. elegans Cell and Anatomy Ontology
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Transcript of 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