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.

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Building a C. elegans Cell and Anatomy Ontology

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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


Building a c elegans cell and anatomy ontology

A Nobel Prize for Worms!

Sydney Brenner

John E. Sulston

H. Robert Horvitz


Building a c elegans cell and anatomy ontology

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]


Follow cells with green fluorescent proteins in a live animal

Follow Cells With Green Fluorescent Proteins in a Live Animal

[WormAtlas.org]


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


Building a c elegans cell and anatomy ontology

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.


Building a c elegans cell and anatomy ontology

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


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