Building the Process Ontology One Branch at a Time

Building the Process Ontology One Branch at a Time

David Hill

Tanya Berardini

Rebecca Foulger

Norberto de la Cruz

The Problems

The Gene Ontology (GO) is used by a wide variety of model organism databases that represent related but distinct biological processes– How can we incorporate species-specific

concepts into the GO? How can we represent these processes, but maintain the true path rule?

– How can we represent related but distinct processes and maintain the true path rule?

Starting Point

Many terms are lumped together, such as embryogenesis and morphogenesis.

This places terms such as pattern specification in the wrong context for some circumstances.

Our solutions For species-specific concepts that contain

elements orthogonal to the GO, we will use the Cross-product solution

What about concepts that are more universal?– Create high-level “sensu” terms representing the

variation of each organism?

– Factor out common things and create “sensu” terms further down the graph

A reminder of the Cross-Product Approach

neural_crest_cell cell differentiation <neural_crest_cell cell fate commitment <neural_crest_cell cell fate determination <neural_crest_cell cell fate specification <neural_crest_cell cellular morphogenesis during…

Factor out common things and create “sensu” terms as far down the graph

as possible What elements of

biological processes are shared?

–We started with development

•Cellular processes

•Timing processes

•Shaping processes

Details of development changes

http://www.geneontology.org/email-go/go-arc/go-2002/1245.html

http://www.geneontology.org/email-go/go-arc/go-2002/1690.html

Eyes are eyes:it depends on how you look at it

MOUSE FLY

Wolff and Ready in The development of Drosophila melanogaster, Bate, M. and Martinez-Arias, A., Editors. 1993, Cold Spring Harbor Laboratory Press. p. 1277-1325 and The Moses lab webite

From Rugh

The commonality in eye development is morphogenesis

The differences are when the process occurs– Mammals:embryonic

– Insects:embryonic and post-embryonic

– Vertebrates:both

Mammals:embryonicPart of mammalian embryonic

development viaVertebrates and animals

Part of embryonicdevelopment via embryonic

eye morphogenesis

Type of morphogenesis via embryonic morphogenesis

Type of organogenesis via eye morphogenesis

Type of vertebrate eye morphogenesis

Insects:embryonic and post-embryonic

Embryonic Post-embryonic

“As a trivial aside, the eye of the potato is really a depression containing a bud in the periderm ("skin") of the potato tuber.  Thedepression is the axil of a scalelike leaf.”T. Berardini, March 28,2003

What about Physiology?

Use the development example to create a consistent physiology graph– Create graph structures for cellular physiology– Create graph structures for organismal

physiology

A Slice of What’s to

Come:The Physiology

graph

Conclusions The ontology should be broken down to

factor out commonalities– In development, the processes of creating form

needed to be separated from when it happens– Create “sensu” terms once we reach an

appropriate level– For physiology we needed to split out processes

that were happening at a systems level. One major subdivision of all Biological

Processes is what happens on a cellular level vs. an organismal level.