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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 - PowerPoint PPT Presentation
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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.