2. Building the Process Ontology One Branch at a Time David Hill Tanya Berardini Rebecca Foulger Norberto de la Cruz

3. 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?

4. 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.

5. 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

6. 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…

7. 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

8. 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-2002/1245.html  http://www.geneontology.org/email-go/go- arc/go-2002/1690.html http://www.geneontology.org/email-go/go- arc/go-2002/1690.html

9. 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

10.  The commonality in eye development is morphogenesis  The differences are when the process occurs –Mammals:embryonic –Insects:embryonic and post-embryonic –Vertebrates:both

11. Mammals:embryonic Part of mammalian embryonic development via Vertebrates and animals Part of embryonic development via embryonic eye morphogenesis Type of morphogenesis via embryonic morphogenesis Type of organogenesis via eye morphogenesis Type of vertebrate eye morphogenesis

12. Insects:embryonic and post- embryonic EmbryonicPost-embryonic

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

14. 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

15. A Slice of What’s to Come: The Physiology graph

16. 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.