1. Challenges to Representing Pathways Nancy R. Gough, Ph.D. Editor, Science Signaling, AAAS

2. Challenges to Representing Pathways 2

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6. Challenges to Representing Pathways 6 Challenges to Representing Information in Pathways Size of the data set of a pathway or experimental data sets to which pathway information is applied Number of feedback loops Crosstalk with other pathways Temporal changes Spatial reorganization

7. Challenges to Representing Pathways 7 Challenges: Size of the Experimental of Pathway Data Sets Computers can handle and process large data sets easily– people can’t Details overwhelm the message AND different messages are important to different people for different purposes Ontologies a solution? Filtering by species, localization, protein interaction domains can divide the data into interpretable chunks. This is only as effective and as accurate as the assignments of these attributes to the data.

8. Challenges to Representing Pathways 8 Challenges: Number of Feedback Loops When there are many feedback loops, identifying what is upstream from what is downstream becomes very challenging in a visual representation for people. It also means that the pathway changes over time. Is there a solution from ontologies?

9. Challenges to Representing Pathways 9 Challenges: Crosstalk with Other Pathways Pathway boundaries for cell signaling are human constructions. How do we know which is the “primary” pathway or the most relevant for biological question? Is that even an appropriate question? Ontologies may help by allowing humans to collapse “pathways” into functional units.

10. Challenges to Representing Pathways 10 Challenges: Temporal Changes As the pathway proceeds, the system changes. Example: Proteins synthesized, proteins degraded, proteins modified posttranslationally How can ontologies help?

11. Challenges to Representing Pathways 11 Challenges: Spatial Reorganization This another dynamic aspect to pathways. Components in pathways move. Cell structures and morphologies change. This can lead to multiple instances of a component in a pathway. A good choice? How can ontologies help?

12. Challenges to Representing Pathways 12 Challenges to Representing Information in Pathways Size of the data set Number of feedback loops Crosstalk with other pathways Temporal changes Spatial reorganization

13. Challenges to Representing Pathways 13 Nancy R. Gough, ngough@aaas.org