1. The ‘regulates’ relationships Chris, David, Tanya

2. The Nature of Biological Regulation Gene products execute molecular functions Executions of functions can be regulatory (ex. protease inhibitor activity) or can take part in regulatory biological processes (ex. TGF beta receptor activity)

3. In the Beginning, There Were Two Relationships is_a part_of

4. There Were Also ‘Regulation’ Terms

5. We made the ‘regulation of X’ a part_of ‘X’ But, it’s not really part_of, is it?

6. Why not part_of ? Regulation of X = “Any process that modulates the frequency, rate or extent of X.” A process can regulate X without being an integral part of X. We needed ‘regulates.’

7. Three kinds types of regulation were described by the original regulation terms in GO Biological regulation --[i] regulation of biological process --[i] regulation of biological quality --[i] regulation of molecular function

8. Intra- and Inter-ontology Links Occurrents can regulate occurrents Occurrent = biological process OR (execution of a) molecular function Does not require any additional relationship types (like has_part, for instance)

9. BMP Signaling Pathway The biological objective of BMP signaling is to regulate transcription

10. Biological Process Intraontology Links

11. Signal Transduction The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately effecting a change in the functioning of the cell.

12. BMP Signaling Pathway The biological objective of BMP signaling is to regulate transcription

13. BMP Signaling Pathway The biological objective of BMP signaling is to regulate transcription

14. More Intraontology Links Molecular function to molecular function –There is NO relationship between enzyme regulators and the enzyme activities themselves –Will change MF ontology from being a strict is_a hierarchy Regulator activity (66 terms) Activator activity (60 terms) Inhibitor activity (90 terms)

15. Molecular Function Intraontology Links

16. Inter-ontology Links BP->MF

17. Inter-ontology Links MF->BP Molecular functions that always occur in a single type of biological process are a part of that biological process.