#86 Promoters

[Chris Myers]

I would like to be able to indicate that a modifier is a promoter in a composite reaction for genetic production.

participant role -> modifier -> stimulator -> promoter

I would also like to be able to indicate that this species represents a promoter.

physical entity representation -> functional entity -> unit of genetic information -> gene regulatory region -> promoter

Not sure if you are allowed the same term in different places in the hierarchy. If not, then perhaps the second one could be "gene promoter".

[Chris Myers]

Since only material entities can be used to annotation species, then what I actually need is:

physical entity representation -> material entity -> informational molecule segment -> promoter

[Nick Juty]

One thing we need to do a bit better is separate the effects at the gene and protein level. When you say promoter, do you mean a promoter in the sense of a stretch of DNA to which various factors can bind to regulate gene expression?

a) For participant role we suggest the following:
SBO:0000003 - participant role
|---SBO:0000019 - modifier
|---NEW TERM - promoter
|---|---SBO:0000020 - inhibitor
|---|---|---SBO:0000206 - competitive inhibitor / SBO:0000207 - non-competitive inhibitor
|---|---NEW TERM silencer
|---|---SBO:0000459 - stimulator
|---|---|---SBO:0000013 - catalyst / SBO:0000461 - essential activator ...
|---|---NEW TERM enhancer

b) For the material entity that you need for annotation, perhaps a term 'transcription factor complex' may be more appropriate. This could fit under 'SBO:0000296 - macromolecular complex'.

For both of these, it may be useful to have a more specific example...

cheers
Nick

[Chris Myers]

For promoter, I do mean location for binding of RNAP. Transcription factors can also bind to enhance or repress.

I do not mean it to be a complex. It is only the unbound form so I prefer it not under macromolecule complex rather informational molecule as it represents a segment of DNA.

[Nick Juty]

The participant role terms are covered in SF #3503716 (regulator request by CM).
For the material entity, I have created the term: 'SBO:0000590 - promoter binding region'

Thanks for the contribution!

--Nick