Ontology meeting 2012-02-15

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MINUTES: BECKY

Discussion item I

Update on CHEBI xps. Where are we up to? Can we set a date for switching to svn? How's the paper looking?

Discussion item II

Regulation by template cont.

AN EXAMPLE OF 'REGULATION BY'

PMID 10591965: FLO8-dependent transcriptional regulation

FLO8 is a transcriptional regulator that up-regulates transcription of numerous genes, whose gene products are required for various yeast processes:

  • FLO8 -> transcription of FLO1 gene -> FLO1 encodes a lectin involved in flocculation
  • FLO8 -> transcription of STA1 gene -> STA1 encodes a glucoamylase responsible for starch degradation
  • FLO8 -> transcription of FLO11 gene -> FLO11 gene encodes a cell-surface protein required for filamentous growth
Example of an existing GO term made to represent this:
positive regulation of starch catabolic process by positive regulation of transcription from RNA polymerase II promoter ; GO:0035957

This GO term doesn't tell the whole story though. You can't tell from GO:35957 that FLO8 is a transcription factor. FLO8 lies at the bottom of a signal transduction pathway. Any gene product in the signaling pathway could be annotated to GO:0035957.

nutrient signal -> receptor --> MAPK cascade --> FLO8 (a TF) -->up-regulation of target genes

For an image of an example pathway, see: http://mcb.asm.org/content/19/7/4874/F10.large.jpg

  • In some cases you know that the annotated gene is a TF. In many cases, they just knock-out a gene and see that expression of STA1 is reduced and therefore starch degradation is impaired. Can we cover both scenarios?


Discussion item III

Can we have 'MF regulates MF'?

E.g.
MAPK activity
--[posreg]MAPKK activity



MINUTES

Present:

  • David Hill
  • Chris Mungall
  • Tanya Berardini
  • Paul Thomas
  • Jane Lomax
  • Rebecca Foulger
  • Paola Roncaglia
  • Karen Christie


CHEBI

  • AI: Jane to send latest copy of paper (version 9) to Chris so Chris can look at the Methods section. Agreed not to include all PIs on authorship.
  • AI: Switch over to using svn to commit GO on MARCH 14th 2012.


REASONING

  • AI: EBI-GO will assume responsibility for checking the Jenkins environment for reasoning.


REGULATION BY REGULATION

  • Main problem is still the order of events (that you need to regulate transcription and then the transcribed GP is involved in a process). You could have extra differentia (starts w/, ends w/) but this doesn't fix it.
  • dual is_a parentage still isn't quite right. Jane suggested instead to have:
positive regulation of starch catabolic process by positive regulation of transcription from RNA polymerase II promoter ; GO:0035957
HAS_PART: positive regulation of transcription from RNA pol II promoter
IS_A: positive regulation of starch catabolism
  • Most of the discussion focussed on whether these terms should be precomposed or captured at annotation level using column 16.
    • E.g. FLO8 TF would be annotated to 'pos reg of transcription' with STA1 in column 16. A separate linkable statement would show that STA1 is an effector of starch degradation.
    • Could also have 'starch catabolism' in column 16.
  • In many cases you only know bits of the full picture, and we need to be able to capture that (e.g. when you don't know that STA1 is the upregulated gene, or you don't know that FLO8 is a TF).
  • Everything is regulated by transcription so we don't want to go replicating the development graph/metabolism graph under transcription. It's not scaleable.
  • Comes down to what is regulation?
    • You are regulating a process if: you're regulating a MF that is part of a process (either directly or indirectly).
    • A process can regulate a process: BMP signaling pathway REGULATES transcription
  • Current annotation limitation is that we can only annotate 1 experiment at a time.

IN SUMMARY: NEED TO GET THIS RIGHT BEFORE WE START MAKING THESE LOGICAL DEFS SO WE DON'T HAVE TO RETROFIT.


MF REGULATES MF

  • This is okay if the regulatory function is the same as the process (DH). For the MAPKKK's this is ok- the function of a MAPKKK is to phosphorylate and activate a MAPKK.
  • AI: Think whether to have an 'activates' relationship as a sub_type of 'positive regulation'. Will need to give community notice.