Ontology meeting 2013-08-22

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Attendees: David, Judy, Becky, Jane, Tanya, Heiko

Minutes: Becky

AGENDA ITEMS

Mirroring generic cytokinesis children under mitotic cytokinesis

SF item from Val

Val probably wants these so she can slim up to mitotic terms. We don't want meiosis and mitosis terms, if the process ONLY occurs in mitosis. It will also look odd to have mitotic children, but no corresponding meiotic child.

AI: Ask Val to tell us which of those processes ONLY occur in mitosis. (Val is visiting the EBI soon, so we'll add that to the list)

AI: Look at 'barrier septum assembly': what is it referring to, since a google search only picks up the GO term. Also the definition says barrier septum formation occurs AFTER cytokinesis, but the term is PART_OF cytokinesis.


build-go-assert-inferences

Do these just contain the new inferences in the last week, or all? (some look a bit familiar).

At the moment, the 'ADD' and 'REMOVE' lines are the only ones we need to look at, as the others are old. Heiko is planning to get rid of the 'regulation' messages to tidy up the list. At at some point we'll refresh the 'EXISTS, TAGGED-INFERRED, NOT_ENTAILED' ones so we only see new ones.



protein-DNA-complexes

One for Harold: Can we come up with guidelines for when a complex is a protein-DNA complex? Does the complex have to be assembled on DNA and ONLY exist when bound to DNA?

Presumably a complex that preforms and then binds DNA is not considered a protein-DNA complex?

It relates to many of Birgits new complex terms. E.g. DNA bending complex ; GO:1990104

WE NEED HAROLD!!!!.... bump to next week's agenda.

Questions that arose:

  • Do PRO define the complex based on activity, or do they defer to the generic GO complex?
  • If we're defining complexes as being CAPABLE_OF an activity, then they don't need to be DNA-bound (if they're acting on DNA)
  • Do we really want protein-DNA complexes where the DNA is a SUBSTRATE (E.g. DNA helicase complex)? We think not.
  • In experiments, can you accurately tell if the proteins are DNA-bound, or is it just an in-vivo assay used to detect the complex?
  • 'protein-DNA complex' isn't a child of 'protein complex'.
  • One option is to obsolete 'protein-DNA-complex' and broaden the definition of protein complex so it can be a grouping parent.
  • The most genuine protein-DNA complex we can think of is the NUCLEOSOME.



RNA stabilization

Our current definition of the 'regulation of RNA stability' 'RNA stabilization' and 'RNA destabilization' terms currently just refer to regulating degradation of the RNA:

regulation of RNA stability ; GO:0043487
Any process that modulates the propensity of RNA molecules to degradation. Includes processes that both stabilize and destabilize RNAs.
RNA destabilization ; GO:0050779
Any process that decreases the stability of an RNA molecule, making it more vulnerable to degradative processes.
RNA stabilization ; GO:0043489
Prevention of degradation of RNA molecules.

There's no relationship between these terms and the 'RNA catabolic process' terms yet. Before I add the relationships in, is stabilization more than just preventing degradation? E.g. maintaining the folded structure of an RNA (PMID 19616559).

In GO, RNA stability refers to regulation of degradation. Therefore Becky will go ahead and connect the stability and the catabolism terms. Regulation of RNA structure and folding is separate.