SourceForge meeting 2015-04-22

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Gene silencing and miRNA

(David OS)

https://sourceforge.net/p/geneontology/ontology-requests/11638/

Does silencing have to be long term or not?

Silencing suggests turning off completely, whereas miRNA action is more negative modulation.

TPVs under RNA processing

https://sourceforge.net/p/geneontology/ontology-requests/6208/ https://sourceforge.net/p/geneontology/ontology-requests/11642/

RNA processing is defined as:

The maturation clause allows it to live under 'gene expression', but it has various subclasses for which this restriction has been lost/ignored.

Proposed solution: keep maturation clause for processing. Where relevant, split out leaf nodes => more general term under RNA metabolism. But, it would be good to have a differentium for the subclass that is part of maturation. I initially thought we could do this with SO terms for primary vs mature transcript. The problem is, we'd need to request SO terms for immature versions of various transcripts, and even then we wouldn't be able to reliably infer for conversion of immature to immature (But if we had 'results in maturation of' that is applicable to molecules????).

We could define RNA maturation terms using SO:

e.g.

label "RNA maturation" definition "The process whose outcome is the formation of a mature (funcational or translatable) RNA molecule, starting from a primary transcript." equivalentTo: 'RNA metabolic process' that 'has input' some S0:primary_transcript and 'has output' some SO:mature_transcript

(SO has other terms we can use to automatically define subclasses)

One possibility is to use these maturation terms to replace the current processing terms. And to make the various subclasses part_of processing. The other option is to keep the processing terms as:

RNA processing EquivalentTo: 'RNA metabolic process' that part_of some 'RNA maturation'

But in this case the maturation terms should probably be flagged as 'do not annotate'.

Note - we are currently using SO terms mRNA and ncRNA for both mature and immature states. This will need to be changed (SO has the additional problem that we don't have a link up from these terms to ribonucleic acid, which we take from ChEBI => some very serious gaps in inference. We need SO molecular - but can we have an interim fix?).

So - which tack to take? The SO solution looks best, but a comprehensive solution would require getting SO fixed first (perhaps getting SO molecular sorted too????)

Should the use of cleavage to refer to nuclease activity be restricted to endonuclease activity?

https://sourceforge.net/p/geneontology/ontology-requests/11642/

We currently have

'RNA cleavage' is_a 'nucleic acid phosphodiester bond hydrolysis' - so cleavage could be endo or exo in this case. I assumed endo. If we keep it ambiguous, is it OK to differentiate child terms in def where necessary. How to do so formally? has_part some 'endonuclease activity' ?


envenomation diff by species target

Should we allow these under 'envenomation resulting in modification of morphology or physiology' envenomation resulting in mammal intoxication envenomation resulting in insect intoxication ?

https://sourceforge.net/p/geneontology/ontology-requests/8453/#e8fc

Regulation of homeostasis

'homeostatic process' is_a 'regulation of biological quality'. Therefore I was under the impression that we wouldn't want to create further regulation terms for homeostasis (reg of reg?). But I see that we have 'regulation of homeostatic process' with children and descendants. I'm sure we've discussed this before...

Stemming from terms in the TG queue e.g. 'regulation of triglyceride homeostasis'