Revision as of 11:42, 19 August 2019

Agenda

After USC hackathon in June, we formed a small working group to fully articulate the GO-CAM model specifications
This will allow for consistent GO-CAM curation using Noctua workbenches, import projects (e.g. Reactome and MOD imports)
Will also allow us to move forward with harmonizing AE relations used in GO-CAM and conventional annotation
- On today's call, we will review the annotation extension relations that need further discussion, starting with happens_during
- Google summary spreadsheet of MF extensions

Current recommendations are that 'happens during' is used to define a biological phase or life stage during which a molecular function occurs
However, happens_during is not defined in the relations ontology
There is a comment, however:
- X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
- This implies that the start and end of the molecular function and phase are known
- For things like cell cycle phases or development stages this seems fairly straightforward
But what about annotations that referred to a function that 'happens during' a biological process, such as 'response to oxidative stress'?
What do we mean when we make these statements?

@@ Line 17: / Line 17: @@
 ** X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
 ** This implies that the start and end of the molecular function and phase are known
-** For things like cell cycle phases, this seems fairly straightforward
+** For things like cell cycle phases or development stages this seems fairly straightforward
-* What about annotations that referred to a function that 'happens during' a biological process?
+* But what about annotations that referred to a function that 'happens during' a biological process, such as 'response to oxidative stress'?
+* What do we mean when we make these statements?
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