SourceForge meeting 2014-04-23

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Extracellular vesicle terms

See email thread "GO and vesicle nomenclature"

 TODO: Jane to contact group working on these to ask for clarification 
 about two intermediate classes which are both parent classes to all leaf nodes in membrane bound extracellular vesicle branch.

flocculation & aggregation - cell-cell adhesion, or process mediated by cell-cell adhesion ?

Currently flocculation is a process resulting in formation of aggregates (flocs) of single celled organism that is mediated by cell-cell adhesion. Related cell adhesion terms have a part of relationship to flocculation terms. Val would prefer it to be a type of cell-cell adhesion. I can see the case for keeping two types of terms. While probably most or all annotations should probably be to the adhesion terms, it is certainly possible to imagine other components to floc formation, such as cell communication (important to keep these open if we want broad applicability for these terms. The adhesion processes themselves are also likely to occur at low levels in the absence of floc formation (e.g. if cultures are insufficiently dense).

OTOH, we are not very consistent about this, as other terms for types of aggregation, e.g. 'Type IV pili-dependent aggregation' GO:0052000, is a type of cell adhesion.

  Decision:  Flocculation stays as two terms. Make new general term for aggregation single cell organisms
  to bring in "Type IV pili-dependent aggregation" - making new class for the cell-cell adhesion involved.  
  (but then how to distinguish this from flocculation?  Is it on type of aggregate formed?)

viral protein binding

Big thumbs down?

Yup.  Suggest they simply use protein-protein interaction or one of its children and record the interacting protein in a with.


This SF ticket requests a general term for depalmitoylation - one that is neutral about what palmitate is being removed from:

Wondering whether I should create the general class at all (rather than just new specific classes. e.g. for CoA depalmitoylation - see PMID: 12855696), and if so how it should be classified. As far as I can tell, catabolic process are all defined by substrate, rather than by what moiety the substrate carries (unless that moitey defines a chemical class itself).

 Seems to be a reasonable case for adding general classes such as deacylation & depalmitoylation - after all we do have dephosphorylation
 But we need to be careful to populate the class hierarchy under these properly.  We can't rely on autoclassification using CHEBI and may not
 be able to reliably find all subclasses by string searching.  
 For this ticket - Make only the new specific process classes required for papers mentioned.
 Make a new ticket for for deacylation and its children bringing in Peter D'Eustachio for advice on finding all subclasses.