SourceForge meeting 2014-05-14

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Do we need a separate 'multicellular organism senescence' term, or does 'multicellular organismal aging' suffice?

PO need this term for defining some of their processes e.g. 4 leaf senescence stage ; PO:0001054. This is the ticket: https://sourceforge.net/p/geneontology/ontology-requests/10381/

Are we going to create specific terms for proteins with modified residues?

Boundaries of protein complex:

This ticket requires deciding whether spindles are protein complexes:

https://sourceforge.net/p/geneontology/ontology-requests/10824/

'protein complex' currently has the def: "Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules."

Can we tighten up the definition to make clear what components are allowed. How about:

"Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccaride) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical."

?

Note - centrosome part of spindle & centrosome *may* have other components besides protein: http://download.springer.com/static/pdf/10/art%253A10.1007%252Fs10577-011-9186-7.pdf?auth66=1400247153_36a440116ffd10fb172a63495c67c10a&ext=.pdf

trans golgi network - part of golgi apparatus or not?

It is not right now, but Jim Hu asks if it should be: https://sourceforge.net/p/geneontology/ontology-requests/10800/

The term has a comment: "The TGN is not considered part of the Golgi apparatus but is a separate organelle." But no indication of where this comes from. The ref in the definition is Alberts et al. Molecular Biology of the Cell. But this appears to treat the trans-network as part of the Golgi, as does Wikipedia.

What counts as an amino acid

https://sourceforge.net/p/geneontology/ontology-requests/10798/


Any opinions?