Cellular component processes

At the meeting on July 9, 2008, we identified thins to be done on processes affecting cellular components. This is a rough list of action items.

Personnel: Jane, David, Midori, Val, others as needed (e.g. Jen, Tanya for plant meristem terms)

Timeframe: late July or early August 2008??

To do:

• Rename all "organization and biogenesis" terms: remove "and biogenesis".
• Split CC maintenance terms out so that no maintenance term is under development. Obsolete or rename "assembly and maintenance" terms.
• Look at all maintenance terms to see whether they should have homeostasis parent/ancestor.

Notes:

cellular component organization [and biogenesis] covers CC morphogenesis and CC maintenance

the meaning is essentially "a process that affects a cellular component"; can we come up with a better name? (rejected "cellular component process" as too vague)

Also (tangential):

• Check for any stray "and" terms. Split, rename, etc. as appropriate.
• Rename the few remaining "and/or" terms to use "or."

Comments

Val (July 11): Would people definitely think of the processing of a peptide as part of the biosynthetic process? I can see that it would be part of the 'biogenesis of the complex', but not part of its biosynthesis. I would think of biogenesis as including the processing and modification and assembly, but biosynthesis as the 'formation' would this make sense? (prerhaps not...)

• organization/or morphogenesis (if part of development)
  • biogenesis
    • biosynthesis/formation (biosynthesis would have a cellular process parent)
    • assembly
    • modification/processing
  • disassembly
    • catabolism
• maintenance

I'm thinking that macromolecule biosynthetic process (which is a metabolic process) would be a cellular process, but that macromolecule biogenesis would not. I am looking at the children of 'macromolecule biosynthetic process', and they all appear to be cellular. Although a lot don't currently have this parent. Check out hemoglobin biosynthetic process, which has cellular process and biosynthesic process, but not cellular biosynthetic process.

Midori (July 11): For a single macromolecule, it'll be a challenge to do definitions that distinguish biogenesis from biosynthesis (also, I thought we decided to purge "biogenesis" from the ontology 'cos we couldn't pin down what it meant generally).

Also, there's no assembly or disassembly for a single macromolecule ... a lot of the terms in the structure only apply to complexes/subcellular anatomical structures.

For the same reason, I don't think we can put catabolism under disassembly. Catabolism refers to individual molecules, whereas disassembly refers to multi-subunit complexes and structures.