Cellular component processes

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At the meeting on July 9, 2008, we identified things 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.
  • Move complex assembly terms out from under metabolism. Can we come up with a parent for 'macromolecular complex assembly' and macromolecular complex disassembly', or should they be siblings directly under 'biological process'?

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); roughly same applies to macromolecular complex assembly and disassembly, as noted above

Also (tangential):

  • Check for any stray "and" terms. Split, rename, etc. as appropriate.
  • Def of "cellular component assembly" (GO:00226070) is a bit circular; see if we can improve it.
  • Should the assembly and disassembly terms have metabolism-ish synonyms? For example, 'spindle disassembly' has 'spindle breakdown', 'spindle catabolism', and 'spindle degradation' as exact synonyms, but some other disassembly terms have no synonyms.

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.

Val(14th July)

I had another thought. I was thinking more about Davids example of biosynthesis which wasn't cellular (the hormome biosynthesis) and I'm still thinking that "macromolecule biosynthestic process" should be cellular.

The definition of biosynthesis (Wikepedia) Biosynthesis is a phenomenon wherein chemical compounds are produced from simpler reagents. Biosynthesis, unlike chemosynthesis, takes place within living organisms and is generally catalyzed by enzymes. The process is a vital part of metabolism.

I wonder if this provides a distinction between biosynthesis and formation. Biosynthesis seems to be more specific and refer to the 'building part' as synthesiszing is specifically 'combining elements', this would exclude the proteolytic cleavage to make an active hormone, although this could be considered part of hormone formation.

also synthesis definition combines together two or more pre-existing elements resulting in the formation of something new


This would make

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

Midori (July 14): David sent a few examples by email ...

SourceForge items

tangentially related - cell morphogenesis

Cross product definitions

See biological_process_xp_cellular_component

Meeting notes

Sept. 9, 2008

David, Midori, Jane

Reviewed wiki; agreed to start with renaming 'CC organization and biogenesis' terms. Reason: 'biogenesis' doesn't really add anything, and isn't consistent with the fact that 'organization' includes disassembly as well as assembly and maintenance.

  • Each term will be renamed 'CC organization'.
  • Add RELATED synonym 'CC biogenesis'.
  • Check definition - it should use standardized wording and include at least some of the CC definition.
  • Make sure there is a CC term for every component mentioned in an 'organization' term.

David edited, starting with 'cellular component organization' (GO:0016043) and proceeding top-down. We got as far as 'periplasmic space organization' (GO:0043580). Next week David and Jane will continue where we left off, and Midori will join if the workshop ends in time.

Note: The ribosome is an exception, because the community thinks of ribosome biogenesis as including the synthesis of ribosomal RNA and proteins as well as their assembly into ribosomal subunits. So we'll keep 'ribosome biogenesis', and make sure the parents work for that situation.

(midori 2008-09-09)

Sept. 16, 2008

David, Midori, Jane

Continued renaming 'organization and biogenesis' terms to just 'organization'.

Also decided to deal with 'assembly and maintenance' terms by:

  • renaming to 'organization' if there isn't another 'organization' term for the component; or
  • merging with the 'organization' term if there is one.

Agreed that every cellular component organization term should have 4 children:

  • assembly
  • maintenance
  • disassembly
  • morphogenesis

Added a high-level term 'cellular component maintenance' and crafted a definition (see the .obo file).

Plan to make sure all assembly, disassembly, maintenance and morphogenesis remodeling terms are correctly placed under corresponding organization terms, and that there is a CC term.

For cellular components, remodeling = morphogenesis; think about whether to rename terms.

(midori 2008-09-16)