Cellular component processes
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??
- 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'?
- Check 'cell projection biogenesis' (GO:0030031) and child terms -- can they be renamed to 'assembly'?
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
- 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.
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...)
OLD proposal (now superseded - Oct. 2008; see below for updated structure)
- organization/or morphogenesis (if part of development)
- biosynthesis/formation (biosynthesis would have a cellular process parent)
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.
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)
- biosynthesis (biosynthesis would have a cellular process parent)
Midori (July 14): David sent a few examples by email ...
- insulin http://www.vivo.colostate.edu/hbooks/pathphys/endocrine/pancreas/insulin.html
- chymotrypsin (secreted, then cleaved)
- "that plant one that jane was talking about that gets synthesized in different compartments" [Jane: I think this was C4 photosynthesis]
- https://sourceforge.net/tracker/index.php?func=detail&aid=2004397&group_id=36855&atid=440764 - DONE
- https://sourceforge.net/tracker/index.php?func=detail&aid=2015015&group_id=36855&atid=440764 - DONE
- https://sourceforge.net/tracker/index.php?func=detail&aid=2019739&group_id=36855&atid=440764 - DONE
tangentially related - cell morphogenesis
Cross product definitions
We have generated logical computable definitions of many of the terms under study here. This allows us to use a reasoner to automatically place terms in the is_a hierarchy, or to check existing placement
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.
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:
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.
Sept. 24, 2008
David, Midori, Jane
Short meeting due to jam-packed schedules ...
Continued renaming "organization and biogenesis" terms as at previous meetings. Got as far as "capsule organization" (is_a external encapsulating structure organization).
When we get to cytoskeleton organization, move some terms, probably up to is_a cellular process:
- actin filament-based process GO:0030029
- intermediate filament-based process GO:0045103
- microtubule-based process GO:0007017
These refer to processes that use the cytoskeleton but don't alter it. (Is it worth making a parent to group them?)
Everyone: Look at maintenance terms, not just in CC organization. Maintenance is usually a homeostatic process -- any exceptions?
David and Tanya have tried to use a standard structure for maintenance terms in the regulation work.
Next week: David will show Jane & Midori what he and Tanya do with maintenance and regulation.
Aim is to to coordinate what's done with "maintenance" between CC organization and regulates.
Sept. 30, 2008
Fixed parentage of 'actin filament-based process' and similar terms (closes SF 2114093).
Continued renaming 'organization and biogenesis' to 'organization'; finished nucleus organization and its is_a children. CVS revision 1.240
Considered whether we need a term for maintenance of a biological process (aka biological process homeostasis). If we do, we have to make sure that
- The names are consistent -- the biological process name should be univocal; and
- The maintenance/homeostasis process should be is_a regulation of the process.
That said, we think there aren't any homeostasis-of-process terms so far. We looked specifically at maintenance of sister chromatid cohesion -- which isn't under homeostasis at present -- and decided that we could think of it as maintaining the state in which sister chromatids are attached (as opposed to maintaining the process of cohesion).
Also, if we add homeostasis of a process, then the parent, homeostatic process, could no longer go under regulation of biological quality.
We do want univocal use of 'maintenance', so continue thinking about whether it covers maintenance of a process. If we need another term, we could, er, maintain univocity by renaming the X maintenance terms under homeostasis to (wait for it) X homeostasis.
Keep in mind that 'cellular homeostasis' means homeostasis of something at the level of a cell; it's defined as a collection of processes.
New task (to do after 'organization' renaming is finished): For all maintenance terms, check whether they have homeostasis ancestor. If not, add parent, or note why it's an exception.
Can Chris add new reports to check for consistent structure with organization terms, homeostasis terms, etc.?
Standard CC organization structure
The standard structure for cellular component biogenesis, organization, etc. as of October 21, 2008 (from email and meetings) is:
- [i] assembly
- [i] disassembly
- [i] maintenance
- [i] morphogensis
- [p] assembly
- [p] part biosynthesis
Definitions: CC biogenesis includes biosynthesis of constituent parts, whereas CC organization does not.
Jan. 26, 2009: added protein complex biogenesis, with relationships consistent with above. (mah)
Feb. 6, 2009: if we ever get a chance to revisit this, we need to sort out 'plant-type cell wall organization' and its children. (jl)