GONUTS has been updated to MW1.31 Most things seem to be working but be sure to report problems.

Have any questions? Please email us at ecoliwiki@gmail.com

Is a General Notes Summary

Jump to: navigation, search

Rules and some Examples

  • Metabolic process is defined as a collection of processes. Therefore, is_a children of metabolic process can be specific metabolic processes.
  • Cell division terms should be children of the related cell proliferation terms.
    • Example: Endothelial cell division is part of endothelial cell proliferation.
    • COMMENT: Double-check this in light of the long discussions about cell division vs. cell proliferation that we've had in the past. X cell division part_of X cell proliferation is probably fine where X cell is some kind of cell in a multicellular organism tissue, but there has been resistance to making the relationship between the generic parents. See SF 1219649 and this thread in the email archive for many gory details. (MAH)
  • A term should not be an is_a child of two top level granularity terms but it can be an is_a of one and a part_of the other.
    • Example: A term can be an is_a cellular and part of organismal but not an is_a of both cellular and organismal.
  • Define each specific process as having a discrete beginning and end.
  • regulation of xx process and is_a vs. part_of relationship to xx process: It can be an is_a child if the parent is a collection of processes in which any instance of the regulation of a process is an instance of the parent. If the parent process is a specific process and an instance of the regulation is not a complete instance of the parent but rather contributes to an instance of the parent's whole then the regulation is a part_of that process. (Verbatim quote from DH.)
  • Sometimes a parent can have only an is_a relationship but its is_a children can have part of relationships to other parents.
    • Example: sex determination is_a children, mating type determination (part of cell differentiation) , female sex determination (part of multicellular organismal development).
  • A term can be a part of organismal development and is_a cell development.
    • Example: dopaminergic neuron development is_a cell development and part_of multicellular organismal development
  • For BP process terms that refers to a collection of processes, use this string “xxx biological process” or "xxx process"
    • Example: metabolism becomes ‘metabolic biological process’ and 'developmental process'. The distinction is still vague because all types represent collections, but the idea is that more generic processes will be distinguished in this way.

Other Notes

  • We did not create separate terms for 'development' and 'developmental process' because their definitions would essentially be the same. If we want to use development to refer to the development of XXX then we will create that specific XXX development term. We don't need a generic term for binning purposes only.
    • Example: Cell development is_a developmental process.
  • We need to be very clear about what's happening at the level of the cell and what is happening at the level of the tissue.
    • Examples: meristem vs. meristem cell
    • Cell migration vs. cell motility
    • Cell division vs. cell proliferation
  • Cell development and cell developmental process are different things.
  • Many terms that were is_a organismal development were made part_of organismal development and is_a developmental process. This is not a hard and fast rule because some of these children terms need to go to deeper terms than organismal development.
  • Problems arise from single cell organisms = organisms. Therefore, we’ve gone with single cell organisms = cell.
  • We don't want to have cell types of single celled organisms.

More Clarification

  • In other words, a cell cycle process (or can think of it as a cell cycle subprocess) is a process that forms part of the cell cycle
    • Any other cycle can be treated the same way; the parent of 'X cycle process' will be either cellular process (GO:0009987) or multicellular organismal process (GO:0032501), as appropriate. Furthermore, this approach can also be applied to non-cyclical processes!
  • Development
    • There was much discussion of whether the existing 'development' term (GO:0007275) should remain 'development' (i.e. the e complete developmental program of any organisms; the whole process), 'developmental process' (a collection of processes involved in development), or 'multicellular organismal development' (as for 'development', but excluding single-celled organisms. (Note that there was never any doubt that we want all of these terms; the question was which one we already have.) **Despite the fact that option 3 (multicellular organismal development) is the name GO:0007275 has in the final IsaComplete.obo file from the meeting, Midori votes for GO:0007275 to be 'development', and for 'developmental process' to get a new ID, because there is less risk of any existing annotations going wrong. There are two S. pombe gene products annotated directly to GO:0007275!
    • Whichever way we do it, the current children of GO:0007275 will have to be examined to see which ones should go under 'developmental process and which under multicellular organismal development (also see to-do list).
  • Morphogenesis
    • Morphogenesis is equivalent to morphogenesis of an anatomical structure, so we don't need two separate terms. note, however, that we do need separate terms for 'development' and 'anatomical structure development' because (a) 'development' includes both morphogenesis and maturation, and (b) development of an anatomical structure can be distinguished from development of an entire organism.
    • Anatomical structure development is_a developmental process.
    • Morphogenesis is_a developmental process, and part_of anatomical structure development.
    • For GO's purposes, define 'anatomical structure' as part of an organism (note: FMA has organism is_a anatomical structure).
  • Reproduction
    • Much discussion of how cellular reproduction (GO:0032505) should relate to reproductive cellular process (GO:0048610); result was to keep both, refine defs, rename GO:0032505 to 'reproduction of a single-celled organism', and add two children to GO:0048610, 'reproductive process in single-celled organism' and 'reproductive cellular process in multicellular organism'.
  • Metabolism
    • Note that the existing term, GO:0008152, will become 'metabolic process' because we've used it with essentially that meaning, i.e. a collection of processes.
    • Now that 'X metabolism' terms are defined as 'The chemical reactions and pathways involving X', perhaps we can make X transport a child of X metabolism ... an idea for further discussion. We would NOT make transport of anything other than X itself (precursors 7 whatnot) a child of X metabolism.

Problematic GO terms

  • All processes are in and of themselves processes and those processes regulate processes. I.e. phosphorylation regulates transcription. If possible, we should have the most specific terms possible, i.e. regulation of transcription by phosphorylation.
  • DNA topological change (GO:0006265) def and relationship to unwinding
    • Of these, only the linking number is a topological property; twist and writhe are geometrical. DNA molecules with the same linking number are topologically equivalent, regardless of the twist and writhe values. So the mention of linking number in the GO:0006265 def is correct. I'm inclined to delete the part of the def that mentions helicases, because helicases don't change the linking number of a DNA molecule. A true change in topology requires breaking one or both strands, as topoisomerases do.
    • DNA unwinding by helicases causes "local" changes in twist and writhe such that the linking number, and therefore the topology, of the entire molecule or segment remains unchanged; topoisomerases then act to relieve tension caused by the twist/writhe changes.
    • The local effects on geometry are thus very much biologically relevant, though I'm not sure how we might represent them in the process ontology. I am very reluctant to do it by changing the definition of 'DNA topological change' in a way that makes it inaccurate.
    • I'm also not much the wiser as to how to represent the relationship between unwinding (i.e., strand separation) and topological change. They are related, but one isn't a type or part of the other either way round. They're coupled in vivo because topology has to change to accommodate geometrical changes and allow unwinding.
    • Relevant quotes from Chapter 10:
      • "The linking number is a topological quantity, which remains unchanged so long as the DNA backbone remains continuous. In contrast, Tw and Wr are geometrical quantities, which may change as the shape of the DNA changes through bending, twisting, or kinking."
      • "Molecules that differ only in a topological quantity such as Lk are called topoisomers."
      • [ Topological change occurs during DNA replication ] "... to separate the two single strands of DNA from one another during semiconservative replication, Lk must be reduced to zero." [mah 10/10/06]
  • Homeostasis
    • New Rule: The maiteneance of a cell is_a homeostasis. Actually in almost all cases I can find, it refers to the maintenance of the tissue the cell is found in. For example, meristem, amniosera, muscle etc.
  • Organismal attachment & Puparia attachment
    • Made new term for organismal attachment. Needed a home for 'puparia attachment' and many of the PAMGO terms that describe attachment of an organism to a host will fit under this term as well.
  • Division of glycoprotein catabolism
    • Glycoprotein catabolism is broken down in two ways. One by what is being broken down and one by the actual chemical reaction.
  • Every time we use organismal, we need to be explicit about multicellular or single-celled organism

Other Terms Discussed

  • Prospores: I'm not quite sure I understand what the question is, but here's what I've found: A bacterial forespore (also called a prespore) is the smaller of two cells resulting from an asymmetric division. During the conversion of the forespore to a mature spore, the forespore remains attached to the mother cell (the larger of the two), and then is engulfed by the mother cell. When the spore is mature the mother cell cytoplasm and membrane are lost. In fungi, prospores are formed after meiosis when the four haploid nuclei are surrounded by a specialized membrane that eventually matures into spore walls. (mah)
  • "Cell maintenance": Five terms fall into this category: germ-line stem cell maintenance, maintenance of meristem identity, photoreceptor cell maintenance, somatic stem cell maintenance, and stem cell maintenance. All except photoreceptor cell maintenance refer to the prevention of differentiation or retention of stem cell population. PCR = Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light. Maybe this should be renamed as something NOT cell maintenance? The term was Becky's - we could consult her. (tzb) - RESOLVED: will leave PCR where it is, definition makes it clear that it is not stem cell maintenance. (tzb 12-11-06)
  • Root and shoot system development: Were we going to add in these terms? I can't see them in the is_a complete file. IIRC, they were meant to be parents of 'root development' and 'shoot development' and children of 'system development.' (tzb)
  • Cell motility = "Any process involved in the controlled movement of a cell.". What was decided wrt movement in place vs movement from one place to another? The current definition of cell motility suggests that 'stomatal movement' (opening and closing of stomatal pore) would be an appropriate child. (tzb)
  • Looks like we created 'reproductive cellular process in single-celled organism' as a child of reproductive cellular process and also 'reproductive process in multicellular organism' but the latter has no children. What do we envision as children for that term? (tzb)