Meeting Notes

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February 1st, 2007

Jen Clark, David Hill, Midori Harris, Jane Lomax (8:00am EST- 12:55pm EST)

Strategy ideas:

  1. Maybe we should do all the cell component terms first. Then we can do all other terms that are differentiated by those components.


To do:

  1. Midori to check if peptidoglycans are in cell walls of fungi and to see if there are any that don't have chitin. DONE!
  2. Jen will clean up the plant cell wall terms to indicate that they both contain pectin.
  3. Change cell wall biosynthetic processes to reflect assembly and metabolism. Jane will look into this.
  4. Have Becky confirm that it is ok to change insect aorta to dorsal vessel aorta.
  5. Is it o.k to say insect appendage development? It is really the only way to distinguish this term. Perhaps we can distinguish *

wings in a more stuctural way. Perhaps arthropod appendage develoment. Exoskeleton-containing appendage development.

  1. We need to rearrange wing development. Q: Does a wing have an exoskeleton?
  2. Check ATP synthesis coupled proton transport in bacteria vs eukaryotes.
  3. Check the pubmed ID from spore wall assembly to (GO:0030476) to get at good defs for the spore wall component terms (Midori).
  4. Ask Michelle about the difference between the eukaryotic and prokaryotic ATP transporters.
  5. As for bacterial capsule, could it be referred to as a semisolid-capsule or gelatious capsule? There is a problem distinguishing this term from its sib which is slime layer. Also need to distinguish it from the fungal capsule. Michelle.
  6. Ask Tanya about the cell surface sensu Magnoliophyta terms. How are they really different from the generic cell surface parent. If not, can we just merge and add a new part of term external side of cell wall.
From meeting minutes, Cambridge, Sept. 2002:
"Cell surface" and related terms: these were added recently by TAIR curators, to capture information from experiments in plants that can narrow down localization to plasma membrane or cell wall but can't distinguish between the two (that's what's meant by "cell surface" in plant literature). The definitions and placement of the cell surface terms were discussed, and changes recommended.
action item 25: TAIR curators to improve definitions of "cell surface" and its children.
    1. Action item: Tanya to review old SF items for cell surface and implement changes suggested if deemed appropriate. Changes suggested are:
      1. merge cell surface and cell surface(s. M.)
      2. create new term 'external side of cell wall' as a part_of child of cell surface
      3. make new term above and is_a child of cell wall part
      4. make 'longitudinal side of cell surface' an is_a child of cell part and remove (s. M.) from main term string (retain as synonym?) leave as part_of child of cell surface
      5. make 'external side of plasma membrane' and is_a child of plasma membrane part
  1. Note that we are using logical "or" in definitions and term names. Make sure this is in the web documentation somewhere.

February 6, 2007

David Hill, Jane Lomax, Jen Clark, Midori Harris (intermittently) 9:30EST-12:30EST


Strategy
Do the cellular component terms first.

Dealt with

  • cortical microtubules
  • DNA-dependent RNA polymerase, cytosolic, nuclear and plastid
  • Rearranged the thylakoids and their children quite a bit.
  • Did pyruvate dehydrogenases. Made the bacterial one cytosolic.



Action Items:

  1. Do we really need archaebacterial and bacterial cytosolic ribosomes? Ask Harold about how to distinguish these.
  2. Can we obsolete spore wall (sensu Fungi) and make 2 new terms, one to describe the 2-layered pombe and one describing the 4-layered one in cerevisiae. Inform Val et al.
  3. Ask tanya if she is happy with lignin containing spore wall and cellulose containing cell wall.
  4. Ask Kimberly what the C. elegans dosage compensation complex is composed of. Is it just protein?

February 7, 2007

Jen Clark, Jane Lomax, David Hill Strategy

Continue with the component terms.

Dealt with: