Notes for cc xp self

• All of the 'cytosolic X' terms have a surrounded_by relationship to cytosol. This doesn't seem right because surrounded_by is an intersection of has_part and bounded_by, so would imply that e.g. a cytosolic complex has_part cytosol. located_in might be better here, or part_of? Same problem with the lumen terms and cytoplasmic X terms.
  • Chris to fix
• Need the email thread for this one:

[Term]
id: GO:0031676 ! plasma membrane-derived thylakoid membrane
intersection_of: GO:0016020 ! membrane
intersection_of: surrounds GO:0030075 ! plasma membrane-derived thylakoid
!!!!  intersection_of: surrounds GO:0034357 ! photosynthetic membrane - see email thread Re: thylakoid membrane question

(Got it.)

• Does it make sense to say that something is bounded_by an envelope? An envelope is a double-layered (inner and outer) membrane with a space in between - is it okay to say that space is bounded by the envelope? Or would it make more sense to say the space was bounded_by the outer membrane and bounds the inner membrane?
  • Should use bounded_by inner membrane rather than envelope. The envelope lumen is bounded_by outer membrane, and bounds inner membrane.
• Terms which contain 'intracellular' have been given the def 'contained_by cell'. The def of contained_by would imply that cell is an immaterial continuant like a cavity - don't think that's really true - would say a cell is a material entity? Can we not use part_of here?
• Inwards_of and outwards_of - can't find definitions of these anywhere? Would it be possible to say 'extracellular region' outwards_of cell wall, cell membrane?
• extracellular space is a bit of a headache - outside plasma membrane but within multicellular organism, part_of extracellular region. Can we use non_GO terms in xps? IS there a term multicellular organism elsewhere? Also, can we say 'extracellular space' contained_in 'extracellular region'? That is, does contained_in make sense when referring to two spaces?

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