#115 polarity - orientation vs charge

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6
2009-09-18
2007-04-11
Chris Mungall
No

currently we have:

PATO:0001769 polarity [DEF: "Orientantion to similar coordinates."]

but nothing for polarity w.r.t charge...

I think both should be disambiguated in their term names

Discussion

  • Chris Mungall
    Chris Mungall
    2007-07-27

    • priority: 5 --> 6
     
  • Chris Mungall
    Chris Mungall
    2007-07-27

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    [increased priority of this item - required for GO polarization terms]

     
  • Chris Mungall
    Chris Mungall
    2007-07-27

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    I guess the orientation and structural alignment is closely related to opposite charges. But not all structural alignment is due to electrical charges?

     
  • Jane Lomax
    Jane Lomax
    2007-07-27

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    I'd say that polarity is the orientation of a substance to similar co-ordinates to itself along an axis or across a membrane (it's odd that the PATO def doesn't mention an axis - I'd say that was crucial to any defintion of polarity), while electrical polarity is the generation of charge *caused by* polarity of ions across a membrane (is it always across a membrane?). So they're not subtypes of one another, rather electrical polarity is caused by a type of structural polarity - does that sound sensible?

    Jane

     
  • Valerie Wood
    Valerie Wood
    2007-07-27

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    I agree with Jane
    -the eisting 'spatial' polarity terms in GO (cell polarity and cytoskeletal polarity, possibly others) should also specify an axis....it seems like organ polarity already does

     
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    Rhetorical questions:
    Do cells ever have more than two poles?
    Does an axis necessarily imply a straight line? In vivo cells are always in the context of other cells, pressed into tight spaces. It's easy to imagine one pole being at a angle to to the other pole, even a right angle. Does the axis necessarily run through the center of a cell?

    We need to be careful about basing the definition too much on an abstract, idealized view of what a cell is.

    I would point out that horseshoe magnets have two poles, but not on a straight axis.

    I agree that polarity across a membrane is different from polarity that defines regions of the cell surface that are distinct from each other.

    Some of the current cell polarity definitions in the GO use the word "anisotropic" defined by Biology Online as "describes a structure whose appearance varies with the angle of observation," (http://www.biology-online.org/dictionary/Anisotropic). Although this is true, it is arguably true about most biological structures at some level, and thus the word is probably not precise enough.

    These are my thoughts, but not a solution, unfortunately,

    Alex

     
  • Midori Harris
    Midori Harris
    2007-07-31

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    Following up on Alex's comment on "anisotropic" ... I tend to think more in terms of the definition I've found in the Oxford American Dictionary (bundled with my computer OS, and therefore convenient): "varying in magnitude according to the direction of measurement." I've also often heard researchers refer to isotropic and anisotropic cell growth.

    In the definition of "anisotropic cell growth" (GO:0051211) we include the explanation that "growth rate varies according to the direction of growth" and may be limited to particular axes or locations. Perhaps these passages could also be used for other "structural polarity" definitions?

    m

     
  • Chris Mungall
    Chris Mungall
    2007-07-31

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    OK, so most GO terms are about the structural organization and can be defined using PATO:0001769 polarity (possibly improved def).

    Some, like
    GO:0060081 membrane hyperpolarization [DEF: "The process in which membrane potential changes in the hyperpolarizing direction from the resting potential, usually from negative to more negative."]

    are better defined using PATO:0001462 membrane potential [DEF: "A quality inhering in a cell's plasma membrane by virtue of the electrical potential difference across it."]

    PATO is a little confusing here, membrane and action potential are siblings, but action potential is defined as a property of a plasma membrane....

    +is_a PATO:0001464 electric potential [DEF: "A quality that is equal to the potential energy per unit charge associated with a static (time-invariant) electric field, also called the electrostatic potential."]
    ++is_a PATO:0001462 membrane potential [DEF: "A quality inhering in a cell's plasma membrane by virtue of the electrical potential difference across it."]
    ++is_a PATO:0001463 action potential [DEF: "A quality inhering in a cell's plasma membrane by virtue of a brief fluctuation in its potential caused by the rapid opening and closing of voltage-gated ion cha

     
    • status: open --> closed