Transporter terms standard definitions

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Standard graph structures

[i]transmembrane transporter activity
---[i]active transporter activity
------[i]primary active transporter activity
---------[i]decarboxylation-driven active transporter activity
---------[i]light-driven active transporter activity
---------[i]methyl transfer-driven active transporter activity
---------[i]oxidoreduction-driven active transporter activity
---------[i]P-P-bond-hydrolysis-driven transporter activity
------[i]secondary active transporter activity
---------[i]antiporter activity
---------[i]symporter activity
---------[i]uniporter activity
[i]transmembrane transporter activity
---[i]passive transmembrane transporter activity
------[i]channel activity
---------[i]gated channel activity
------------[i]dephosphorylation-gated channel activity
------------[i]ion gated channel activity
------------[i]ligand-gated channel activity
------------[i]mechanically gated channel activity
------------[i]phosphorylation-gated channel activity
------------[i]voltage-gated channel activity
[i]transporter activity
---[i]substrate-specific transporter activity
------[i]substrate-specific transmembrane transporter activity
---[i]transmembrane transporter activity
------[i]substrate-specific transmembrane transporter activity
[i]transmembrane transporter activity
---[i]efflux transmembrane transporter activity
---[i]uptake transmembrane transporter activity


[i]antiporter activity
---[i] X antiporter activity
------[i] X:Y antiporter activity
[i]symporter activity
---[i] X symporter activity
------[i] X:Y symporter activity



Standard definitions - Active transporters

X transmembrane transporter activity
def: Enables the transfer of X from one side of a membrane to the other. X is [insert description]. (Updated definition and made consistent across all term 2017-11-02 Pascale; added design pattern 2017-11-14)

X uptake transmembrane transporter activity
def: Catalysis of the transfer of X from the outside of a cell to the inside of a cell across a membrane. X is [insert description].

X efflux transmembrane transporter activity
def: Catalysis of the transfer of X from the inside of a cell to the outside of the cell across a membrane. X is [insert description].

active transmembrane X transporter activity
def: Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction. X is [insert description].

primary active transmembrane X transporter activity
def: Catalysis of the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by a primary energy source. Primary energy sources known to be coupled to transport are chemical, electrical and solar sources. X is [insert description].

decarboxylation-driven active transmembrane X transporter activity
def: Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by decarboxylation of a cytoplasmic substrate. X is [insert description].

light-driven active transmembrane X transporter activity
def: Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by light. X is [insert description].

methyl transfer-driven active transmembrane X transporter activity
def: Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by a methyl transfer reaction. X is [insert description].

oxidoreduction-driven active transmembrane X transporter activity
def: Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by an exothermic flow of electrons from a reduced substrate to an oxidized substrate. X is [insert description].

P-P-bond-hydrolysis-driven transmembrane X transporter activity
def: Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated. X is [insert description].

secondary active transmembrane X transporter activity
def: Enables the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Secondary active transporters include symporters and antiporters'. X is [insert description]. (Updated definition: https://github.com/geneontology/go-ontology/issues/14458)

X:solute antiporter activity
def: Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a antiport mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. X is [insert description].

X:solute symporter activity
def: Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a symport mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. X is [insert description].

X uniporter activity
def: Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a uniport mechanism which is independent of the movement of any other molecular species. X is [insert description].

In secondary active transporter defs include a reaction where possible. For excample:

Catalysis of the reaction: sugar(out) + H+(out) = sugar(in) + H+(in). Catalysis of the reaction: solute(out) + H+(out) = solute(in) + H+(in).


Standard definitions - Passive transporters

passive transmembrane X transporter activity
def: Catalysis of the transfer of X from one side of the membrane to the other, down the solute's concentration gradient. X is [insert description].

X channel activity
def: Enables the energy-independent facilitated diffusion of %s from one side of a membrane to the other, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules. (Updated definition and made consistent across all term 2017-11-14 Pascale; added design pattern)


gated X channel activity
def: Catalysis of the transmembrane transfer of X by a channel that opens in response to a specific stimulus.

dephosphorylation-gated X channel activity
def: Catalysis of the transmembrane transfer of X by a channel that opens in response to dephosphorylation of one of its constituent parts.

ion-gated X channel activity
def: Catalysis of the transmembrane transfer of X by a channel that opens in response to a specific ion stimulus.

ligand-gated X channel activity
def: Catalysis of the transmembrane transfer of X by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.

mechanically-gated X channel activity
def: Catalysis of the transmembrane transfer of X by a channel that opens in response to a mechanical stress.

phosphorylation-gated X channel activity
def: Catalysis of the transmembrane transfer of X by a channel that opens in response to phosphorylation of one of its constituent parts.

voltage-gated X channel activity
def: Catalysis of the transmembrane transfer of X by a channel whose open state is dependent on the voltage across the membrane in which it is embedded.

X channel activity
def:Catalysis of facilitated diffusion of X (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.

x gated y channel activity
def:Catalysis of the transmembrane transfer of y by a channel that opens in response to stimulus by x. Transport by a channel involves catalysis of facilitated diffusion of a solute (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel, without evidence for a carrier-mediated mechanism.

Other standard definitions

L-amino acid
def:L-Y is the levorotatory isomer of [insert systematic name].

D-amino acid
def:D-Y is the dextrorotatory isomer of [insert systematic name].

constituitive activity
def:This activity is constituitive and therefore always present, regardless of demand.

inducible activity
def:This activity is inducible and therefore only present when there is demand.

high affinity:
def:In high affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations.

Low affinity
def:In low affinity transport the transporter is able to bind the solute only if it is present at very high concentrations.


Standard definitions Process

Transport:
The directed movement of %s into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore."

(https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/cc_transport.yaml)

Transmembrane transport:
The process in which a x is transported across a membrane.

Organelle transmembrane transport:
The process in which a x is transported across a o membrane into or out of the o. x = compound; o = organelle