Plasma lipoprotein particle ontology

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This work has been completed. Comments can be found on the SourceForge entry (SF 3019819).

Process ontology broad parent term

In the process ontology it would be very helpful to have a parent term which groups together plasma lipoprotein particle remodeling, assembly and clearance terms, at present some of these are under cellular process and some are under multicellular organismal process. These processes involve the transport of the lipoprotein to or from the extracellular space so it seems more sensible for all of these terms need to be child terms of multicellular organismal process.

Please could the following terms be created/repositioned in the ontology:

New Term: plasma lipoprotein particle organization

Definition: A process which results in the assembly, remodeling, arrangement of constituent parts, or disassembly of a plasma lipoprotein particle.

With the is_a parent GO:0032501 multicellular organismal process

dbxrf: BHF

New term: apolipoprotein E recycling

Definition: The process by which chylomicron remnant-associated apolipoprotein E is internalized by endocytosis, localized to recycling endosomes and then secreted in association with a high-density lipoprotein particle .

Exact synonym APOE recycling

See PMID: 16373604 for more details about this process

dbxrf: BHF

is_a parent New term: plasma lipoprotein particle organization

part_of parents: GO:0034380 high-density lipoprotein particle assembly GO:0034382 chylomicron remnant clearance

Is this the correct use of the part_of relationship? Chylomicron remnant clearance will result in APOE recycling. Not all HDL particles are assembled with recycled APOE.

ADD ‘plasma’ to name GO:0034381 lipoprotein particle clearance

all of the annotations to this term (or child terms) relate to clearance of plasma lipoprotein particles and would make this name consistent with plasma lipoprotein particle assembly and plasma lipoprotein particle remodeling

Suggested new ontology arrangement:

GO:0032501 multicellular organismal process

>is_a New term: plasma lipoprotein particle organization

>> is_a GO:0034377 plasma lipoprotein particle assembly

>> is_a GO:0034381 (ADD ‘plasma’ to name) lipoprotein particle clearance

>> is_a GO:0034369 plasma lipoprotein particle remodeling

>> is_a new term apolipoprotein recycling

with no links to GO:0043933 macromolecular complex subunit organization

Lipoprotein clearance ontology

Remove macromolecular complex disassembly as a parent of lipoprotein clearance terms (as this parent has the parent term GO:0016043 cellular component organization.)

New term is_a triglyceride-rich lipoprotein particle clearance

Synonym exact: triacylglycerol-rich lipoprotein particle clearance

Definition: The process by which a triglyceride-rich lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.

dbxrf: BHF

New term is_a intermediate-density lipoprotein particle clearance

Synonym exact: IDL clearance

Definition: The process by which an intermediate-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.

dbxrf: BHF

This will then enable the ontology structure for the clearance terms to follow the already existing ontology structure for remodeling terms:

New term: plasma lipoprotein particle organization

> is_a GO:0034381 (add ‘plasma’ to name) lipoprotein particle clearance

>>GO:0034383 low-density lipoprotein particle

>>GO:0034384 high-density lipoprotein particle clearance

>> New term is_a triglyceride-rich lipoprotein particle clearance

>>>GO:0034447 very-low-density lipoprotein particle clearance

>>>GO:0034382 chylomicron remnant clearance

>>> New term is_a intermediate-density lipoprotein particle clearance

Plasma lipoprotein assembly

Change ontology for GO:0034377 plasma lipoprotein particle assembly by removing it from parent: GO:0065005 protein-lipid complex assembly and adding new parent term: plasma lipoprotein particle organization as suggested in section 1:

GO:0032501 multicellular organismal process

>is_a New term: plasma lipoprotein particle organization

>> is_a GO:0034377 plasma lipoprotein particle assembly

To GO:0034380 high-density lipoprotein particle assembly

ADD exact synonym HDL formation

Plasma lipoprotein remodeling

Change ontology for GO:0034369 plasma lipoprotein particle remodeling by removing it from parent term GO:0034368 protein-lipid complex remodeling and adding new parent term: plasma lipoprotein particle organization as suggested in section 1:

Add parent GO:0032501 multicellular organismal process

>is_a New term: plasma lipoprotein particle organization

>GO:0034369 plasma lipoprotein particle remodeling

To GO:0034374 low-density lipoprotein particle remodeling

ADD synonym related: small dense LDL formation

synonym related: small dense low-density lipoprotein particle formation

To GO:0034375 high-density lipoprotein particle remodeling

Add as an is_a parent to GO:0034376 conversion of discoidal high-density lipoprotein to spherical high-density lipoprotein as follows:

GO:0034375 high-density lipoprotein particle remodeling

>is_a GO:0034376 conversion of discoidal high-density lipoprotein to spherical high-density lipoprotein.

Lipoprotein binding

New term: protein-lipid complex binding

Definition: Interacting selectively and non-covalently with any protein-lipid complex.

dbxrf: BHF

New term: intermediate-density lipoprotein binding

Definition: Interacting selectively and non-covalently with a intermediate-density lipoprotein particle, one of the classes of lipoprotein particles found in blood plasma in many animals.

synonym exact: IDL binding

dbxrf: BHF

GO:0008034 lipoprotein binding (Definition: Interacting selectively and non-covalently with any conjugated, water-soluble protein in which the nonprotein moiety consists of a lipid or lipids) is not an appropriate parent term for HDL binding, LDL binding and VLDL binding terms. Although some of the proteins in the plasma lipoprotein particle are conjugated with lipid, this is not necessarily the protein bound when an HDL, LDL or VLDL particle is bound.

Therefore remove GO:0008034 lipoprotein binding as parent from HDL binding, LDL binding, and VLDL binding and create new ontology:

GO:0032403 protein complex binding

>New term: protein-lipid complex binding

>>New term: intermediate-density lipoprotein binding

>>GO:0030169 low-density lipoprotein binding

>>GO:0008035 high-density lipoprotein binding

>>GO:0030228 lipoprotein receptor activity

>>GO:0035478 chylomicron binding

>>GO:0034189 very-low-density lipoprotein binding

Add ‘particle’ and ‘plasma’ in the definitions of terms below, as the binding is to the protein in the particle not necessarily to the lipoprotein:

GO:0030169 low-density lipoprotein binding

  • New definition: Interacting selectively and non-covalently with a low-density lipoprotein particle, one of the classes of plasma lipoprotein particles found in blood plasma in many animals (data normally relate to humans).

GO:0008035 high-density lipoprotein binding

  • New definition: Interacting selectively and non-covalently with a high-density lipoprotein particle: one of the classes of plasma lipoprotein particles found in blood plasma in many animals (data normally relate to humans).

GO:0030228 lipoprotein receptor activity (the definition for this is very wrong)

  • New definition: Combining with a plasma lipoprotein particle to initiate a change in cell activity. Plasma lipoprotein particles transport lipids, which are non-covalently associated with the particles, in the blood or lymph.

GO:0035478 chylomicron binding

  • New definition: Interacting selectively and non-covalently with a chylomicron, a class of plasma lipoprotein particles found in blood plasma in many animals. Chylomicrons are the largest plasma lipoprotein particles, with diameters of 75-600 nanometers and have the lowest protein-to-lipid ratio and therefore the lowest density.

GO:0034189 very-low-density lipoprotein binding

  • New definition: Interacting selectively and non-covalently with a very-low-density lipoprotein particle, one of the classes of plasma lipoprotein particles found in blood plasma in many animals.

GO:0005041 low-density lipoprotein receptor activity

  • New definition: Combining with a low-density lipoprotein particle to initiate a change in cell activity.

GO:0030229 very-low-density lipoprotein receptor activity

  • New definition: Combining with a very-low-density lipoprotein particle to initiate a change in cell activity.

GO:0070506 high-density lipoprotein receptor activity

  • New definition: Combining with a high-density lipoprotein particle to initiate a change in cell activity.

Thanks

Ruth