format-version: 1.0
date: 04:06:2009 12:32
saved-by: saubin
auto-generated-by: OBO-Edit 1.101
default-namespace: default_namespace

[Term]
id: GO:0000000
name: transport system
namespace: transport
def: "The system that regulates the moving of biochemicals and other atomic or molecular substances from and into the cell." [SA:sa]

[Term]
id: GO:0000001
name: import system
def: "The system that regulates the entrance of biochemicals and other atomic or molecular substances into the cell." [SA:sa]
is_a: GO:0000000 ! transport system

[Term]
id: GO:0000002
name: export system
namespace: transport
def: "The system that regulates the entrance of biochemicals and other atomic or molecular substances out of the cell." [SA:sa]
is_a: GO:0000000 ! transport system

[Term]
id: GO:0000003
name: TAT pathway
namespace: transport
def: "Is a protein export, or secretion pathway found in plants, bacteria, and archaea. It serves to actively translocate folded proteins across a lipid membrane bilayer." [wikipedia:sa]
is_a: GO:0000004 ! protein export

[Term]
id: GO:0000004
name: protein export
namespace: transport
def: "Protein export is a process whereby protein that has been manufactured in a cell is routed to the surface of the cell." [ENCY:encyclopedia.com]
is_a: GO:0000002 ! export system

[Term]
id: GO:0000005
name: Sec pathway
namespace: transport
def: "Transports proteins in an unfolded state." [prot:proteomics]
is_a: GO:0000004 ! protein export

[Term]
id: GO:0000006
name: ABC exporter system
namespace: transport
def: "Is a ABC tranporter system specialized in the export." [SA:sa]
is_a: GO:0000004 ! protein export

[Term]
id: GO:0000007
name: ABC transport system
namespace: transport
def: "The ABC (ATP binding cassette) transporter is one of the active transport systems of the cell, which is widespread in archaea, eubacteria, and eukaryotes (Higgins 1992)." [OR:oralgen]
is_a: GO:0000000 ! transport system

[Term]
id: GO:0000008
name: outer membrane
namespace: compartment
def: "The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites." [GOC:go_curators]
is_a: ID:0000001 ! membrane

[Term]
id: GO:0000009
name: cell wall
namespace: compartment
def: "The rigid outermost cell layer found in plants and certain algae, bacteria, and fungi but characteristically absent from animal cells." [AHDEL:ahdel]
is_a: ID:0000004 ! cell part

[Term]
id: GO:0000010
name: periplasm
def: "Space between the inner cytoplasmic membrane and external outer membrane of Gram-negative bacteria or the equivalent space between the cell membrane and cell wall in Gram-positive bacteria." [wikipedia:wi]
exact_synonym: "periplasmic space" [wikipedia:wi]
is_a: ID:0000004 ! cell part

[Term]
id: GO:0000011
name: extracellular medium
namespace: compartment
def: "Space or region out of the cell." [SA:sa]
is_a: ID:0000000 ! cellular component

[Term]
id: GO:0000012
name: cytoplasm
namespace: compartment
def: "The jellylike material that makes up much of a cell inside the cell membrane, and, in eukaryotic cells, surrounds the nucleus." [AHSD:ahsd]
is_a: ID:0000004 ! cell part

[Term]
id: GO:0000013
name: translocase
namespace: compartment
def: "Translocase is a general term for an enzyme that assists in moving another molecule, usually across a membrane." [wikipedia:sa]
is_a: ID:0000037 ! protein complex

[Term]
id: GO:0000014
name: Sec translocase
namespace: compartment
is_a: GO:0000013 ! translocase

[Term]
id: GO:0000015
name: protein translocation
def: "Mechanism by which a cell transports proteins to the appropriate positions in the cell or outside of it." [wikipedia:sa]
is_a: ID:0000022 ! transport

[Term]
id: ID:0000000
name: cellular component
namespace: compartment
def: "The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together." [GOC:go_curators, nlm:iupac]

[Term]
id: ID:0000001
name: membrane
namespace: compartment
def: "The cell membrane (also called the plasma membrane or plasmalemma) is the biological membrane separating the interior of a cell from the outside environment." [wikipedia:wi]
is_a: ID:0000004 ! cell part

[Term]
id: ID:0000002
name: inner membrane
namespace: compartment
def: "The inner membrane is the biological membrane (phospholipid bilayer) of an organelle or Gram-negative bacteria that is within an outer membrane." [wikipedia:wi]
exact_synonym: "cytoplasmic membrane" [wikipedia:wi]
xref_analog: wikipedia:http\://en.wikipedia.org
is_a: ID:0000001 ! membrane

[Term]
id: ID:0000003
name: biological process
def: "A recognized series of events or molecular functions." [GO:go]
created_by: sophie
creation_date: 2009-06-02T10:51:16Z

[Term]
id: ID:0000004
name: cell part
namespace: compartment
def: "Any constituent part of a cell, the basic structural and functional unit of all organisms." [GOC:jl]
is_a: ID:0000000 ! cellular component
created_by: sophie
creation_date: 2009-06-03T11:31:08Z

[Term]
id: ID:0000005
name: protein structure
def: "Description of the conformation of the protein." [SA:sa]
related_synonym: "protein topology" []
created_by: sophie
creation_date: 2009-06-02T11:01:36Z

[Term]
id: ID:0000006
name: primary structure
def: "The primary structure of a protein is its linear sequence of amino acids and the location of any disulfide (-S-S-) bridges." [KBP:kbp "http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/"]
xref_analog: SA:sa
is_a: ID:0000005 ! protein structure
created_by: sophie
creation_date: 2009-06-02T11:03:35Z

[Term]
id: ID:0000007
name: secondary structure
def: "Local inter-residue interactions mediated by hydrogen bonds, or not." [wikipedia:sa]
is_a: ID:0000005 ! protein structure
created_by: sophie
creation_date: 2009-06-02T11:06:58Z

[Term]
id: ID:0000008
name: tertiary structure
def: "Refers to the three-dimensional structure of the entire polypeptide chain." [KBP:kbp "http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/"]
is_a: ID:0000005 ! protein structure
created_by: sophie
creation_date: 2009-06-02T11:10:40Z

[Term]
id: ID:0000009
name: quaternary structure
def: "The arrangement of multiple folded protein molecules in a multi-subunit complex." [wikipedia:sa]
is_a: ID:0000005 ! protein structure
created_by: sophie
creation_date: 2009-06-02T11:11:48Z

[Term]
id: ID:0000010
name: alpha helix
def: "The coiled structure of many proteins consisting of a single chain of amino acids stabilized by hydrogen bonds." [MN:mn "medterms.com"]
related_synonym: "alpha-helical structure " []
exact_synonym: "alpha-helical conformation" []
is_a: ID:0000019 ! helix
created_by: sophie
creation_date: 2009-06-02T11:21:08Z

[Term]
id: ID:0000011
name: beta sheet
def: "A three-dimensional structure of a protein that takes on a flat, pleated appearance." [HG:hg "HOPES Glossary"]
is_a: ID:0000007 ! secondary structure
created_by: sophie
creation_date: 2009-06-02T11:24:14Z

[Term]
id: ID:0000012
name: biological adhesion
def: "The attachment of a cell or organism to a substrate or other organism." [GOC:isa_complete]
is_a: ID:0000003 ! biological process
created_by: sophie
creation_date: 2009-06-03T09:42:44Z

[Term]
id: ID:0000013
name: organic compound
namespace: compound
def: "A compound containing hydrocarbon groups." [AHMD:ahmd]

[Term]
id: ID:0000014
name: protein
namespace: compound
def: "A macromolecule composed of one or more polypeptides, each comprising a chain of amino acids linked by peptide bonds." [BB:bb "biobasics.gc.ca"]
is_a: ID:0000013 ! organic compound

[Term]
id: ID:0000015
name: cell-wall protein
namespace: compound
def: "A protein molecule that is attached to, or associated with the cell-wall of a cell." [SA:sa]
is_a: ID:0000014 ! protein

[Term]
id: ID:0000016
name: membrane protein
namespace: compound
def: "A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle." [wikipedia:wi]
is_a: ID:0000014 ! protein

[Term]
id: ID:0000017
name: transmembrane protein
def: "A transmembrane protein is a protein that spans the entire biological membrane." [wikipedia:wi]
is_a: ID:0000014 ! protein

[Term]
id: ID:0000018
name: gene
namespace: compound
def: "A sequence of DNA that either codes for the synthesis of a specific protein or has a specific regulatory function." [BO:bo "biotechnologyonline"]
is_a: ID:0000013 ! organic compound
relationship: codes_for ID:0000014 ! protein

[Term]
id: ID:0000019
name: helix
related_synonym: "helix content" []
exact_synonym: "helical conformation" []
exact_synonym: "helical structure" []
is_a: ID:0000007 ! secondary structure
created_by: sophie
creation_date: 2009-06-03T06:16:35Z

[Term]
id: ID:0000020
name: oligomeric complex
def: "A complex made of two or more subunits." [SA:sa]
is_a: ID:0000009 ! quaternary structure
created_by: sophie
creation_date: 2009-06-02T11:53:30Z

[Term]
id: ID:0000021
name: establishment of localization
def: "The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location." [GOC:ai]
is_a: ID:0000003 ! biological process
created_by: sophie
creation_date: 2009-06-03T09:44:22Z

[Term]
id: ID:0000022
name: transport
def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells, or within a multicellular organism." [GOC:mah]
is_a: ID:0000021 ! establishment of localization
created_by: sophie
creation_date: 2009-06-03T09:47:24Z

[Term]
id: ID:0000023
name: protein region
def: "Specific localisation in the protein structure." [SA:sa]
related_synonym: "protein domain" []
related_synonym: "protein segment" []
related_synonym: "protein sequence" []
created_by: sophie
creation_date: 2009-06-03T11:34:39Z

[Term]
id: ID:0000024
name: signal sequence
def: "A segment of about 15 to 30 amino acids at the N terminus of a protein, that enables the protein to be secreted (pass through a cell membrane)." [BTG:btg "biotech.fyicenter.com"]
related_synonym: "signal peptide" []
is_a: ID:0000023 ! protein region
created_by: sophie
creation_date: 2009-06-03T11:44:36Z

[Term]
id: ID:0000025
name: N-terminus
def: "The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) refers to the end of a protein or polypeptide terminated by an amino acid with a free amine group (-NH2)." [wikipedia:sa]
exact_synonym: "amino-terminus " []
is_a: ID:0000023 ! protein region
created_by: sophie
creation_date: 2009-06-03T11:46:51Z

[Term]
id: ID:0000026
name: C-terminus
def: "The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal end, or COOH-terminus) of a protein or polypeptide is the end of the amino acid chain terminated by a free carboxyl group (-COOH)." [wikipedia:sa]
is_a: ID:0000023 ! protein region
created_by: sophie
creation_date: 2009-06-03T11:54:54Z

[Term]
id: ID:0000027
name: N-terminal signal sequence
def: "A signal sequence specifically located in the N-terminus." [SA:sa]
is_a: ID:0000024 ! signal sequence
created_by: sophie
creation_date: 2009-06-03T12:00:44Z

[Term]
id: ID:0000028
name: physico-chemical property
def: "Object properties relating to physical chemistry." [Wordnet:wn]
xref_analog: GOC:go_curators
created_by: sophie
creation_date: 2009-06-03T12:04:44Z

[Term]
id: ID:0000029
name: hydrophobicity
def: "The property of being water-repellent; tending to repel and not absorb water." [Wordnet:wn]
is_a: ID:0000028 ! physico-chemical property
created_by: sophie
creation_date: 2009-06-03T01:33:02Z

[Term]
id: ID:0000030
name: hydrophilicity
def: "The tendency of a molecule to be solvated by water." [CHEM:def "chemicool.com"]
is_a: ID:0000028 ! physico-chemical property
created_by: sophie
creation_date: 2009-06-03T01:35:37Z

[Term]
id: ID:0000031
name: protein complex assembly
def: "The aggregation, arrangement and bonding together of a set of components to form a protein complex." [GOC:ai]
is_a: ID:0000032 ! macromolecular complex assembly
created_by: sophie
creation_date: 2009-06-03T01:37:16Z

[Term]
id: ID:0000032
name: macromolecular complex assembly
def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a complex." [GOC:jl]
is_a: ID:0000033 ! cellular component assembly
created_by: sophie
creation_date: 2009-06-03T01:40:00Z

[Term]
id: ID:0000033
name: cellular component assembly
def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete]
is_a: ID:0000034 ! anatomical structure formation
intersection_of: GO:0000006 ! ABC exporter system
created_by: sophie
creation_date: 2009-06-03T01:42:21Z

[Term]
id: ID:0000034
name: anatomical structure formation
def: "The process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structure is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph, GOC:tb]
comment: GO:0010926.
is_a: ID:0000003 ! biological process
created_by: sophie
creation_date: 2009-06-03T01:56:31Z

[Term]
id: ID:0000035
name: protein insertion
def: "The process by which a protein is incorporated into a cellular component." [SA:sa]
is_a: ID:0000003 ! biological process
created_by: sophie
creation_date: 2009-06-03T02:00:46Z

[Term]
id: ID:0000036
name: macromolecular complex
namespace: compartment
def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together." [GOC:mah]
is_a: ID:0000000 ! cellular component
created_by: sophie
creation_date: 2009-06-03T02:51:12Z

[Term]
id: ID:0000037
name: protein complex
namespace: compartment
def: "Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or carbohydrate groups." [GOC:go_curators]
is_a: ID:0000036 ! macromolecular complex
created_by: sophie
creation_date: 2009-06-03T02:51:43Z

[Term]
id: ID:0000038
name: protein-lipid complex
namespace: compartment
def: "A macromolecular complex containing both protein and lipid molecules." [GOC:mah]
is_a: ID:0000036 ! macromolecular complex
created_by: sophie
creation_date: 2009-06-03T02:54:07Z

[Term]
id: ID:0000039
name: transmembrane helix
is_a: ID:0000019 ! helix
created_by: sophie
creation_date: 2009-06-03T06:17:44Z

[Term]
id: ID:0000040
name: amphipathic helix
is_a: ID:0000019 ! helix
created_by: sophie
creation_date: 2009-06-03T06:18:25Z

[Term]
id: ID:0000041
name: amphiphilic alpha-helix
is_a: ID:0000010 ! alpha helix
created_by: sophie
creation_date: 2009-06-03T06:19:50Z

[Term]
id: ID:0000042
name: double helix
is_a: ID:0000019 ! helix
created_by: sophie
creation_date: 2009-06-03T06:20:31Z

[Term]
id: ID:0000043
name: entrance helix
is_a: ID:0000019 ! helix
created_by: sophie
creation_date: 2009-06-03T06:21:10Z

[Term]
id: ID:0000044
name: bent alpha-helix
is_a: ID:0000010 ! alpha helix
created_by: sophie
creation_date: 2009-06-03T06:21:35Z

[Term]
id: ID:0000045
name: N-terminal alpha-helix
is_a: ID:0000010 ! alpha helix
created_by: sophie
creation_date: 2009-06-03T06:21:56Z

[Term]
id: ID:0000046
name: N-terminal helix
is_a: ID:0000019 ! helix
created_by: sophie
creation_date: 2009-06-03T06:22:21Z

[Term]
id: ID:0000047
name: minihelix
is_a: ID:0000019 ! helix
created_by: sophie
creation_date: 2009-06-04T08:19:19Z

[Term]
id: ID:0000048
name: amphipathic alpha-helix
is_a: ID:0000010 ! alpha helix
created_by: sophie
creation_date: 2009-06-04T08:19:44Z

[Term]
id: ID:0000049
name: N-terminal transmembrane helix
is_a: ID:0000039 ! transmembrane helix
created_by: sophie
creation_date: 2009-06-04T08:21:31Z

[Term]
id: ID:0000050
name: membrane-associated protein
namespace: compound
is_a: ID:0000014 ! protein
created_by: sophie
creation_date: 2009-06-04T11:31:59Z

[Term]
id: ID:0000051
name: SecA
namespace: compound
is_a: ID:0000050 ! membrane-associated protein
relationship: participates_to GO:0000005 ! Sec pathway
created_by: sophie
creation_date: 2009-06-04T11:32:25Z

[Typedef]
id: codes_for
name: codes for
def: "A gene CODES FOR a protein." [SA:sa]

[Typedef]
id: is_part_of_complex
name: is part of complex
def: "Protein IS PART OF COMPLEX complex." [SA:sa]

[Typedef]
id: participates_to
name: participates to
created_by: sophie
creation_date: 2009-06-04T11:35:53Z