format-version: 1.0
date: 11:09:2006 14:54
autogenerated-by: /Users/cjm/cvs/go-dev/go-perl/scripts/go2fmt.pl
format-version: 1.0
date: 28:06:2006 17:39
saved-by: midori
auto-generated-by: OBO-Edit 1.001
default-namespace: gene_ontology
remark: cvs version: $Revision: 1.1 $
remark: GO_slim_name: Generic GO slim
remark: GO_slim_authors: Suparna Mundodi and Amelia Ireland
remark: GO_slim_contact: smundodi@acoma.stanford.edu
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_goa "GOA and proteome slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"

[Term]
id: GO:0000003
name: reproduction
alt_id: GO:0019952
namespace: biological_process
def: "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." [GOC:go_curators, ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008150

[Term]
id: GO:0000004
name: biological process unknown
namespace: biological_process
def: "Used for the annotation of gene products whose process is not known or cannot be inferred." [GOC:sgd_curators]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0008150

[Term]
id: GO:0000166
name: nucleotide binding
namespace: molecular_function
def: "Interacting selectively with a nucleotide\, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety." [GOC:mah, ISBN:0198547684]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0005488

[Term]
id: GO:0000228
name: nuclear chromosome
namespace: cellular_component
def: "A chromosome found in the nucleus of a eukaryotic cell." [GOC:mah]
subset: goslim_generic
is_a: GO:0005694
relationship: part_of GO:0005634
synonym: "nuclear interphase chromosome" NARROW []

[Term]
id: GO:0000229
name: cytoplasmic chromosome
namespace: cellular_component
def: "A chromosome found in the cytoplasm." [GOC:mah]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0005694
relationship: part_of GO:0005737
synonym: "cytoplasmic interphase chromosome" NARROW []

[Term]
id: GO:0003674
name: molecular_function
namespace: molecular_function
def: "Elemental activities\, such as catalysis or binding\, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok

[Term]
id: GO:0003676
name: nucleic acid binding
namespace: molecular_function
def: "Interacting selectively with any nucleic acid." [GOC:jl]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0005488

[Term]
id: GO:0003677
name: DNA binding
namespace: molecular_function
def: "Interacting selectively with DNA (deoxyribonucleic acid)." [GOC:jl]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003676
synonym: "microtubule/chromatin interaction" RELATED []
synonym: "plasmid binding" NARROW []

[Term]
id: GO:0003682
name: chromatin binding
namespace: molecular_function
def: "Interacting selectively with chromatin\, the network of fibers of DNA and protein that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC:jl, ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
is_a: GO:0005488
synonym: "microtubule/chromatin interaction" RELATED []
synonym: "nuclear membrane vesicle binding to chromatin" NARROW []
synonym: "lamin/chromatin binding" BROAD []

[Term]
id: GO:0003700
name: transcription factor activity
alt_id: GO:0000130
namespace: molecular_function
def: "The function of binding to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:curators]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0003677
is_a: GO:0030528

[Term]
id: GO:0003723
name: RNA binding
namespace: molecular_function
def: "Interacting selectively with an RNA molecule or a portion thereof." [GOC:mah]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003676

[Term]
id: GO:0003774
name: motor activity
namespace: molecular_function
def: "Catalysis of movement along a polymeric molecule such as a microfilament or microtubule\, coupled to the hydrolysis of a nucleoside triphosphate." [GOC:mah, ISBN:0815316194]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003674

[Term]
id: GO:0003779
name: actin binding
namespace: molecular_function
def: "Interacting selectively with monomeric or multimeric forms of actin\, including actin filaments." [GOC:clt]
subset: goslim_generic
is_a: GO:0008092
synonym: "membrane associated actin binding" NARROW []

[Term]
id: GO:0003824
name: catalytic activity
namespace: molecular_function
def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions\, the reactants are known as substrates\, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates\, and are usually composed wholly or largely of protein\, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0003674
synonym: "enzyme activity" RELATED []

[Term]
id: GO:0004518
name: nuclease activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN:0198547684]
comment: Consider also annotating to the molecular function term 'nucleic acid binding ; GO:0003676'.
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0016787
xref: EC:3.1.-.-

[Term]
id: GO:0004672
name: protein kinase activity
alt_id: GO:0050222
namespace: molecular_function
def: "Catalysis of the transfer of a phosphate group\, usually from ATP\, to a protein substrate." [GOC:jl]
subset: goslim_generic
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0016301
synonym: "protamine kinase activity" NARROW []
xref: EC:2.7.1.37
xref: MetaCyc:PROTEIN-KINASE-RXN
xref: Reactome:4030

[Term]
id: GO:0004721
name: phosphoprotein phosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases\, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity." [EC:3.1.3.16, ISBN:0198547684]
subset: goslim_generic
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0016787
synonym: "protein phosphatase activity" EXACT []
xref: EC:3.1.3.16
xref: MetaCyc:3.1.3.16-RXN
xref: Reactome:113432
xref: Reactome:113757
xref: Reactome:115322
xref: Reactome:115328
xref: Reactome:115332
xref: Reactome:117849
xref: Reactome:117855
xref: Reactome:117859
xref: Reactome:117862
xref: Reactome:120480
xref: Reactome:120488
xref: Reactome:122808
xref: Reactome:122814
xref: Reactome:122818
xref: Reactome:124864
xref: Reactome:124870
xref: Reactome:1887
xref: Reactome:69198
xref: Reactome:69262
xref: Reactome:69735
xref: Reactome:69742

[Term]
id: GO:0004871
name: signal transducer activity
namespace: molecular_function
def: "Mediates the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell." [GOC:jl, ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003674
synonym: "SAP kinase 3 activity" NARROW []
synonym: "SAP kinase 4 activity" NARROW []
synonym: "SAP kinase 5 activity" NARROW []

[Term]
id: GO:0004872
name: receptor activity
namespace: molecular_function
def: "Combining with an extracellular or intracellular messenger to initiate a change in cell activity." [GOC:ceb, ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0004871
synonym: "immunophilin" RELATED []
synonym: "endoplasmic reticulum receptor activity" NARROW []
synonym: "GPI-anchored membrane-bound receptor" NARROW []
synonym: "peroxisome integral membrane receptor" NARROW []
synonym: "peroxisome receptor" NARROW []
synonym: "receptor guanylate cyclase activity" NARROW []

[Term]
id: GO:0005102
name: receptor binding
namespace: molecular_function
def: "Interacting selectively with one or more specific sites on a receptor molecule\, a macromolecule that undergoes combination with a hormone\, neurotransmitter\, drug or intracellular messenger to initiate a change in cell function." [GOC:bf, GOC:ceb, ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0004871
is_a: GO:0005515
synonym: "adrenocorticotropin" RELATED []
synonym: "allatostatin" RELATED []
synonym: "alpha-2 macroglobulin receptor-associated protein activity" RELATED []
synonym: "bacteriocin activity" RELATED []
synonym: "cell adhesion molecule activity" RELATED []
synonym: "cell adhesion receptor inhibitor activity" RELATED []
synonym: "cell adhesion receptor regulator activity" RELATED []
synonym: "colicin" RELATED []
synonym: "insulin" RELATED []
synonym: "membrane-associated guanylate kinase" RELATED []
synonym: "N-methyl-D-aspartate receptor-associated protein activity" RELATED []
synonym: "nicotinic acetylcholine receptor-associated protein activity" RELATED []
synonym: "receptor-associated protein activity" RELATED []
synonym: "selectin" RELATED []
synonym: "tachykinin" RELATED []
synonym: "transmembrane receptor protein serine/threonine kinase related_receptor-associated protein activity" RELATED []
synonym: "receptor ligand" NARROW []

[Term]
id: GO:0005198
name: structural molecule activity
namespace: molecular_function
def: "The action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cell." [GOC:mah]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003674
synonym: "colicin" RELATED []
synonym: "pore-forming toxin activity" RELATED []
synonym: "puparial glue (sensu Diptera)" RELATED []
synonym: "yolk protein" RELATED []

[Term]
id: GO:0005215
name: transporter activity
namespace: molecular_function
def: "Enables the directed movement of substances (such as macromolecules\, small molecules\, ions) into\, out of\, within or between cells." [GOC:ai, GOC:df]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003674
synonym: "small-molecule carrier or transporter" RELATED []
synonym: "peroxisomal membrane transporter" NARROW []
xref: Reactome:1391

[Term]
id: GO:0005216
name: ion channel activity
namespace: molecular_function
def: "Allows the regulatable energy-independent passage of ions across a lipid bilayer down a concentration gradient." [GOC:cy]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0005215

[Term]
id: GO:0005326
name: neurotransmitter transporter activity
namespace: molecular_function
def: "Enables the directed movement of a neurotransmitter into\, out of\, within or between cells. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [GOC:ai, ISBN:0198506732]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0005215

[Term]
id: GO:0005488
name: binding
namespace: molecular_function
def: "The selective\, often stoichiometric interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732]
comment: Note that ligand is being used in its broadest biological sense. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0003674
synonym: "ligand" NARROW []

[Term]
id: GO:0005509
name: calcium ion binding
namespace: molecular_function
def: "Interacting selectively with calcium ions (Ca2+)." [GOC:ai]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0005488
synonym: "calcium ion storage activity" RELATED []
synonym: "fibrillin" RELATED []

[Term]
id: GO:0005515
name: protein binding
alt_id: GO:0045308
namespace: molecular_function
def: "Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC:go_curators]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0005488
synonym: "alpha-2 macroglobulin receptor-associated protein activity" RELATED []
synonym: "calcium-dependent cell adhesion molecule activity" RELATED []
synonym: "calcium-independent cell adhesion molecule activity" RELATED []
synonym: "cell adhesion molecule activity" RELATED []
synonym: "death receptor adaptor protein activity" RELATED []
synonym: "death receptor interacting protein activity" RELATED []
synonym: "death receptor-associated factor activity" RELATED []
synonym: "glycine receptor-associated protein" RELATED []
synonym: "N-methyl-D-aspartate receptor-associated protein activity" RELATED []
synonym: "nicotinic acetylcholine receptor-associated protein activity" RELATED []
synonym: "protein degradation tagging activity" RELATED []
synonym: "protein tagging activity" RELATED []
synonym: "receptor-associated protein activity" RELATED []
synonym: "protein amino acid binding" EXACT []

[Term]
id: GO:0005554
name: molecular function unknown
namespace: molecular_function
def: "Used for the annotation of gene products whose function is not known or cannot be inferred." [GOC:sgd_curators]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003674

[Term]
id: GO:0005575
name: cellular_component
namespace: cellular_component
def: "The part of a cell of which a gene product is a component; for purpose of GO includes the extracellular environment of cells; a gene product may be a component of one or more parts of a cell; this term includes gene products that are parts of macromolecular complexes\, by the definition that all members of a complex normally copurify under all except extreme conditions." [GOC:go_curators]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok

[Term]
id: GO:0005576
name: extracellular region
namespace: cellular_component
def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators]
comment: Note that this term is intended to annotate gene products that are not attached to the cell surface.
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0005575
synonym: "extracellular" EXACT []

[Term]
id: GO:0005578
name: extracellular matrix (sensu Metazoa)
namespace: cellular_component
def: "A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. As in\, but not restricted to\, the multicellular animals (Metazoa\, ncbi_taxonomy_id:33208)." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
relationship: part_of GO:0005576
synonym: "adhesive extracellular matrix constituent" NARROW []

[Term]
id: GO:0005615
name: extracellular space
namespace: cellular_component
def: "That part of a multicellular organism outside the cells proper\, usually taken to be outside the plasma membranes\, and occupied by fluid." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
relationship: part_of GO:0005576
synonym: "intercellular space" RELATED []

[Term]
id: GO:0005618
name: cell wall
namespace: cellular_component
def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant\, fungal\, and most prokaryotic cells\, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and\, often\, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0030312

[Term]
id: GO:0005622
name: intracellular
namespace: cellular_component
def: "The living contents of a cell; the matter contained within (but not including) the plasma membrane\, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
relationship: part_of GO:0005623
synonym: "protoplasm" EXACT []

[Term]
id: GO:0005623
name: cell
namespace: cellular_component
def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0005575

[Term]
id: GO:0005634
name: nucleus
namespace: cellular_component
def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells\, the nucleus contains all of the cell's chromosomes except the organellar chromosomes\, and is the site of RNA synthesis and processing. In some species\, or in specialized cell types\, RNA metabolism or DNA replication may be absent." [GOC:go_curators]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
is_a: GO:0043226
relationship: part_of GO:0005622

[Term]
id: GO:0005635
name: nuclear envelope
alt_id: GO:0005636
namespace: cellular_component
def: "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space\, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_plant
relationship: part_of GO:0005634

[Term]
id: GO:0005654
name: nucleoplasm
namespace: cellular_component
def: "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC:ma, ISBN:0124325653]
subset: goslim_generic
subset: goslim_plant
relationship: part_of GO:0005634

[Term]
id: GO:0005694
name: chromosome
namespace: cellular_component
def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_goa
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0043226
relationship: part_of GO:0005622
synonym: "chromatid" RELATED []
synonym: "interphase chromosome" NARROW []
synonym: "prophase chromosome" NARROW []

[Term]
id: GO:0005730
name: nucleolus
namespace: cellular_component
def: "A small\, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein\, is not bounded by a limiting membrane\, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA\, the processing of this RNA into 5.8S\, 18S\, and 28S components of ribosomal RNA\, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
relationship: part_of GO:0005634

[Term]
id: GO:0005737
name: cytoplasm
namespace: cellular_component
def: "All of the contents of a cell excluding the plasma membrane and nucleus\, but including other subcellular structures." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
relationship: part_of GO:0005622

[Term]
id: GO:0005739
name: mitochondrion
namespace: cellular_component
def: "A semiautonomous\, self replicating organelle that occurs in varying numbers\, shapes\, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
is_a: GO:0043226
relationship: part_of GO:0005737
synonym: "mitochondria" EXACT []

[Term]
id: GO:0005764
name: lysosome
namespace: cellular_component
def: "Any of a group of related cytoplasmic\, membrane bound organelles that are found in most animal cells and that contain a variety of hydrolases\, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
is_a: GO:0005773
synonym: "lysosomal cysteine-type endopeptidase" RELATED []
synonym: "lysosomal protein stabilization" RELATED []

[Term]
id: GO:0005768
name: endosome
namespace: cellular_component
def: "A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
is_a: GO:0043226
relationship: part_of GO:0005737
synonym: "endosomal oligosaccharide transporter" RELATED []

[Term]
id: GO:0005773
name: vacuole
namespace: cellular_component
def: "A closed structure\, found only in eukaryotic cells\, that is completely surrounded by unit membrane and contains liquid material." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0043226
relationship: part_of GO:0005737
synonym: "vacuolar carboxypeptidase Y" RELATED []

[Term]
id: GO:0005777
name: peroxisome
alt_id: GO:0019818
namespace: cellular_component
def: "A small\, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2)." [ISBN:0815316194]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
is_a: GO:0043226
relationship: part_of GO:0005737
synonym: "peroxisomal fatty acyl transporter" RELATED []
synonym: "peroxisomal membrane transporter" RELATED []
synonym: "peroxisome receptor" RELATED []
synonym: "peroxisome vesicle" BROAD []

[Term]
id: GO:0005783
name: endoplasmic reticulum
namespace: cellular_component
def: "The irregular network of unit membranes\, visible only by electron microscopy\, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels\, which are often expanded into slitlike cavities called cisternae. The ER takes two forms\, rough (or granular)\, with ribosomes adhering to the outer surface\, and smooth (with no ribosomes attached)." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
is_a: GO:0043226
relationship: part_of GO:0005737
synonym: "ER" EXACT []

[Term]
id: GO:0005794
name: Golgi apparatus
namespace: cellular_component
def: "A compound membranous cytoplasmic organelle of eukaryotic cells\, consisting of flattened\, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes\, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum\, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle\, while in invertebrates and plants\, where they are known usually as dictyosomes\, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins\, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis\, in the vicinity of the cis face\, trans\, in the vicinity of the trans face\, and medial\, lying between the cis and trans regions." [ISBN:0198506732]
comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
is_a: GO:0043226
relationship: part_of GO:0005737
synonym: "Golgi" EXACT []
synonym: "Golgi complex" EXACT []
synonym: "Golgi ribbon" NARROW []

[Term]
id: GO:0005811
name: lipid particle
namespace: cellular_component
def: "Any particle of coalesced lipids in the cytoplasm of a cell. May include associated proteins." [GOC:mah]
comment: Note that this term does not refer to vesicle, but instead to structures in which lipids do not necessarily form bilayers.
subset: goslim_generic
relationship: part_of GO:0005737
synonym: "lipid droplet" EXACT []

[Term]
id: GO:0005815
name: microtubule organizing center
namespace: cellular_component
def: "A region in a eukaryotic cell\, such as a centrosome or basal body\, from which microtubules grow." [ISBN:0815316194]
subset: goslim_generic
subset: goslim_yeast
relationship: part_of GO:0005737
synonym: "microtubule organising centre" EXACT []
synonym: "MTOC" EXACT []

[Term]
id: GO:0005829
name: cytosol
namespace: cellular_component
def: "That part of the cytoplasm that does not contain membranous or particulate subcellular components." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
relationship: part_of GO:0005737

[Term]
id: GO:0005840
name: ribosome
namespace: cellular_component
def: "An intracellular organelle\, about 200 A in diameter\, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits\, one large and one small\, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients\, expressed in Svedberg units (symbol: S). Hence\, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit\, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation\, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes\, eukaryotes\, mitochondria\, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0043226
is_a: GO:0043234
relationship: part_of GO:0005737
synonym: "ribosomal RNA" NARROW []

[Term]
id: GO:0005856
name: cytoskeleton
namespace: cellular_component
def: "Any of the various filamentous elements within the cytoplasm of eukaryotic cells that remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments\, microfilaments\, microtubules\, and the microtrabecular lattice. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions\, including cellular movement\, cell division\, endocytosis\, and movement of organelles." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0043226
relationship: part_of GO:0005622

[Term]
id: GO:0005886
name: plasma membrane
namespace: cellular_component
def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
relationship: part_of GO:0005623
synonym: "plasma membrane cation-transporting ATPase" RELATED []
synonym: "plasma membrane copper transporter" RELATED []
synonym: "plasma membrane long-chain fatty acid transporter" RELATED []
synonym: "cell membrane" EXACT []
synonym: "cytoplasmic membrane" EXACT []
synonym: "plasmalemma" EXACT []
synonym: "bacterial inner membrane" NARROW []
synonym: "juxtamembrane" BROAD []

[Term]
id: GO:0005929
name: cilium
namespace: cellular_component
def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane\, and contains a regular longitudinal array of microtubules\, anchored basally in a centriole." [GOC:kva, ISBN:0198547684]
subset: goslim_generic
is_a: GO:0043226
relationship: part_of GO:0005622

[Term]
id: GO:0005941
name: unlocalized protein complex
namespace: cellular_component
def: "Used as a holding place for cellular components whose precise localization is\, as yet\, unknown\, or has not been determined by GO (the latter is the major reason for nodes to have this parent); this term should not be used for annotation of gene products." [GOC:ma]
comment: See also the cellular component term 'cellular component unknown ; GO:0008372'.
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0043234

[Term]
id: GO:0005975
name: carbohydrate metabolism
namespace: biological_process
def: "The chemical reactions and pathways involving carbohydrates\, any of a group of organic compounds based of the general formula Cx(H2O)y." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0044238

[Term]
id: GO:0006091
name: generation of precursor metabolites and energy
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of precursor metabolites\, substances from which energy is derived\, and the processes involved in the liberation of energy from these substances." [GOC:jl]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0008152
synonym: "energy pathways" BROAD []

[Term]
id: GO:0006118
name: electron transport
namespace: biological_process
def: "The transport of electrons from an electron donor to an electron acceptor." [URL:http://cancerweb.ncl.ac.uk/]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0006091
is_a: GO:0006810
synonym: "6-phosphofructokinase reduction" RELATED []
synonym: "dihydrobiopterin reduction" RELATED []
synonym: "dihydrolipoamide reduction" RELATED []
synonym: "dihydrolipoylprotein reduction" RELATED []
synonym: "dihydropteridine reduction" RELATED []
synonym: "other pathways of electron transport" RELATED []
synonym: "oxidized glutathione reduction" RELATED []
synonym: "protein-disulfide reduction" RELATED []
synonym: "electron transfer" EXACT []

[Term]
id: GO:0006139
name: nucleobase, nucleoside, nucleotide and nucleic acid metabolism
namespace: biological_process
def: "The chemical reactions and pathways involving nucleobases\, nucleosides\, nucleotides and nucleic acids." [GOC:ai]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0044238

[Term]
id: GO:0006259
name: DNA metabolism
namespace: biological_process
def: "The chemical reactions and pathways involving DNA\, deoxyribonucleic acid\, one of the two main types of nucleic acid\, consisting of a long\, unbranched macromolecule formed from one\, or more commonly\, two\, strands of linked deoxyribonucleotides." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0006139

[Term]
id: GO:0006350
name: transcription
namespace: biological_process
def: "The synthesis of either RNA on a template of DNA or DNA on a template of RNA." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0006139
xref: Reactome:74159

[Term]
id: GO:0006412
name: protein biosynthesis
alt_id: GO:0006416
alt_id: GO:0006453
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of a protein\, rather than of proteins in general." [GOC:go_curators]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0009058
is_a: GO:0019538
synonym: "protein-synthesizing GTPase activity" RELATED []
synonym: "protein-synthesizing GTPase activity\, elongation" RELATED []
synonym: "protein-synthesizing GTPase activity\, initiation" RELATED []
synonym: "protein-synthesizing GTPase activity\, termination" RELATED []
synonym: "protein anabolism" EXACT []
synonym: "protein formation" EXACT []
synonym: "protein synthesis" EXACT []

[Term]
id: GO:0006464
name: protein modification
namespace: biological_process
def: "The covalent alteration of one or more amino acid residues within a protein\, resulting in a change in the properties of that protein." [GOC:go_curators]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0019538
synonym: "protein tagging activity" RELATED []
synonym: "protein-pyrroloquinoline-quinone linkage" NARROW []
xref: Reactome:163841

[Term]
id: GO:0006519
name: amino acid and derivative metabolism
namespace: biological_process
def: "The chemical reactions and pathways involving amino acids\, organic acids containing one or more amino substituents\, and compounds derived from amino acids." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0044238

[Term]
id: GO:0006629
name: lipid metabolism
namespace: biological_process
def: "The chemical reactions and pathways involving lipids\, compounds soluble in an organic solvent but not\, or sparingly\, in an aqueous solvent. Includes fatty acids; neutral fats\, other fatty-acid esters\, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids\, phospholipids and sphingolipids; and carotenes\, polyprenols\, sterols\, terpenes and other isoprenoids." [GOC:ma]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0044238

[Term]
id: GO:0006810
name: transport
namespace: biological_process
def: "The directed movement of substances (such as macromolecules\, small molecules\, ions) into\, out of\, within or between cells." [GOC:mah]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
relationship: part_of GO:0007582
synonym: "hydrolase activity\, acting on acid anhydrides\, acting on GTP\, involved in cellular and subcellular movement" RELATED []
synonym: "small molecule transport" NARROW []
synonym: "solute:solute exchange" NARROW []

[Term]
id: GO:0006811
name: ion transport
namespace: biological_process
def: "The directed movement of charged atoms or small charged molecules into\, out of\, within or between cells." [GOC:ai]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0006810

[Term]
id: GO:0006950
name: response to stress
namespace: biological_process
def: "A change in state or activity of a cell or an organism (in terms of movement\, secretion\, enzyme production\, gene expression\, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually\, but not necessarily\, exogenous (e.g. temperature\, humidity\, ionizing radiation)." [GOC:mah]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0008150

[Term]
id: GO:0006996
name: organelle organization and biogenesis
namespace: biological_process
def: "The assembly and arrangement of any organelle within a cell." [GOC:mah]
subset: goslim_generic
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0016043
synonym: "organelle organisation and biogenesis" EXACT []

[Term]
id: GO:0007005
name: mitochondrion organization and biogenesis
namespace: biological_process
def: "The assembly and arrangement of a mitochondrion\, including mitochondrial morphology and distribution\, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components." [GOC:mah, GOC:sgd_curators, PMID:9786946]
subset: goslim_generic
is_a: GO:0006996
synonym: "mitochondria organization and biogenesis" EXACT []
synonym: "mitochondrion organisation and biogenesis" EXACT []

[Term]
id: GO:0007010
name: cytoskeleton organization and biogenesis
namespace: biological_process
def: "The assembly and arrangement of cytoskeletal structures." [GOC:mah]
subset: goslim_generic
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0006996
synonym: "cytoskeletal regulator activity" RELATED []
synonym: "negative regulation of cytoskeleton" RELATED []
synonym: "positive regulation of cytoskeleton" RELATED []
synonym: "regulation of cytoskeleton" RELATED []
synonym: "Rho small monomeric GTPase activity" RELATED []
synonym: "cytoskeleton organisation and biogenesis" EXACT []

[Term]
id: GO:0007028
name: cytoplasm organization and biogenesis
namespace: biological_process
def: "The assembly and arrangement of the cytoplasm and its components." [GOC:ems]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0016043
synonym: "cytoplasm organisation and biogenesis" EXACT []

[Term]
id: GO:0007049
name: cell cycle
namespace: biological_process
def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically\, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell\, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0007582
synonym: "cell-division cycle" EXACT []

[Term]
id: GO:0007154
name: cell communication
namespace: biological_process
def: "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell\, between a cell and an extracellular matrix\, or between a cell and any other aspect of its environment." [GOC:mah]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008150

[Term]
id: GO:0007165
name: signal transduction
namespace: biological_process
def: "The cascade of processes by which a signal interacts with a receptor\, causing a change in the level or activity of a second messenger or other downstream target\, and ultimately effecting a change in the functioning of the cell." [GOC:go_curators]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0007154
synonym: "activation of MAPK during sporulation (sensu Fungi)" NARROW []
synonym: "activation of MAPK during sporulation (sensu Saccharomyces)" NARROW []
synonym: "activation of MAPKK during sporulation (sensu Fungi)" NARROW []
synonym: "activation of MAPKK during sporulation (sensu Saccharomyces)" NARROW []
synonym: "activation of MAPKKK during sporulation (sensu Fungi)" NARROW []
synonym: "activation of MAPKKK during sporulation (sensu Saccharomyces)" NARROW []
synonym: "inactivation of MAPK during sporulation (sensu Fungi)" NARROW []
synonym: "inactivation of MAPK during sporulation (sensu Saccharomyces)" NARROW []
synonym: "MAPKKK cascade during sporulation (sensu Fungi)" NARROW []
synonym: "MAPKKK cascade during sporulation (sensu Saccharomyces)" NARROW []

[Term]
id: GO:0007267
name: cell-cell signaling
namespace: biological_process
def: "Any process that mediates the transfer of information from one cell to another." [GOC:mah]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0007154
synonym: "cell-cell signalling" EXACT []

[Term]
id: GO:0007275
name: development
namespace: biological_process
def: "The biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote\, a young adult or a young single celled organism) to a later condition (e.g. a multicellular animal\, an aged adult or a mature single celled organism)." [GOC:ems]
comment: Note that this term was 'developmental process'.
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008150

[Term]
id: GO:0007582
name: physiological process
namespace: biological_process
def: "Those processes specifically pertinent to the functioning of integrated living units: cells\, tissues\, organs\, and organisms." [GOC:ems, ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008150

[Term]
id: GO:0007610
name: behavior
namespace: biological_process
def: "The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [GOC:ems, ISBN:0395448956]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
is_a: GO:0008150
synonym: "behavioral response to stimulus" EXACT []
synonym: "behaviour" EXACT []
synonym: "behavioural response to stimulus" EXACT []

[Term]
id: GO:0008037
name: cell recognition
namespace: biological_process
def: "The process by which a cell in a multicellular organism interprets its surroundings." [GOC:go_curators]
subset: goslim_generic
is_a: GO:0008150

[Term]
id: GO:0008092
name: cytoskeletal protein binding
namespace: molecular_function
def: "Interacting selectively with any protein component of any cytoskeleton (actin\, microtubule\, or intermediate filament cytoskeleton)." [GOC:mah]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0005515

[Term]
id: GO:0008135
name: translation factor activity, nucleic acid binding
namespace: molecular_function
def: "Functions during translation by binding nucleic acids during polypeptide synthesis at the ribosome." [GOC:ai]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0003676
is_a: GO:0045182
synonym: "protein-synthesizing GTPase activity" RELATED []

[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
def: "A phenomenon marked by changes that lead to a particular result\, mediated by one or more gene products." [GOC:go_curators]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok

[Term]
id: GO:0008152
name: metabolism
namespace: biological_process
def: "Processes that cause many of the chemical changes in living organisms\, including anabolism and catabolism. Metabolic processes typically transform small molecules\, but also include macromolecular processes such as DNA repair and replication\, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684]
comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0007582
synonym: "metabolic process" EXACT []
synonym: "fat body metabolism (sensu Insecta)" NARROW []
synonym: "metabolism resulting in cell growth" NARROW []
xref: Reactome:71408

[Term]
id: GO:0008219
name: cell death
namespace: biological_process
def: "The specific activation or halting of processes within a cell so that its vital functions markedly cease\, rather than simply deteriorating gradually over time\, which culminates in cell death." [GOC:ems]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0016265
synonym: "necrosis" RELATED []

[Term]
id: GO:0008233
name: peptidase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of peptide bonds." [GOC:jl]
subset: goslim_generic
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0016787
synonym: "hydrolase\, acting on peptide bonds" EXACT []
synonym: "peptide hydrolase" EXACT []
synonym: "protease" EXACT []
synonym: "proteasome endopeptidase activity" NARROW []
xref: EC:3.4.-.-

[Term]
id: GO:0008283
name: cell proliferation
namespace: biological_process
def: "The multiplication or reproduction of cells\, resulting in the rapid expansion of a cell population." [GOC:mah, GOC:mb]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0007582

[Term]
id: GO:0008289
name: lipid binding
namespace: molecular_function
def: "Interacting selectively with a lipid." [GOC:ai]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0005488

[Term]
id: GO:0008372
name: cellular component unknown
namespace: cellular_component
def: "Used for the annotation of gene products whose localization is not known or cannot be inferred." [GOC:ma]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0005575

[Term]
id: GO:0009055
name: electron carrier activity
namespace: molecular_function
def: "Any molecular entity that serves as an electron acceptor and electron donor in an electron transport system." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: gosubset_prok
is_a: GO:0003824
synonym: "electron carrier\, chlorophyll electron transport system" RELATED []
synonym: "electron transporter activity" EXACT []
synonym: "2Fe-2S electron transfer carrier" NARROW []
synonym: "3Fe-4S/4Fe-4S electron transfer carrier" NARROW []
synonym: "adrenodoxin-type ferredoxin" NARROW []
synonym: "amicyanin" NARROW []
synonym: "azurin" NARROW []
synonym: "bacterial-type ferredoxin" NARROW []
synonym: "chloroplast-type ferredoxin" NARROW []
synonym: "copper electron carrier" NARROW []
synonym: "dicluster bacterial-type ferredoxin" NARROW []
synonym: "electron transfer flavoprotein" NARROW []
synonym: "electron transfer flavoprotein\, group I" NARROW []
synonym: "electron transfer flavoprotein\, group II" NARROW []
synonym: "high-potential iron-sulfur carrier" NARROW []
synonym: "iron-sulfur electron transfer carrier" NARROW []
synonym: "monocluster bacterial-type ferredoxin" NARROW []
synonym: "mononuclear iron electron carrier" NARROW []
synonym: "polyferredoxin" NARROW []
synonym: "redox-active disulfide bond electron carrier" NARROW []
synonym: "rubredoxin" NARROW []
synonym: "small blue copper electron carrier" NARROW []
synonym: "thioredoxin-like 2Fe-2S ferredoxin" NARROW []

[Term]
id: GO:0009056
name: catabolism
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of substances\, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008152
synonym: "breakdown" EXACT []
synonym: "degradation" EXACT []

[Term]
id: GO:0009058
name: biosynthesis
namespace: biological_process
def: "The energy-requiring part of metabolism in which simpler substances are transformed into more complex ones\, as in growth and other biosynthetic processes." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008152
synonym: "anabolism" EXACT []
synonym: "formation" EXACT []
synonym: "synthesis" EXACT []

[Term]
id: GO:0009536
name: plastid
namespace: cellular_component
def: "Any member of a family of organelles found in the cytoplasm of plants and some protists\, which are membrane-bounded and contain DNA. Plant plastids develop from a common type\, the proplastid." [GOC:jl, ISBN:0198547684]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0043226
relationship: part_of GO:0005737

[Term]
id: GO:0009579
name: thylakoid
namespace: cellular_component
def: "A sac-like vesicle that bears the photosynthetic pigments in photosynthetic organisms. In prokaryotes the thylakoids are of various shapes and are attached to the plasma membrane. In eukaryotes they are flattened\, membrane-bound disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0043226
relationship: part_of GO:0005622
synonym: "photosynthetic membrane" RELATED []

[Term]
id: GO:0009605
name: response to external stimulus
namespace: biological_process
def: "A change in state or activity of a cell or an organism (in terms of movement\, secretion\, enzyme production\, gene expression\, etc.) as a result of an external stimulus." [GOC:hb]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008150
synonym: "response to environmental stimulus" EXACT []

[Term]
id: GO:0009607
name: response to biotic stimulus
namespace: biological_process
def: "A change in state or activity of a cell or an organism (in terms of movement\, secretion\, enzyme production\, gene expression\, etc.) as a result of a biotic stimulus\, a stimulus caused or produced by a living organism." [GOC:hb]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008150

[Term]
id: GO:0009628
name: response to abiotic stimulus
namespace: biological_process
def: "A change in state or activity of a cell or an organism (in terms of movement\, secretion\, enzyme production\, gene expression\, etc.) as a result of an abiotic (non-living) stimulus." [GOC:hb]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008150

[Term]
id: GO:0009653
name: morphogenesis
namespace: biological_process
def: "The process by which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:go_curators, ISBN:0521436125]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
relationship: part_of GO:0007275
synonym: "embryogenesis and morphogenesis" BROAD []

[Term]
id: GO:0009719
name: response to endogenous stimulus
namespace: biological_process
def: "A change in state or activity of a cell or an organism (in terms of movement\, secretion\, enzyme production\, gene expression\, etc.) as a result of an endogenous stimulus." [GOC:sm]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008150

[Term]
id: GO:0009790
name: embryonic development
alt_id: GO:0009795
namespace: biological_process
def: "The process whose specific outcome is the progression of an embryo from zygote formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific and may be somewhat arbitrary. For example\, it would be at birth for mammals\, larval hatching for insects and seed dormancy in plants." [GOC:go_curators]
subset: goslim_generic
subset: goslim_plant
is_a: GO:0007275
synonym: "embryogenesis" EXACT []
synonym: "embryonal development" EXACT []
synonym: "embryogenesis and morphogenesis" BROAD []

[Term]
id: GO:0015031
name: protein transport
alt_id: GO:0015831
namespace: biological_process
def: "The directed movement of proteins into\, out of\, within or between cells." [GOC:ai]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0006810
synonym: "enzyme transport" NARROW []

[Term]
id: GO:0016023
name: cytoplasmic membrane-bound vesicle
namespace: cellular_component
def: "A membrane-bound vesicle found in the cytoplasm of the cell." [GOC:ai, GOC:mah]
subset: goslim_generic
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0043226
relationship: part_of GO:0005737
synonym: "cytoplasmic membrane bound vesicle" EXACT []

[Term]
id: GO:0016032
name: viral life cycle
namespace: biological_process
def: "A set of processes by which a virus reproduces. Usually\, this is by infection of a host cell\, replication of the viral genome\, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently\, under particular circumstances\, 'complete' its life cycle." [GOC:mah]
comment: See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'.
subset: goslim_generic
is_a: GO:0008150
synonym: "viral infection" RELATED []
synonym: "virulence" RELATED []
synonym: "viral replication cycle" EXACT []

[Term]
id: GO:0016043
name: cell organization and biogenesis
namespace: biological_process
def: "The processes involved in the assembly and arrangement of cell structures\, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0007582
synonym: "cell organisation and biogenesis" EXACT []

[Term]
id: GO:0016049
name: cell growth
namespace: biological_process
def: "The process by which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:ai]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0040007
relationship: part_of GO:0009653
relationship: part_of GO:0016043
synonym: "cell expansion" RELATED []
synonym: "metabolism resulting in cell growth" RELATED []
synonym: "cellular growth" EXACT []
synonym: "growth of cell" EXACT []

[Term]
id: GO:0016209
name: antioxidant activity
namespace: molecular_function
def: "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals\, thereby breaking the chain reaction that normally leads to extensive biological damage." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: gosubset_prok
is_a: GO:0003674

[Term]
id: GO:0016265
name: death
namespace: biological_process
def: "A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism." [GOC:mah, ISBN:0877797099]
comment: See also the biological process term 'apoptosis ; GO:0006915'.
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0007582

[Term]
id: GO:0016301
name: kinase activity
namespace: molecular_function
def: "Catalysis of the transfer of a phosphate group\, usually from ATP\, to a substrate molecule." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0016740
synonym: "phosphokinase" EXACT []
xref: Reactome:113431
xref: Reactome:113433
xref: Reactome:114246
xref: Reactome:115027
xref: Reactome:115715
xref: Reactome:115932
xref: Reactome:115944
xref: Reactome:115947
xref: Reactome:115951
xref: Reactome:115974
xref: Reactome:115991
xref: Reactome:116605
xref: Reactome:117491
xref: Reactome:118310
xref: Reactome:118568
xref: Reactome:118583
xref: Reactome:118586
xref: Reactome:118589
xref: Reactome:118596
xref: Reactome:118617
xref: Reactome:118965
xref: Reactome:119356
xref: Reactome:120179
xref: Reactome:120930
xref: Reactome:121183
xref: Reactome:121192
xref: Reactome:121216
xref: Reactome:121239
xref: Reactome:121274
xref: Reactome:121543
xref: Reactome:122577
xref: Reactome:123125
xref: Reactome:123301
xref: Reactome:123309
xref: Reactome:123312
xref: Reactome:123316
xref: Reactome:123331
xref: Reactome:124636
xref: Reactome:125197
xref: Reactome:125408
xref: Reactome:125423
xref: Reactome:125426
xref: Reactome:125441
xref: Reactome:1423
xref: Reactome:68385
xref: Reactome:68401
xref: Reactome:69194
xref: Reactome:69222
xref: Reactome:69246
xref: Reactome:69254
xref: Reactome:69603
xref: Reactome:69607
xref: Reactome:69716
xref: Reactome:69904
xref: Reactome:69913
xref: Reactome:75047
xref: Reactome:75051
xref: Reactome:75052
xref: Reactome:75053
xref: Reactome:75054
xref: Reactome:75225
xref: Reactome:75371
xref: Reactome:75808
xref: Reactome:75819
xref: Reactome:83536

[Term]
id: GO:0016740
name: transferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a group\, e.g. a methyl group\, glycosyl group\, acyl group\, phosphorus-containing\, or other groups\, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003824
xref: EC:2

[Term]
id: GO:0016787
name: hydrolase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of various bonds\, e.g. C-O\, C-N\, C-C\, phosphoric anhydride bonds\, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003824
xref: EC:3

[Term]
id: GO:0019538
name: protein metabolism
alt_id: GO:0006411
namespace: biological_process
def: "The chemical reactions and pathways involving a specific protein\, rather than of proteins in general. Includes protein modification." [GOC:ma]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0044238
synonym: "protein metabolism and modification" EXACT []

[Term]
id: GO:0019725
name: cell homeostasis
namespace: biological_process
def: "Any of the processes involved in the maintenance of an internal equilibrium within a cell or between a cell and its external environment." [GOC:jl, ISBN:0395825172]
subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0007582

[Term]
id: GO:0019748
name: secondary metabolism
namespace: biological_process
def: "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells\, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types\, and may be useful for the organism as a whole. In unicellular organisms\, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients." [GOC:go_curators]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008152

[Term]
id: GO:0019825
name: oxygen binding
namespace: molecular_function
def: "Interacting selectively with oxygen (O2)." [GOC:jl]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0005488
synonym: "cytochrome P450 activity" RELATED []
synonym: "cytochrome P450" NARROW []
xref: Reactome:4477

[Term]
id: GO:0030154
name: cell differentiation
namespace: biological_process
def: "The process whereby relatively unspecialized cells\, e.g. embryonic or regenerative cells\, acquire specialized structural and/or functional features that characterize the cells\, tissues\, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
relationship: part_of GO:0007275

[Term]
id: GO:0030188
name: chaperone regulator activity
namespace: molecular_function
def: "Modulates the activity of a molecular chaperone." [GOC:mah]
subset: goslim_generic
subset: goslim_goa
subset: gosubset_prok
is_a: GO:0003674

[Term]
id: GO:0030234
name: enzyme regulator activity
namespace: molecular_function
def: "Modulates the activity of an enzyme." [GOC:mah]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003674
synonym: "enzyme modulator" EXACT []

[Term]
id: GO:0030246
name: carbohydrate binding
namespace: molecular_function
def: "Interacting selectively with any carbohydrate." [GOC:mah]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0005488
synonym: "cell adhesion molecule activity" RELATED []
synonym: "cell adhesion receptor activity" RELATED []
synonym: "selectin" RELATED []

[Term]
id: GO:0030312
name: external encapsulating structure
namespace: cellular_component
def: "A structure that lies outside the plasma membrane and surrounds the entire cell." [GOC:go_curators]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
relationship: part_of GO:0005623

[Term]
id: GO:0030313
name: cell envelope
namespace: cellular_component
def: "Everything external to\, but not including\, the cytoplasmic membrane of bacteria\, encompassing the periplasmic space\, cell wall\, and outer membrane if present." [GOC:jl, URL:http://pathmicro.med.sc.edu/fox/cell_envelope.htm]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0030312

[Term]
id: GO:0030528
name: transcription regulator activity
namespace: molecular_function
def: "Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor." [GOC:mah]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003674

[Term]
id: GO:0030533
name: triplet codon-amino acid adaptor activity
namespace: molecular_function
def: "Mediates the insertion of an amino acid at the correct point in the sequence of a nascent polypeptide chain during protein synthesis." [ISBN:0198506732]
comment: Note that this term can be used in place of the obsolete term 'transfer RNA ; GO:0005563'.
subset: goslim_generic
is_a: GO:0003674
synonym: "transfer RNA" EXACT []
synonym: "tRNA" EXACT []

[Term]
id: GO:0031386
name: protein tag
namespace: molecular_function
def: "Acting as an indicator or marker to facilitate recognition by other molecules in the cell. Recognition of the tag\, which can be covalently attached to the target molecule\, may result in modification\, sequestration\, transport or degradation of the molecule in question." [GOC:go_curators]
subset: goslim_generic
is_a: GO:0003674
synonym: "protein tagging activity" RELATED []
synonym: "ubiquitin" RELATED []

[Term]
id: GO:0040007
name: growth
namespace: biological_process
def: "The increase in size or mass of an entire organism\, a part of an organism or a cell." [GOC:bf, GOC:ma]
comment: See also the biological process term 'cell growth ; GO:0016049'.
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0008150
synonym: "growth pattern" RELATED []

[Term]
id: GO:0040029
name: regulation of gene expression, epigenetic
namespace: biological_process
def: "Any process that modulates the frequency\, rate or extent of gene expression; the process is mitotically or meiotically heritable\, or is stably self-propagated in the cytoplasm of a resting cell\, and does not entail a change in DNA sequence." [PMID:10521337, PMID:11498582]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0050789

[Term]
id: GO:0043226
name: organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function. Includes the nucleus\, mitochondria\, plastids\, vacuoles\, vesicles\, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0005575

[Term]
id: GO:0043234
name: protein complex
namespace: cellular_component
def: "Any protein group composed of two or more subunits\, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups\, such as nucleic acids\, metal ions or carbohydrate groups." [GOC:go_curators]
comment: Note that although at some level almost all cellular components can be thought of as protein complexes, this term is intended to exclude structures composed of the same repeating subunit or subunits, for example microtubules. Protein complexes encompassed by this term are generally not structural, and usually have a defined set of subunits.
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0005575

[Term]
id: GO:0044238
name: primary metabolism
namespace: biological_process
def: "Reactions involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most\, if not all\, cells of the organism." [GOC:go_curators, URL:http://www.metacyc.org]
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0008152

[Term]
id: GO:0044403
name: symbiosis, encompassing mutualism through parasitism
alt_id: GO:0043298
alt_id: GO:0044404
namespace: biological_process
def: "An interaction between two organisms living together in more or less intimate association. The term host is usually used for the larger (macro) of the two members of a symbiosis. The smaller (micro) member is called the symbiont. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism\, in which the association is disadvantageous or destructive to one of the organisms; mutualism\, in which the association is advantageous\, or often necessary to one or both and not harmful to either; and commensalism\, in which one member of the association benefits while the other is not affected. However\, mutualism\, parasitism\, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact\, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs." [URL:http://www.free-definition.com, PAMGO:cc]
comment: Note that this term encompasses all symbiotic relationships between species along a continuum from mutualism through to parasitism, as outlined in the definition.
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0008150
synonym: "host-pathogen interaction" RELATED []
synonym: "symbiotic interaction between host and other organism" RELATED []
synonym: "symbiotic interaction with other non-host organism" RELATED []
synonym: "symbiotic interaction between organisms" EXACT []
synonym: "symbiotic interaction between species" EXACT []

[Term]
id: GO:0045182
name: translation regulator activity
namespace: molecular_function
def: "Any substance involved in the initiation\, activation\, perpetuation\, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
is_a: GO:0003674

[Term]
id: GO:0045735
name: nutrient reservoir activity
namespace: molecular_function
def: "Functions in the storage of nutritious substrates." [GOC:ai]
comment: Note that this term can be used in place of the obsolete terms 'storage protein ; GO:0005187' and 'storage protein of fat body (sensu Insecta) ; GO:0008041'.
subset: goslim_generic
subset: gosubset_prok
is_a: GO:0003674
synonym: "storage protein" RELATED []
synonym: "storage protein of fat body (sensu Insecta)" RELATED []
synonym: "yolk protein" RELATED []

[Term]
id: GO:0050789
name: regulation of biological process
namespace: biological_process
def: "Any process that modulates the frequency\, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression\, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators]
subset: goslim_generic
subset: goslim_goa
subset: gosubset_prok
is_a: GO:0008150
synonym: "regulation" BROAD []

[Typedef]
id: part_of
name: part of
namespace: gene_ontology
is_transitive: 1

