[Term]
id: GO:0000166
name: nucleotide binding
namespace: molecular_function
def: "Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC:mah, ISBN:0198547684]
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
is_a: GO:0005488 ! binding

[Term]
id: GO:0003674
name: molecular_function
namespace: molecular_function
alt_id: GO:0005554
def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt]
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "molecular function" EXACT []

[Term]
id: GO:0003676
name: nucleic acid binding
namespace: molecular_function
alt_id: GO:0000496
def: "Binding to a nucleic acid." [GOC:jl]
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "base pairing" NARROW []
is_a: GO:0005488 ! binding

[Term]
id: GO:0003677
name: DNA binding
namespace: molecular_function
alt_id: GO:0043566
def: "Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "microtubule/chromatin interaction" RELATED []
synonym: "plasmid binding" NARROW []
synonym: "structure specific DNA binding" RELATED []
synonym: "structure-specific DNA binding" RELATED []
is_a: GO:0003676 ! nucleic acid binding

[Term]
id: GO:0003682
name: chromatin binding
namespace: molecular_function
def: "Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC:jl, ISBN:0198506732, PMID:20404130]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "lamin/chromatin binding" NARROW []
synonym: "microtubule/chromatin interaction" NARROW []
synonym: "nuclear membrane vesicle binding to chromatin" NARROW []
is_a: GO:0005488 ! binding

[Term]
id: GO:0003700
name: DNA-binding transcription factor activity
namespace: molecular_function
alt_id: GO:0000130
alt_id: GO:0001071
alt_id: GO:0001130
alt_id: GO:0001131
alt_id: GO:0001151
alt_id: GO:0001199
alt_id: GO:0001204
def: "A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons." [GOC:txnOH-2018]
comment: Usage guidance: Most DNA-binding transcription factors do not have enzymatic activity. The presence of specific DNA-binding domains known to be present in DNA-binding transcription factors (HOX, GATA etc) should be used to help decide whether a protein is a DNA binding transcription factor or a coregulator. If a protein has an enzymatic activity (for example, ubiquitin ligase, histone acetyl transferase) and no known DNA binding domain, consider annotating to GO:0003712 transcription coregulator activity. Special care should be taken with proteins containing zinc fingers, Myb/SANT and ARID domains, since only a subset of proteins containing these domains directly and selectively bind to regulatory DNA motifs in cis-regulatory regions.
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_plant
subset: goslim_yeast
synonym: "bacterial-type DNA binding transcription factor activity" NARROW []
synonym: "bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity" NARROW []
synonym: "bacterial-type RNA polymerase transcription enhancer sequence-specific DNA binding transcription factor activity" NARROW []
synonym: "bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding" NARROW []
synonym: "bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding" NARROW []
synonym: "DNA binding transcription factor activity" EXACT []
synonym: "gene-specific transcription factor activity" EXACT []
synonym: "metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity" NARROW []
synonym: "metal ion regulated sequence-specific DNA binding transcription factor activity" NARROW []
synonym: "nucleic acid binding transcription factor activity" BROAD []
synonym: "sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity" NARROW []
synonym: "sequence-specific DNA binding transcription factor activity" EXACT []
synonym: "transcription factor activity" BROAD []
synonym: "transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding" NARROW []
synonym: "transcription factor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding" NARROW []
synonym: "transcription factor activity, bacterial-type RNA polymerase transcription enhancer sequence-specific binding" NARROW []
synonym: "transcription factor activity, metal ion regulated sequence-specific DNA binding" NARROW []
is_a: GO:0140110 ! transcription regulator activity
relationship: has_part GO:0003677 ! DNA binding
relationship: part_of GO:0008150 ! biological_process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15704" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16534" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20253" xsd:anyURI
created_by: krc
creation_date: 2010-10-21T04:37:54Z

[Term]
id: GO:0003723
name: RNA binding
namespace: molecular_function
alt_id: GO:0000498
alt_id: GO:0044822
def: "Binding to an RNA molecule or a portion thereof." [GOC:jl, GOC:mah]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "base pairing with RNA" NARROW []
synonym: "poly(A) RNA binding" RELATED []
synonym: "poly(A)-RNA binding" RELATED []
synonym: "poly-A RNA binding" RELATED []
xref: Reactome:R-HSA-203922 "Exportin-5 recognizes 3' overhang of pre-miRNA"
is_a: GO:0003676 ! nucleic acid binding

[Term]
id: GO:0003774
name: cytoskeletal motor activity
namespace: molecular_function
def: "Generation of force resulting in movement, for example along a microfilament or microtubule, or in torque resulting in membrane scission or rotation of a flagellum. The energy required is obtained either from the hydrolysis of a nucleoside triphosphate or by an electrochemical proton gradient (proton-motive force)." [GOC:mah, GOC:vw, PMID:11242086, PMID:29716949]
subset: goslim_candida
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "motor activity" BROAD []
xref: Reactome:R-HSA-1861595 "Extension of pseudopodia by myosin-X in a PI3K dependent manner"
is_a: GO:0003674 ! molecular_function
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19590" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21756" xsd:anyURI

[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." [GOC:vw, ISBN:0198506732]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote_ribbon
synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb]
xref: Wikipedia:Enzyme
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0004518
name: nuclease activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN:0198547684]
comment: Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', and 'DNA-(apurinic or apyrimidinic site) lyase activity ; GO:0003906' do not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis.
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_plant
subset: goslim_yeast
is_a: GO:0016787 ! hydrolase activity

[Term]
id: GO:0005102
name: signaling receptor binding
namespace: molecular_function
def: "Binding to 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]
comment: Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'.
subset: goslim_agr
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_mouse
subset: goslim_plant
synonym: "receptor binding" BROAD []
synonym: "receptor ligand" NARROW []
synonym: "receptor-associated protein activity" RELATED []
xref: Wikipedia:Ligand_(biochemistry)
is_a: GO:0005515 ! protein binding

[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." [GOC:mah, GOC:vw]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
is_a: GO:0003674 ! molecular_function
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24130" xsd:anyURI

[Term]
id: GO:0005215
name: transporter activity
namespace: molecular_function
alt_id: GO:0005478
def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells." [GOC:ai, GOC:dgf]
comment: Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.
subset: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "carrier" RELATED []
is_a: GO:0003674 ! molecular_function
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27621" xsd:anyURI

[Term]
id: GO:0005488
name: binding
namespace: molecular_function
def: "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732]
comment: Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
subset: goslim_pir
subset: goslim_plant
synonym: "ligand" NARROW []
xref: Wikipedia:Binding_(molecular)
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0005515
name: protein binding
namespace: molecular_function
alt_id: GO:0001948
alt_id: GO:0045308
def: "Binding to a protein." [GOC:go_curators]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote_ribbon
synonym: "glycoprotein binding" NARROW []
synonym: "protein amino acid binding" EXACT []
is_a: GO:0005488 ! binding

[Term]
id: GO:0005575
name: cellular_component
namespace: cellular_component
alt_id: GO:0008372
def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt]
comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "cell or subcellular entity" EXACT []
synonym: "cellular component" EXACT []
synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315]
xref: NIF_Subcellular:sao1337158144
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17729" xsd:anyURI

[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. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "extracellular" EXACT []
xref: Wikipedia:Extracellular
is_a: GO:0005575 ! cellular_component

[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, most prokaryotic cells and some protozoan parasites, 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; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins." [GOC:giardia, ISBN:0198547684, PMID:15134259, Wikipedia:Microbial_cyst]
comment: Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for plants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995).
subset: gocheck_do_not_annotate
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
xref: Wikipedia:Cell_wall
is_a: GO:0030312 ! external encapsulating structure
property_value: RO:0002161 NCBITaxon:33208
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21669" xsd:anyURI

[Term]
id: GO:0005622
name: intracellular anatomical structure
namespace: cellular_component
def: "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732]
subset: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_plant
synonym: "internal to cell" EXACT []
synonym: "intracellular" EXACT []
synonym: "nucleocytoplasm" RELATED [GOC:mah]
synonym: "protoplasm" EXACT []
synonym: "protoplast" RELATED [GOC:mah]
xref: Wikipedia:Intracellular
is_a: GO:0005575 ! cellular_component
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI

[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_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_yeast
synonym: "cell nucleus" EXACT []
synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757]
xref: NIF_Subcellular:sao1702920020
xref: Wikipedia:Cell_nucleus
is_a: GO:0005575 ! cellular_component
relationship: has_part GO:0016020 ! membrane
relationship: part_of GO:0005622 ! intracellular anatomical structure

[Term]
id: GO:0005635
name: nuclear envelope
namespace: cellular_component
alt_id: GO:0005636
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_chembl
subset: goslim_generic
subset: goslim_plant
xref: Wikipedia:Nuclear_envelope
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005634 ! nucleus

[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_chembl
subset: goslim_generic
subset: goslim_plant
xref: NIF_Subcellular:sao661522542
xref: Wikipedia:Nucleoplasm
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005634 ! nucleus

[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_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
xref: NIF_Subcellular:sao1820400233
xref: Wikipedia:Nucleolus
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0005737
name: cytoplasm
namespace: cellular_component
def: "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
xref: Wikipedia:Cytoplasm
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005622 ! intracellular anatomical structure
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI

[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." [GOC:giardia, ISBN:0198506732]
comment: Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_yeast
synonym: "mitochondria" EXACT []
xref: NIF_Subcellular:sao1860313010
xref: Wikipedia:Mitochondrion
is_a: GO:0005575 ! cellular_component
relationship: has_part GO:0016020 ! membrane
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0005764
name: lysosome
namespace: cellular_component
def: "A small lytic vacuole that has cell cycle-independent morphology found in most animal cells and that contains 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." [GOC:mah, ISBN:0198506732]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_plant
xref: NIF_Subcellular:sao585356902
xref: Wikipedia:Lysosome
is_a: GO:0005773 ! vacuole
property_value: RO:0002161 NCBITaxon:4751

[Term]
id: GO:0005768
name: endosome
namespace: cellular_component
def: "A vacuole to which materials ingested by endocytosis are delivered." [ISBN:0198506732, PMID:19696797]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
xref: NIF_Subcellular:sao1720343330
xref: Wikipedia:Endosome
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005575 ! cellular_component

[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. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_yeast
synonym: "vacuolar carboxypeptidase Y" RELATED []
xref: Wikipedia:Vacuole
is_a: GO:0005575 ! cellular_component
relationship: has_part GO:0016020 ! membrane
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0005777
name: peroxisome
namespace: cellular_component
alt_id: GO:0019818
def: "A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism." [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_yeast
synonym: "peroxisomal" RELATED []
synonym: "peroxisome vesicle" BROAD []
xref: NIF_Subcellular:sao499555322
xref: Wikipedia:Peroxisome
is_a: GO:0005575 ! cellular_component
relationship: has_part GO:0016020 ! membrane
relationship: part_of GO:0005737 ! cytoplasm

[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_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_yeast
synonym: "ER" EXACT []
xref: NIF_Subcellular:sao1036339110
xref: Wikipedia:Endoplasmic_reticulum
is_a: GO:0005575 ! cellular_component
relationship: has_part GO:0016020 ! membrane
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0005794
name: Golgi apparatus
namespace: cellular_component
def: "A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways." [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_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_yeast
synonym: "Golgi" BROAD []
synonym: "Golgi complex" EXACT []
synonym: "Golgi ribbon" NARROW []
xref: NIF_Subcellular:sao451912436
xref: Wikipedia:Golgi_apparatus
is_a: GO:0005575 ! cellular_component
relationship: has_part GO:0016020 ! membrane
relationship: part_of GO:0005622 ! intracellular anatomical structure
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0005829
name: cytosol
namespace: cellular_component
def: "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC:hjd, GOC:jl]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
xref: NIF_Subcellular:sao101633890
xref: Wikipedia:Cytosol
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0005840
name: ribosome
namespace: cellular_component
alt_id: GO:0033279
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_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "free ribosome" NARROW [NIF_Subcellular:sao1139385046]
synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653]
synonym: "ribosomal RNA" RELATED []
xref: NIF_Subcellular:sao1429207766
xref: Wikipedia:Ribosome
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005622 ! intracellular anatomical structure

[Term]
id: GO:0005856
name: cytoskeleton
namespace: cellular_component
def: "A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. 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." [GOC:mah, PMID:16959967, PMID:27419875]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_yeast
xref: Wikipedia:Cytoskeleton
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005622 ! intracellular anatomical structure

[Term]
id: GO:0005886
name: plasma membrane
namespace: cellular_component
alt_id: GO:0005887
alt_id: GO:0005904
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_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "bacterial inner membrane" NARROW []
synonym: "cell membrane" EXACT []
synonym: "cellular membrane" EXACT [NIF_Subcellular:sao6433132645]
synonym: "cytoplasmic membrane" EXACT []
synonym: "inner endospore membrane" NARROW []
synonym: "integral component of plasma membrane" NARROW []
synonym: "integral to plasma membrane" NARROW []
synonym: "juxtamembrane" BROAD []
synonym: "plasma membrane lipid bilayer" NARROW [GOC:mah]
synonym: "plasmalemma" EXACT []
xref: NIF_Subcellular:sao1663586795
xref: Wikipedia:Cell_membrane
is_a: GO:0016020 ! membrane
relationship: part_of GO:0005575 ! cellular_component

[Term]
id: GO:0005975
name: carbohydrate metabolic process
namespace: biological_process
alt_id: GO:0044261
alt_id: GO:0044723
def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC:mah, ISBN:0198506732]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "carbohydrate metabolism" EXACT []
xref: Wikipedia:Carbohydrate_metabolism
is_a: GO:0008152 ! metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22880" xsd:anyURI
created_by: jl
creation_date: 2012-10-23T15:40:34Z

[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 any process involved in the liberation of energy from these substances." [GOC:jl]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "energy pathways" BROAD []
synonym: "intermediary metabolism" RELATED [GOC:mah]
synonym: "metabolic energy generation" RELATED []
is_a: GO:0008152 ! metabolic process
is_a: GO:0009987 ! cellular process

[Term]
id: GO:0006139
name: nucleobase-containing compound metabolic process
namespace: biological_process
alt_id: GO:0055134
def: "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai]
subset: goslim_pir
subset: goslim_plant
synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT []
synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT []
synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED []
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb]
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006259
name: DNA metabolic process
namespace: biological_process
alt_id: GO:0055132
def: "Any cellular metabolic process involving deoxyribonucleic acid. This is 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_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote_ribbon
synonym: "cellular DNA metabolism" EXACT []
synonym: "DNA metabolism" EXACT []
is_a: GO:0006139 ! nucleobase-containing compound metabolic process

[Term]
id: GO:0006412
name: translation
namespace: biological_process
alt_id: GO:0006416
alt_id: GO:0006453
alt_id: GO:0043037
def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "protein anabolism" EXACT []
synonym: "protein biosynthesis" EXACT []
synonym: "protein biosynthetic process" EXACT []
synonym: "protein formation" EXACT []
synonym: "protein synthesis" EXACT []
synonym: "protein translation" EXACT []
xref: Wikipedia:Translation_(genetics)
is_a: GO:0009058 ! biosynthetic process
is_a: GO:0009987 ! cellular process
is_a: GO:0019538 ! protein metabolic process
relationship: has_part GO:0009058 ! biosynthetic process
relationship: has_part GO:0009987 ! cellular process

[Term]
id: GO:0006629
name: lipid metabolic process
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_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "lipid metabolism" EXACT []
xref: Wikipedia:Lipid_metabolism
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006810
name: transport
namespace: biological_process
alt_id: GO:0015457
alt_id: GO:0015460
alt_id: GO:0044765
def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
subset: gocheck_do_not_annotate
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "single-organism transport" RELATED []
is_a: GO:0008150 ! biological_process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI
created_by: jl
creation_date: 2012-12-13T16:25:32Z

[Term]
id: GO:0006950
name: response to stress
namespace: biological_process
def: "Any process that results in 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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "response to abiotic stress" RELATED []
synonym: "response to biotic stress" RELATED []
is_a: GO:0008150 ! biological_process

[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, GOC:mtg_cell_cycle]
subset: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "cell-division cycle" EXACT []
xref: Wikipedia:Cell_cycle
is_a: GO:0009987 ! cellular process

[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_pir
subset: goslim_plant
xref: Wikipedia:Cell_signaling
is_a: GO:0009987 ! cellular process

[Term]
id: GO:0007165
name: signal transduction
namespace: biological_process
alt_id: GO:0023014
alt_id: GO:0023015
alt_id: GO:0023016
alt_id: GO:0023033
alt_id: GO:0023045
def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11]
comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "signaling cascade" NARROW []
synonym: "signaling pathway" RELATED []
synonym: "signalling cascade" NARROW []
synonym: "signalling pathway" RELATED []
xref: Wikipedia:Signal_transduction
is_a: GO:0009987 ! cellular process
relationship: part_of GO:0007154 ! cell communication
relationship: regulates GO:0009987 ! cellular process

[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. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions." [GOC:dos, GOC:mah]
subset: goslim_chembl
subset: goslim_plant
synonym: "cell-cell signalling" EXACT []
is_a: GO:0007154 ! cell communication
relationship: regulates GO:0008150 ! biological_process

[Term]
id: GO:0007275
name: multicellular organism development
namespace: biological_process
def: "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
comment: Note that this term was 'developmental process'.
subset: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_plant
is_a: GO:0048856 ! anatomical structure development
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21234" xsd:anyURI

[Term]
id: GO:0007623
name: circadian rhythm
namespace: biological_process
alt_id: GO:0050895
def: "Any biological process in an organism that recurs with a regularity of approximately 24 hours." [GOC:bf, GOC:go_curators]
subset: goslim_drosophila
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "circadian process" EXACT []
synonym: "circadian response" RELATED []
synonym: "response to circadian rhythm" RELATED []
xref: Wikipedia:Circadian_rhythm
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0008135
name: translation factor activity, RNA binding
namespace: molecular_function
def: "Functions during translation by binding to RNA during polypeptide synthesis at the ribosome." [GOC:ai, GOC:vw]
subset: goslim_chembl
subset: goslim_plant
subset: goslim_yeast
synonym: "translation factor activity, nucleic acid binding" BROAD [GOC:mah]
is_a: GO:0003676 ! nucleic acid binding
is_a: GO:0045182 ! translation regulator activity
relationship: has_part GO:0003723 ! RNA binding
relationship: part_of GO:0006412 ! translation

[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
alt_id: GO:0000004
alt_id: GO:0007582
alt_id: GO:0044699
def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
synonym: "biological process" EXACT []
synonym: "physiological process" EXACT []
synonym: "single organism process" RELATED []
synonym: "single-organism process" RELATED []
xref: Wikipedia:Biological_process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI
created_by: jl
creation_date: 2012-09-19T15:05:24Z

[Term]
id: GO:0008152
name: metabolic process
namespace: biological_process
alt_id: GO:0044236
alt_id: GO:0044710
def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. 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: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote_ribbon
synonym: "metabolic process resulting in cell growth" NARROW []
synonym: "metabolism" EXACT []
synonym: "metabolism resulting in cell growth" NARROW []
synonym: "multicellular organism metabolic process" NARROW []
synonym: "single-organism metabolic process" RELATED []
xref: Wikipedia:Metabolism
is_a: GO:0008150 ! biological_process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI
created_by: jl
creation_date: 2012-10-17T15:46:40Z

[Term]
id: GO:0008289
name: lipid binding
namespace: molecular_function
def: "Binding to a lipid." [GOC:ai]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
is_a: GO:0005488 ! binding

[Term]
id: GO:0009056
name: catabolic process
namespace: biological_process
alt_id: GO:0044243
alt_id: GO:0044712
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_agr
subset: goslim_chembl
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "breakdown" EXACT []
synonym: "catabolism" EXACT []
synonym: "degradation" EXACT []
synonym: "multicellular organismal catabolic process" NARROW []
synonym: "single-organism catabolic process" RELATED []
xref: Wikipedia:Catabolism
is_a: GO:0008152 ! metabolic process
created_by: jl
creation_date: 2012-10-17T15:52:35Z

[Term]
id: GO:0009058
name: biosynthetic process
namespace: biological_process
alt_id: GO:0044274
alt_id: GO:0044711
def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684]
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "anabolism" EXACT []
synonym: "biosynthesis" EXACT []
synonym: "formation" BROAD []
synonym: "multicellular organismal biosynthetic process" NARROW []
synonym: "single-organism biosynthetic process" RELATED []
synonym: "synthesis" EXACT []
xref: Wikipedia:Anabolism
is_a: GO:0008152 ! metabolic process
created_by: jl
creation_date: 2012-10-17T15:52:18Z

[Term]
id: GO:0009416
name: response to light stimulus
namespace: biological_process
def: "Any process that results in 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 light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light." [GOC:go_curators, ISBN:0582227089]
subset: goslim_plant
is_a: GO:0009628 ! response to abiotic stimulus

[Term]
id: GO:0009507
name: chloroplast
namespace: cellular_component
def: "A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma." [ISBN:0471245208]
subset: goslim_plant
subset: goslim_plant_ribbon
xref: Wikipedia:Chloroplast
is_a: GO:0009536 ! plastid
property_value: RO:0002161 NCBITaxon:28009
property_value: RO:0002161 NCBITaxon:33208
property_value: RO:0002161 NCBITaxon:4751
property_value: RO:0002161 NCBITaxon:554915

[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_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
xref: Wikipedia:Plastid
is_a: GO:0005575 ! cellular_component
relationship: has_part GO:0016020 ! membrane
relationship: part_of GO:0005737 ! cytoplasm
property_value: RO:0002161 NCBITaxon:2
property_value: RO:0002161 NCBITaxon:2157
property_value: RO:0002161 NCBITaxon:28009
property_value: RO:0002161 NCBITaxon:33208
property_value: RO:0002161 NCBITaxon:4751
property_value: RO:0002161 NCBITaxon:554915

[Term]
id: GO:0009579
name: thylakoid
namespace: cellular_component
def: "A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded 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." [GOC:ds, GOC:mtg_sensu, ISBN:0198506732]
comment: A thylakoid is not considered an organelle, but some thylakoids are part of organelles.
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "photosynthetic membrane" RELATED []
xref: Wikipedia:Thylakoid
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005622 ! intracellular anatomical structure
property_value: RO:0002161 NCBITaxon:33208
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13958" xsd:anyURI

[Term]
id: GO:0009605
name: response to external stimulus
namespace: biological_process
def: "Any process that results in 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]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_annotate
subset: goslim_drosophila
subset: goslim_plant
synonym: "response to environmental stimulus" EXACT []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0009606
name: tropism
namespace: biological_process
def: "The movement of an organism, or part of an organism, in response to an external source of stimulus, usually toward or away from it." [GOC:curators, ISBN:0877795088]
subset: goslim_plant
xref: Wikipedia:Tropism
is_a: GO:0009605 ! response to external stimulus

[Term]
id: GO:0009607
name: response to biotic stimulus
namespace: biological_process
def: "Any process that results in 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]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_annotate
subset: goslim_metagenomics
subset: goslim_plant
synonym: "response to biotic stress" NARROW []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0009628
name: response to abiotic stimulus
namespace: biological_process
def: "Any process that results in 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 (not derived from living organisms) stimulus." [GOC:hb]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_annotate
subset: goslim_metagenomics
subset: goslim_plant
synonym: "response to abiotic stress" NARROW []
is_a: GO:0008150 ! biological_process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16572" xsd:anyURI

[Term]
id: GO:0009719
name: response to endogenous stimulus
namespace: biological_process
def: "Any process that results in 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 arising within the organism." [GOC:sm]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_annotate
subset: goslim_plant
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0009790
name: embryo development
namespace: biological_process
alt_id: GO:0009795
def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu]
subset: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_plant
synonym: "embryogenesis" EXACT []
synonym: "embryogenesis and morphogenesis" BROAD []
synonym: "embryonal development" EXACT []
xref: Wikipedia:Embryogenesis
is_a: GO:0007275 ! multicellular organism development

[Term]
id: GO:0009791
name: post-embryonic development
namespace: biological_process
def: "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development." [GOC:go_curators]
subset: goslim_plant
is_a: GO:0008150 ! biological_process
relationship: part_of GO:0007275 ! multicellular organism development

[Term]
id: GO:0009835
name: fruit ripening
namespace: biological_process
def: "An developmental maturation process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal." [GOC:lr]
subset: goslim_plant
synonym: "fruit maturation" RELATED [GOC:PO_curators]
synonym: "fruit senescence" RELATED [GOC:PO_curators]
xref: Wikipedia:Ripening
is_a: GO:0008150 ! biological_process
relationship: part_of GO:0007275 ! multicellular organism development
relationship: part_of GO:0022414 ! reproductive process

[Term]
id: GO:0009838
name: abscission
namespace: biological_process
def: "The controlled shedding of a body part." [ISBN:0140514031]
subset: goslim_plant
xref: Wikipedia:Abscission
is_a: GO:0008150 ! biological_process
relationship: part_of GO:0007275 ! multicellular organism development

[Term]
id: GO:0009856
name: pollination
namespace: biological_process
def: "The cascade of biological processes occurring in plants beginning when the pollen lands on the female reproductive organs of a plant and continuing up to, but not including, fertilization, as defined by sperm-egg cell fusion." [GOC:tb, PMID:10973091]
subset: goslim_plant
subset: goslim_plant_ribbon
xref: Wikipedia:Pollination
is_a: GO:0022414 ! reproductive process
relationship: part_of GO:0008150 ! biological_process

[Term]
id: GO:0009908
name: flower development
namespace: biological_process
alt_id: GO:0048409
def: "The process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. The flower is the reproductive structure in a plant, and its development begins with the transition of the vegetative or inflorescence meristem into a floral meristem." [GOC:tb, ISBN:0879015322]
subset: goslim_plant
subset: goslim_plant_ribbon
is_a: GO:0009791 ! post-embryonic development
is_a: GO:0022414 ! reproductive process
is_a: GO:0048856 ! anatomical structure development

[Term]
id: GO:0009987
name: cellular process
namespace: biological_process
alt_id: GO:0008151
alt_id: GO:0044763
alt_id: GO:0050875
def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete]
comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
subset: gocheck_do_not_annotate
subset: goslim_plant
synonym: "cell growth and/or maintenance" NARROW []
synonym: "cell physiology" EXACT []
synonym: "cellular physiological process" EXACT []
synonym: "single-organism cellular process" RELATED []
is_a: GO:0008150 ! biological_process
created_by: jl
creation_date: 2012-12-11T16:56:55Z

[Term]
id: GO:0012501
name: programmed cell death
namespace: biological_process
alt_id: GO:0016244
def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis]
comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children.
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
synonym: "caspase-independent apoptosis" RELATED []
synonym: "caspase-independent cell death" NARROW []
synonym: "non-apoptotic programmed cell death" NARROW []
synonym: "nonapoptotic programmed cell death" NARROW []
synonym: "PCD" RELATED []
synonym: "RCD" RELATED []
synonym: "regulated cell death" BROAD []
xref: Wikipedia:Programmed_cell_death
is_a: GO:0009987 ! cellular process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24835" xsd:anyURI

[Term]
id: GO:0015979
name: photosynthesis
namespace: biological_process
def: "The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds." [ISBN:0198547684]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
xref: Wikipedia:Photosynthesis
is_a: GO:0008152 ! metabolic process
is_a: GO:0009987 ! cellular process
property_value: RO:0002161 NCBITaxon:33208
property_value: RO:0002161 NCBITaxon:4895

[Term]
id: GO:0016020
name: membrane
namespace: cellular_component
alt_id: GO:0016021
alt_id: GO:0098589
alt_id: GO:0098805
def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "integral component of membrane" NARROW []
synonym: "integral to membrane" NARROW []
synonym: "membrane region" NARROW []
synonym: "region of membrane" NARROW []
synonym: "transmembrane" RELATED [GOC:mah]
synonym: "whole membrane" NARROW []
xref: Wikipedia:Biological_membrane
xref: Wikipedia:Transmembrane_protein
is_a: GO:0005575 ! cellular_component
creation_date: 2014-03-06T11:37:54Z

[Term]
id: GO:0016043
name: cellular component organization
namespace: biological_process
alt_id: GO:0044235
alt_id: GO:0071842
def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah]
subset: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "cell organisation" EXACT []
synonym: "cell organization and biogenesis" RELATED [GOC:mah]
synonym: "cellular component organisation at cellular level" EXACT [GOC:mah]
synonym: "cellular component organisation in other organism" EXACT [GOC:mah]
synonym: "cellular component organization at cellular level" EXACT []
synonym: "cellular component organization in other organism" EXACT []
is_a: GO:0009987 ! cellular process

[Term]
id: GO:0016049
name: cell growth
namespace: biological_process
alt_id: GO:0048591
def: "The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:ai]
subset: gocheck_do_not_annotate
subset: goslim_drosophila
subset: goslim_pir
subset: goslim_plant
synonym: "cell expansion" RELATED []
synonym: "cellular growth" EXACT []
synonym: "growth of cell" EXACT []
synonym: "metabolic process resulting in cell growth" RELATED []
synonym: "metabolism resulting in cell growth" RELATED []
synonym: "non-developmental cell growth" RELATED [GOC:mah]
synonym: "non-developmental growth of a unicellular organism" RELATED [GOC:mah]
is_a: GO:0009987 ! cellular process
is_a: GO:0040007 ! growth

[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]
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_yeast
synonym: "phosphokinase activity" EXACT []
xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm"
xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines"
is_a: GO:0016740 ! transferase activity

[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_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
subset: goslim_yeast
xref: EC:2.-.-.-
xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2"
xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1"
xref: Reactome:R-HSA-5668414 "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK"
xref: Reactome:R-HSA-8868783 "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248"
is_a: GO:0003824 ! catalytic activity

[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." [ISBN:0198506732]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
subset: goslim_yeast
xref: EC:3.-.-.-
xref: Reactome:R-HSA-1236938 "Partial proteolysis of antigen in phagolysosomes"
xref: Reactome:R-HSA-2029475 "Production of AA by iPLA2 upon FCGR activation"
xref: Reactome:R-HSA-5694583 "ABHD4 hydrolyses NAPE"
xref: Reactome:R-HSA-5695964 "ABHD14B hydrolyses PNPB"
xref: Reactome:R-HSA-6786190 "CMBL hydrolyses OM to OLMS"
xref: Reactome:R-HSA-6788295 "HDHD1:Mg2+ dephosphorylates PURIDP"
xref: Reactome:R-HSA-8938314 "ENPPs hydrolyse CoA-SH to PPANT, PAP"
xref: Reactome:R-HSA-8952137 "Phospholipid phosphatase 6 hydrolyses Presqualene diphosphate to presqualene monophosphate"
is_a: GO:0003824 ! catalytic activity

[Term]
id: GO:0019538
name: protein metabolic process
namespace: biological_process
alt_id: GO:0006411
alt_id: GO:0044267
alt_id: GO:0044268
def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_flybase_ribbon
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "cellular protein metabolic process" EXACT []
synonym: "cellular protein metabolism" EXACT []
synonym: "multicellular organismal protein metabolic process" NARROW []
synonym: "protein metabolic process and modification" EXACT []
synonym: "protein metabolism" EXACT []
synonym: "protein metabolism and modification" EXACT []
xref: Wikipedia:Protein_metabolism
is_a: GO:0008152 ! metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI

[Term]
id: GO:0019725
name: cellular homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state at the level of the cell." [GOC:isa_complete, GOC:jl, ISBN:0395825172]
subset: goslim_candida
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_plant
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0019748
name: secondary metabolic process
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_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_pombe
synonym: "secondary metabolism" EXACT []
synonym: "secondary metabolite metabolic process" EXACT []
synonym: "secondary metabolite metabolism" EXACT []
xref: Wikipedia:Secondary_metabolism
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0019825
name: oxygen binding
namespace: molecular_function
def: "Binding to oxygen (O2)." [GOC:jl]
subset: goslim_pir
subset: goslim_plant
synonym: "cytochrome P450" NARROW []
synonym: "cytochrome P450 activity" RELATED []
is_a: GO:0005488 ! binding

[Term]
id: GO:0022414
name: reproductive process
namespace: biological_process
alt_id: GO:0044702
def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete]
subset: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "single organism reproductive process" RELATED []
xref: Wikipedia:Reproduction
is_a: GO:0008150 ! biological_process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI
created_by: jl
creation_date: 2012-09-19T15:56:06Z

[Term]
id: GO:0030154
name: cell differentiation
namespace: biological_process
def: "The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
subset: goslim_plant_ribbon
xref: Wikipedia:Cellular_differentiation
is_a: GO:0009987 ! cellular process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24390" xsd:anyURI

[Term]
id: GO:0030234
name: enzyme regulator activity
namespace: molecular_function
alt_id: GO:0010576
def: "Binds to and modulates the activity of an enzyme." [GOC:dph, GOC:mah, GOC:tb]
comment: This term should only be used in cases when the regulator directly interacts with the enzyme.
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_yeast
synonym: "catalytic regulator activity" EXACT [GOC:dph]
synonym: "enzyme modulator" EXACT []
synonym: "metalloenzyme regulator activity" NARROW []
is_a: GO:0003674 ! molecular_function
relationship: has_part GO:0005515 ! protein binding

[Term]
id: GO:0030246
name: carbohydrate binding
namespace: molecular_function
alt_id: GO:0005529
def: "Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates." [GOC:mah]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_flybase_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "selectin" RELATED []
synonym: "sugar binding" EXACT []
is_a: GO:0005488 ! binding

[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 or cells. This does not include the periplasmic space." [GOC:go_curators]
comment: The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'.
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005575 ! cellular_component

[Term]
id: GO:0036211
name: protein modification process
namespace: biological_process
alt_id: GO:0006464
def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:bf, GOC:jl]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
synonym: "cellular protein modification process" EXACT []
synonym: "process resulting in protein modification" EXACT []
synonym: "protein modification" EXACT [GOC:bf]
is_a: GO:0019538 ! protein metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI
created_by: bf
creation_date: 2012-04-26T01:47:12Z

[Term]
id: GO:0038023
name: signaling receptor activity
namespace: molecular_function
alt_id: GO:0004872
alt_id: GO:0019041
def: "Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:bf, GOC:signaling]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_flybase_ribbon
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "receptor activity" BROAD []
synonym: "receptor activity involved in signal transduction" EXACT [GOC:bf]
synonym: "signalling receptor activity" EXACT []
is_a: GO:0003674 ! molecular_function
created_by: bf
creation_date: 2011-08-01T02:45:27Z

[Term]
id: GO:0040007
name: growth
namespace: biological_process
alt_id: GO:0048590
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: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_pir
subset: goslim_plant
synonym: "growth pattern" RELATED []
synonym: "non-developmental growth" RELATED [GOC:mah]
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0040029
name: epigenetic regulation of gene expression
namespace: biological_process
def: "A process that modulates the frequency, rate or extent of gene expression through chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or cytosine methylation of DNA. Once established, this regulation may be maintained over many cell divisions. It can also be heritable in the absence of the instigating signal." [PMID:10521337, PMID:11498582, PMID:22243696, PMID:34414474]
subset: goslim_plant
synonym: "regulation of gene expression, epigenetic" EXACT []
is_a: GO:0016043 ! cellular component organization
relationship: regulates GO:0009058 ! biosynthetic process
relationship: regulates GO:0009987 ! cellular process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22201" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24794" xsd:anyURI

[Term]
id: GO:0042221
name: response to chemical
namespace: biological_process
def: "Any process that results in 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 chemical stimulus." [GOC:jl]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_annotate
subset: goslim_candida
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_yeast
synonym: "response to chemical stimulus" EXACT [GOC:dos]
synonym: "response to chemical substance" EXACT []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0045182
name: translation regulator activity
namespace: molecular_function
def: "Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai]
subset: goslim_candida
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "translation factor activity" EXACT []
is_a: GO:0003674 ! molecular_function
relationship: part_of GO:0008150 ! biological_process

[Term]
id: GO:0048856
name: anatomical structure development
namespace: biological_process
def: "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. 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." [GO_REF:0000021]
subset: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_generic
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "development of an anatomical structure" EXACT []
is_a: GO:0008150 ! biological_process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI

[Term]
id: GO:0065009
name: regulation of molecular function
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GOC:isa_complete]
subset: gocheck_do_not_annotate
subset: goslim_pir
subset: goslim_plant
synonym: "regulation of a molecular function" EXACT []
is_a: GO:0008150 ! biological_process
relationship: regulates GO:0003674 ! molecular_function

[Term]
id: GO:0140110
name: transcription regulator activity
namespace: molecular_function
def: "A molecular function that controls the rate, timing and/or magnitude of gene transcription. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism. Genes are transcriptional units, and include bacterial operons." [GOC:pg, GOC:txnOH-2018, Wikipedia:Transcription_factor]
subset: gocheck_do_not_annotate
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
is_a: GO:0003674 ! molecular_function
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13588" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23609" xsd:anyURI
created_by: pg
creation_date: 2017-10-18T07:05:44Z

[Typedef]
id: ends_during
name: ends during
namespace: external
xref: RO:0002093

[Typedef]
id: happens_during
name: happens during
namespace: external
xref: RO:0002092
is_transitive: true
is_a: ends_during ! ends during

[Typedef]
id: has_ontology_root_term
name: has ontology root term
namespace: external
xref: IAO:0000700
is_metadata_tag: true
is_class_level: true

[Typedef]
id: has_part
name: has part
namespace: external
xref: BFO:0000051
is_transitive: true

[Typedef]
id: negatively_regulates
name: negatively regulates
namespace: external
xref: RO:0002212
is_a: regulates ! regulates

[Typedef]
id: occurs_in
name: occurs in
namespace: external
xref: BFO:0000066
transitive_over: part_of ! part of

[Typedef]
id: part_of
name: part of
namespace: external
xref: BFO:0000050
is_transitive: true
inverse_of: has_part ! has part

[Typedef]
id: positively_regulates
name: positively regulates
namespace: external
xref: RO:0002213
holds_over_chain: negatively_regulates negatively_regulates
is_a: regulates ! regulates

[Typedef]
id: regulates
name: regulates
namespace: external
xref: RO:0002211
is_transitive: true

[Typedef]
id: starts_during
name: starts during
namespace: external
xref: RO:0002091

[Typedef]
id: term_tracker_item
name: term tracker item
namespace: external
xref: IAO:0000233
is_metadata_tag: true
is_class_level: true
