format-version: 1.2
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
subsetdef: goslim_agr "AGR slim"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_chembl "ChEMBL protein targets summary"
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_metagenomics "Metagenomics GO slim"
subsetdef: goslim_mouse "Mouse GO slim"
subsetdef: goslim_pir "PIR GO slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_pombe "Fission yeast GO slim"
subsetdef: goslim_synapse "synapse GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
synonymtypedef: syngo_official_label "label approved by the SynGO project"
synonymtypedef: systematic_synonym "Systematic synonym" EXACT
ontology: go/subsets/goslim_pir

[Term]
id: GO:0000003
name: reproduction
namespace: biological_process
alt_id: GO:0019952
alt_id: GO:0050876
def: "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
synonym: "reproductive physiological process" EXACT []
xref: Wikipedia:Reproduction
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0000109
name: nucleotide-excision repair complex
namespace: cellular_component
def: "Any complex formed of proteins that act in nucleotide-excision repair." [PMID:10915862]
comment: Note that process information is included in the term and definition for the purpose of describing and distinguishing the complex.
subset: goslim_pir
synonym: "UvrB-UvrC complex" NARROW [PMID:12145219]
synonym: "UvrBC complex" NARROW [GOC:bhm, PMID:12145219]
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0000128
name: flocculation
namespace: biological_process
def: "The reversible, non-sexual aggregation of single-celled organisms in suspension to form aggregates of many cells known as flocs." [GOC:jl, GOC:vw, PMID:21114594, PMID:8740415]
comment: The word floc derives from the Latin word floccus, which means a tuft of wool.
subset: goslim_pir
xref: Wikipedia:Flocculation
is_a: GO:0051704 ! multi-organism process

[Term]
id: GO:0000133
name: polarisome
namespace: cellular_component
def: "Protein complex that plays a role in determining cell polarity by directing the localized assembly of actin filaments at polarization sites; in Saccharomyces the polarisome includes Bni1p, Spa2p, Pea2p, and Bud6p." [PMID:14734532, PMID:14998522, PMID:9632790]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm
relationship: part_of GO:0030427 ! site of polarized growth

[Term]
id: GO:0000151
name: ubiquitin ligase complex
namespace: cellular_component
def: "A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex." [GOC:jh2, PMID:9529603]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0000166
name: nucleotide binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with 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:0000178
name: exosome (RNase complex)
namespace: cellular_component
def: "A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured." [PMID:17174896, PMID:20531386, PMID:26726035]
comment: Note that this term should not be confused with 'exosome' used in the context of vesicles released from multivesicular bodies.
subset: goslim_pir
synonym: "exosome (ribonucleasease complex)" EXACT []
synonym: "exosome multienzyme ribonuclease complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0000280
name: nuclear division
namespace: biological_process
def: "The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei." [GOC:mah]
subset: goslim_pir
synonym: "karyokinesis" RELATED []
is_a: GO:0048285 ! organelle fission

[Term]
id: GO:0000307
name: cyclin-dependent protein kinase holoenzyme complex
namespace: cellular_component
def: "Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner." [GOC:krc, PMID:11602261]
subset: goslim_pir
synonym: "CDK holoenzyme" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0000346
name: transcription export complex
namespace: cellular_component
def: "The transcription export (TREX) complex couples transcription elongation by RNA polymerase II to mRNA export. The complex associates with the polymerase and travels with it along the length of the transcribed gene. TREX is composed of the THO transcription elongation complex as well as other proteins that couple THO to mRNA export proteins. The TREX complex is known to be found in a wide range of eukaryotes, including S. cerevisiae and metazoans." [GOC:krc, PMID:11979277]
subset: goslim_pir
synonym: "TREX complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0000347
name: THO complex
namespace: cellular_component
def: "The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. In S. cerevisiae, it is composed of four subunits: Hpr1p, Tho2p, Thp1p, and Mft1p, while the human complex is composed of 7 subunits." [GOC:krc, PMID:11060033, PMID:11979277, PMID:16983072]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0000375
name: RNA splicing, via transesterification reactions
namespace: biological_process
alt_id: GO:0000385
alt_id: GO:0031202
def: "Splicing of RNA via a series of two transesterification reactions." [GOC:krc]
comment: Note that nuclear mRNA, Group I, Group II, and Group III introns are all spliced by a series of two transesterification reactions that occur within the RNA itself, or between two RNAs in trans splicing. Some of these require one or more proteins to stabilize the catalytic conformation, while others are autocatalytic. Note that tRNA introns are spliced by a different catalytic mechanism.
subset: goslim_pir
synonym: "pre-mRNA splicing factor activity" RELATED [GOC:krc, GOC:mah]
synonym: "RNA splicing factor activity, transesterification mechanism" RELATED [GOC:krc, GOC:mah]
synonym: "spliceosomal catalysis" RELATED []
is_a: GO:0006396 ! RNA processing

[Term]
id: GO:0000439
name: transcription factor TFIIH core complex
namespace: cellular_component
alt_id: GO:0000441
def: "The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD." [GOC:ew, GOC:krc, PMID:14500720, PMID:17215295, PMID:22308316, PMID:22572993, PMID:23028141, PMID:7813015]
subset: goslim_pir
synonym: "core TFIIH complex" EXACT []
synonym: "SSL2-core TFIIH complex" EXACT []
is_a: GO:0005667 ! transcription factor complex
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0000502
name: proteasome complex
namespace: cellular_component
def: "A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core." [GOC:rb, http://en.wikipedia.org/wiki/Proteasome]
subset: goslim_pir
synonym: "26S proteasome" NARROW []
synonym: "proteasome" EXACT [GOC:cjm]
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0000746
name: conjugation
namespace: biological_process
def: "The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms." [GOC:elh]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
subset: goslim_yeast
xref: Wikipedia:Conjugation
is_a: GO:0051704 ! multi-organism process

[Term]
id: GO:0000776
name: kinetochore
namespace: cellular_component
alt_id: GO:0005699
def: "A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules." [GOC:elh]
comment: Note that the kinetochore overlaps the centromeric DNA, but centromeric DNA is not part of the kinetochore.
subset: goslim_pir
xref: Wikipedia:Kinetochore
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
relationship: part_of GO:0005694 ! chromosome

[Term]
id: GO:0000782
name: telomere cap complex
namespace: cellular_component
def: "A complex of DNA and protein located at the end of a linear chromosome that protects and stabilizes a linear chromosome." [GOC:elh]
comment: Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome.
subset: goslim_pir
is_a: GO:0032993 ! protein-DNA complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005694 ! chromosome

[Term]
id: GO:0000786
name: nucleosome
namespace: cellular_component
alt_id: GO:0005718
def: "A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures." [GOC:elh]
subset: goslim_pir
xref: Wikipedia:Nucleosome
is_a: GO:0032993 ! protein-DNA complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005694 ! chromosome

[Term]
id: GO:0000796
name: condensin complex
namespace: cellular_component
alt_id: GO:0005676
alt_id: GO:0008620
def: "A multisubunit protein complex that plays a central role in chromosome condensation." [GOC:elh]
subset: goslim_pir
synonym: "13S condensin complex" NARROW []
synonym: "SMC complex" RELATED []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005694 ! chromosome

[Term]
id: GO:0000808
name: origin recognition complex
namespace: cellular_component
def: "A multisubunit complex that is located at the replication origins of a chromosome." [GOC:elh]
subset: goslim_pir
synonym: "ORC" EXACT []
synonym: "origin of replication recognition complex" EXACT []
xref: Wikipedia:Origin_recognition_complex
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005694 ! chromosome

[Term]
id: GO:0000930
name: gamma-tubulin complex
namespace: cellular_component
def: "A multiprotein complex composed of gamma-tubulin and other non-tubulin proteins. Gamma-tubulin complexes are localized to microtubule organizing centers, and play an important role in the nucleation of microtubules. The number and complexity of non-tubulin proteins associated with these complexes varies between species." [GOC:clt, PMID:12134075]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm
relationship: part_of GO:0005856 ! cytoskeleton

[Term]
id: GO:0001534
name: radial spoke
namespace: cellular_component
def: "Protein complex that links the outer microtubule doublet of the ciliary or flagellum axoneme with the sheath that surrounds the central pair of microtubules. Composed of a stalk that attaches to each doublet microtubule and a globular structure (spoke head) that projects toward the central pair of microtubules." [ISBN:0124325653, PMID:9450971]
subset: goslim_pir
xref: Wikipedia:Radial_spoke
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005930 ! axoneme

[Term]
id: GO:0001775
name: cell activation
namespace: biological_process
def: "A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:mgi_curators]
subset: goslim_pir
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0001816
name: cytokine production
namespace: biological_process
def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149]
comment: Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules.
subset: goslim_pir
synonym: "interferon production" NARROW [GOC:add, GOC:mah]
synonym: "interleukin production" NARROW [GOC:add, GOC:mah, http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F]
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0001871
name: pattern binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a repeating or polymeric structure, such as a polysaccharide or peptidoglycan." [PMID:12072369, PMID:12225919, PMID:12507420, PMID:12925128, PMID:14523544]
comment: Note that this term and its child terms are intended for annotation of gene products which function to recognize (bind) the repeating structural units such as polysaccharides or peptidoglycans commonly found in microbial cell walls and virions. If such binding is coupled to signal transduction, use 'pattern recognition receptor activity ; GO:0008329' instead.
subset: goslim_pir
synonym: "pattern recognition activity" BROAD []
is_a: GO:0005488 ! binding

[Term]
id: GO:0001882
name: nucleoside binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose." [GOC:hjd]
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0001906
name: cell killing
namespace: biological_process
def: "Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions." [GOC:add]
subset: goslim_pir
synonym: "necrosis" RELATED []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0001917
name: photoreceptor inner segment
namespace: cellular_component
def: "The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs." [GOC:add, PMID:12019563]
subset: goslim_pir
is_a: GO:0044464 ! cell part

[Term]
id: GO:0002054
name: nucleobase binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases." [GOC:hjd]
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0002376
name: immune system process
namespace: biological_process
def: "Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
comment: Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022.
subset: goslim_agr
subset: goslim_chembl
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
xref: Wikipedia:Immune_system
is_a: GO:0008150 ! biological_process

[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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [GOC:pdt]
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use 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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
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
def: "Interacting selectively and non-covalently with any nucleic acid." [GOC:jl]
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
is_a: GO:0005488 ! binding

[Term]
id: GO:0003682
name: chromatin binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with 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_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "lamin/chromatin binding" BROAD []
synonym: "microtubule/chromatin interaction" RELATED []
synonym: "nuclear membrane vesicle binding to chromatin" NARROW []
is_a: GO:0005488 ! binding

[Term]
id: GO:0003774
name: motor activity
namespace: molecular_function
def: "Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate." [GOC:mah, GOC:vw, ISBN:0815316194, PMID:11242086]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
subset: goslim_plant
is_a: GO:0016787 ! hydrolase activity

[Term]
id: GO:0003823
name: antigen binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen." [GOC:jl, ISBN:0198506732, ISBN:0721662544]
subset: goslim_chembl
subset: goslim_pir
synonym: "antibody" RELATED []
synonym: "B cell receptor activity" RELATED []
synonym: "immunoglobulin" RELATED []
synonym: "opsonin activity" RELATED []
is_a: GO:0005488 ! binding

[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_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb]
xref: Wikipedia:Enzyme
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0004133
name: glycogen debranching enzyme activity
namespace: molecular_function
def: "Catalysis of the cleavage of branch points in branched glycogen polymers." [ISBN:0198506732]
subset: goslim_pir
is_a: GO:0003824 ! catalytic activity
relationship: part_of GO:0005976 ! polysaccharide metabolic process
relationship: part_of GO:0006112 ! energy reserve metabolic process

[Term]
id: GO:0004386
name: helicase activity
namespace: molecular_function
def: "Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix." [GOC:mah, ISBN:0198506732]
comment: Note that most helicases catalyze processive duplex unwinding.
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_yeast
xref: Reactome:REACT_101111 "Addition of the third nucleotide on the nascent transcript, Saccharomyces cerevisiae"
xref: Reactome:REACT_101247 "Formation of open bubble structure in DNA by helicases, Bos taurus"
xref: Reactome:REACT_101622 "MCM8 mediated fork unwinding, Danio rerio"
xref: Reactome:REACT_101644 "Formation of open bubble structure in DNA by helicases, Oryza sativa"
xref: Reactome:REACT_101823 "MCM2-7 mediated fork unwinding, Plasmodium falciparum"
xref: Reactome:REACT_101994 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Xenopus tropicalis"
xref: Reactome:REACT_102121 "Addition of the third nucleotide on the nascent transcript, Rattus norvegicus"
xref: Reactome:REACT_102441 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Gallus gallus"
xref: Reactome:REACT_102560 "MCM2-7 mediated fork unwinding, Oryza sativa"
xref: Reactome:REACT_1033 "Formation of open bubble structure in DNA by helicases, Homo sapiens"
xref: Reactome:REACT_103861 "MCM8 mediated fork unwinding, Bos taurus"
xref: Reactome:REACT_103881 "RNA Polymerase II Promoter Opening: First Transition, Dictyostelium discoideum"
xref: Reactome:REACT_103897 "MCM8 mediated fork unwinding, Mus musculus"
xref: Reactome:REACT_103959 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Rattus norvegicus"
xref: Reactome:REACT_104221 "MCM2-7 mediated fork unwinding, Rattus norvegicus"
xref: Reactome:REACT_105950 "MCM2-7 mediated fork unwinding, Xenopus tropicalis"
xref: Reactome:REACT_106346 "Formation of open bubble structure in DNA by helicases, Taeniopygia guttata"
xref: Reactome:REACT_107072 "Formation of open bubble structure in DNA by helicases, Mus musculus"
xref: Reactome:REACT_107495 "RNA Polymerase II Promoter Opening: First Transition, Taeniopygia guttata"
xref: Reactome:REACT_108159 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Dictyostelium discoideum"
xref: Reactome:REACT_108648 "Addition of the third nucleotide on the nascent transcript, Arabidopsis thaliana"
xref: Reactome:REACT_108654 "MCM2-7 mediated fork unwinding, Schizosaccharomyces pombe"
xref: Reactome:REACT_109035 "RNA Polymerase II Promoter Opening: First Transition, Schizosaccharomyces pombe"
xref: Reactome:REACT_109161 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Arabidopsis thaliana"
xref: Reactome:REACT_110588 "MCM8 mediated fork unwinding, Xenopus tropicalis"
xref: Reactome:REACT_110827 "Formation of open bubble structure in DNA by helicases, Danio rerio"
xref: Reactome:REACT_110845 "Cap-bound mRNA is activated by helicases, Mus musculus"
xref: Reactome:REACT_112208 "MCM8 mediated fork unwinding, Drosophila melanogaster"
xref: Reactome:REACT_112817 "Cap-bound mRNA is activated by helicases, Schizosaccharomyces pombe"
xref: Reactome:REACT_113177 "Formation of open bubble structure in DNA by helicases, Caenorhabditis elegans"
xref: Reactome:REACT_1521 "Cap-bound mRNA is activated by helicases, Homo sapiens"
xref: Reactome:REACT_1817 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Homo sapiens"
xref: Reactome:REACT_1844 "RNA Polymerase II Promoter Opening: First Transition, Homo sapiens"
xref: Reactome:REACT_28131 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Drosophila melanogaster"
xref: Reactome:REACT_28343 "MCM2-7 mediated fork unwinding, Danio rerio"
xref: Reactome:REACT_28810 "Addition of the third nucleotide on the nascent transcript, Oryza sativa"
xref: Reactome:REACT_28880 "MCM2-7 mediated fork unwinding, Drosophila melanogaster"
xref: Reactome:REACT_29155 "Addition of the third nucleotide on the nascent transcript, Drosophila melanogaster"
xref: Reactome:REACT_29217 "Formation of open bubble structure in DNA by helicases, Xenopus tropicalis"
xref: Reactome:REACT_29818 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Oryza sativa"
xref: Reactome:REACT_29850 "RNA Polymerase II Promoter Opening: First Transition, Saccharomyces cerevisiae"
xref: Reactome:REACT_30013 "MCM8 mediated fork unwinding, Rattus norvegicus"
xref: Reactome:REACT_30989 "MCM8 mediated fork unwinding, Arabidopsis thaliana"
xref: Reactome:REACT_31034 "Cap-bound mRNA is activated by helicases, Danio rerio"
xref: Reactome:REACT_31090 "MCM2-7 mediated fork unwinding, Gallus gallus"
xref: Reactome:REACT_31554 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Schizosaccharomyces pombe"
xref: Reactome:REACT_32533 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Caenorhabditis elegans"
xref: Reactome:REACT_33205 "MCM8 mediated fork unwinding, Canis familiaris"
xref: Reactome:REACT_34016 "Formation of open bubble structure in DNA by helicases, Rattus norvegicus"
xref: Reactome:REACT_34089 "MCM2-7 mediated fork unwinding, Dictyostelium discoideum"
xref: Reactome:REACT_34560 "MCM8 mediated fork unwinding, Sus scrofa"
xref: Reactome:REACT_40 "Addition of the third nucleotide on the nascent transcript, Homo sapiens"
xref: Reactome:REACT_6134 "HIV-1 Promoter Opening: First Transition, Homo sapiens"
xref: Reactome:REACT_6184 "Addition of the fourth nucleotide on the nascent HIV-1 transcript: Second Transition, Homo sapiens"
xref: Reactome:REACT_6325 "Addition of the third nucleotide on the nascent HIV-1 transcript, Homo sapiens"
xref: Reactome:REACT_6758 "Xenopus Mcm8 mediated fork unwinding, Xenopus laevis"
xref: Reactome:REACT_6768 "MCM8 mediated fork unwinding, Homo sapiens"
xref: Reactome:REACT_6853 "Yeast Mcm2-7 mediated fork unwinding, Saccharomyces cerevisiae"
xref: Reactome:REACT_6922 "MCM2-7 mediated fork unwinding, Homo sapiens"
xref: Reactome:REACT_78086 "RNA Polymerase II Promoter Opening: First Transition, Rattus norvegicus"
xref: Reactome:REACT_78462 "Formation of open bubble structure in DNA by helicases, Drosophila melanogaster"
xref: Reactome:REACT_78667 "MCM2-7 mediated fork unwinding, Canis familiaris"
xref: Reactome:REACT_78771 "MCM8 mediated fork unwinding, Dictyostelium discoideum"
xref: Reactome:REACT_79759 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Mus musculus"
xref: Reactome:REACT_80107 "RNA Polymerase II Promoter Opening: First Transition, Arabidopsis thaliana"
xref: Reactome:REACT_80325 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Danio rerio"
xref: Reactome:REACT_80500 "MCM8 mediated fork unwinding, Gallus gallus"
xref: Reactome:REACT_80532 "Addition of the third nucleotide on the nascent transcript, Gallus gallus"
xref: Reactome:REACT_80605 "Addition of the third nucleotide on the nascent transcript, Mus musculus"
xref: Reactome:REACT_81126 "Addition of the third nucleotide on the nascent transcript, Schizosaccharomyces pombe"
xref: Reactome:REACT_81335 "RNA Polymerase II Promoter Opening: First Transition, Gallus gallus"
xref: Reactome:REACT_81427 "MCM8 mediated fork unwinding, Taeniopygia guttata"
xref: Reactome:REACT_81441 "MCM8 mediated fork unwinding, Oryza sativa"
xref: Reactome:REACT_81682 "Formation of open bubble structure in DNA by helicases, Canis familiaris"
xref: Reactome:REACT_82776 "RNA Polymerase II Promoter Opening: First Transition, Danio rerio"
xref: Reactome:REACT_83794 "Formation of open bubble structure in DNA by helicases, Gallus gallus"
xref: Reactome:REACT_84565 "Formation of open bubble structure in DNA by helicases, Schizosaccharomyces pombe"
xref: Reactome:REACT_84574 "Cap-bound mRNA is activated by helicases, Canis familiaris"
xref: Reactome:REACT_84809 "MCM2-7 mediated fork unwinding, Mus musculus"
xref: Reactome:REACT_84907 "MCM2-7 mediated fork unwinding, Taeniopygia guttata"
xref: Reactome:REACT_85111 "Cap-bound mRNA is activated by helicases, Drosophila melanogaster"
xref: Reactome:REACT_85172 "MCM2-7 mediated fork unwinding, Arabidopsis thaliana"
xref: Reactome:REACT_86220 "MCM2-7 mediated fork unwinding, Caenorhabditis elegans"
xref: Reactome:REACT_88362 "Addition of the third nucleotide on the nascent transcript, Caenorhabditis elegans"
xref: Reactome:REACT_89000 "MCM2-7 mediated fork unwinding, Bos taurus"
xref: Reactome:REACT_89030 "Formation of open bubble structure in DNA by helicases, Saccharomyces cerevisiae"
xref: Reactome:REACT_89363 "Addition of the third nucleotide on the nascent transcript, Xenopus tropicalis"
xref: Reactome:REACT_89694 "RNA Polymerase II Promoter Opening: First Transition, Drosophila melanogaster"
xref: Reactome:REACT_91822 "MCM8 mediated fork unwinding, Plasmodium falciparum"
xref: Reactome:REACT_93391 "RNA Polymerase II Promoter Opening: First Transition, Oryza sativa"
xref: Reactome:REACT_93711 "RNA Polymerase II Promoter Opening: First Transition, Mus musculus"
xref: Reactome:REACT_94645 "RNA Polymerase II Promoter Opening: First Transition, Xenopus tropicalis"
xref: Reactome:REACT_94679 "RNA Polymerase II Promoter Opening: First Transition, Caenorhabditis elegans"
xref: Reactome:REACT_95942 "Addition of the fourth nucleotide on the Nascent Transcript: Second Transition, Saccharomyces cerevisiae"
xref: Reactome:REACT_95993 "Formation of open bubble structure in DNA by helicases, Arabidopsis thaliana"
xref: Reactome:REACT_98273 "Addition of the third nucleotide on the nascent transcript, Dictyostelium discoideum"
xref: Reactome:REACT_98302 "Formation of open bubble structure in DNA by helicases, Sus scrofa"
xref: Reactome:REACT_98745 "Cap-bound mRNA is activated by helicases, Xenopus tropicalis"
xref: Reactome:REACT_99120 "Addition of the third nucleotide on the nascent transcript, Danio rerio"
is_a: GO:0016787 ! hydrolase activity

[Term]
id: GO:0004497
name: monooxygenase activity
namespace: molecular_function
def: "Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water." [http://www.onelook.com/, ISBN:0198506732]
subset: goslim_pir
synonym: "hydroxylase activity" RELATED [GOC:mah, GOC:vk]
xref: Reactome:REACT_100875 "FMO2 S-oxidizes the antithyroid drug methimazole, Dictyostelium discoideum"
xref: Reactome:REACT_101711 "CYP2W1 can oxidize indole, Sus scrofa"
xref: Reactome:REACT_106539 "CYP3A43 catalyzes the 6beta-hydroxylation of testosterone, Gallus gallus"
xref: Reactome:REACT_106973 "CYP2W1 can oxidize indole, Mus musculus"
xref: Reactome:REACT_107936 "FMO2 S-oxidizes the antithyroid drug methimazole, Caenorhabditis elegans"
xref: Reactome:REACT_109390 "CYP4F11 omega-hydroxylates 3-hydroxypalmitate, Mus musculus"
xref: Reactome:REACT_110926 "CYP2W1 can oxidize indole, Danio rerio"
xref: Reactome:REACT_113028 "CYP3A43 catalyzes the 6beta-hydroxylation of testosterone, Taeniopygia guttata"
xref: Reactome:REACT_115238 "FMO2 S-oxidizes the antithyroid drug methimazole, Danio rerio"
xref: Reactome:REACT_13511 "CYP4F11 omega-hydroxylates 3-hydroxypalmitate, Homo sapiens"
xref: Reactome:REACT_13592 "CYP2W1 can oxidize indole, Homo sapiens"
xref: Reactome:REACT_13740 "CYP3A43 catalyzes the 6beta-hydroxylation of testosterone, Homo sapiens"
xref: Reactome:REACT_13821 "FMO2 S-oxidizes the antithyroid drug methimazole, Homo sapiens"
xref: Reactome:REACT_30553 "FMO2 S-oxidizes the antithyroid drug methimazole, Canis familiaris"
xref: Reactome:REACT_34685 "FMO2 S-oxidizes the antithyroid drug methimazole, Mus musculus"
xref: Reactome:REACT_78030 "CYP4F11 omega-hydroxylates 3-hydroxypalmitate, Danio rerio"
xref: Reactome:REACT_79048 "CYP3A43 catalyzes the 6beta-hydroxylation of testosterone, Danio rerio"
xref: Reactome:REACT_80846 "CYP2W1 can oxidize indole, Canis familiaris"
xref: Reactome:REACT_82079 "CYP2W1 can oxidize indole, Xenopus tropicalis"
xref: Reactome:REACT_84097 "FMO2 S-oxidizes the antithyroid drug methimazole, Bos taurus"
xref: Reactome:REACT_84242 "CYP2W1 can oxidize indole, Gallus gallus"
xref: Reactome:REACT_86917 "CYP2W1 can oxidize indole, Rattus norvegicus"
xref: Reactome:REACT_88779 "CYP4F11 omega-hydroxylates 3-hydroxypalmitate, Xenopus tropicalis"
xref: Reactome:REACT_90320 "CYP4F11 omega-hydroxylates 3-hydroxypalmitate, Taeniopygia guttata"
xref: Reactome:REACT_90960 "CYP3A43 catalyzes the 6beta-hydroxylation of testosterone, Drosophila melanogaster"
xref: Reactome:REACT_90990 "CYP2W1 can oxidize indole, Bos taurus"
xref: Reactome:REACT_92968 "FMO2 S-oxidizes the antithyroid drug methimazole, Sus scrofa"
xref: Reactome:REACT_95195 "FMO2 S-oxidizes the antithyroid drug methimazole, Rattus norvegicus"
xref: Reactome:REACT_96655 "CYP3A43 catalyzes the 6beta-hydroxylation of testosterone, Mus musculus"
is_a: GO:0016491 ! oxidoreductase activity

[Term]
id: GO:0004803
name: transposase activity
namespace: molecular_function
alt_id: GO:0004804
def: "Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element." [GOC:bm, ISBN:0198506732]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "P-element encoded transposase activity" NARROW []
is_a: GO:0003824 ! catalytic activity

[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 its assembly within or outside a cell." [GOC:mah, GOC:vw]
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
is_a: GO:0003674 ! molecular_function

[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, or 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: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
synonym: "carrier" RELATED []
xref: Reactome:REACT_6315 "Virion-associated M2 protein mediated ion infusion, Homo sapiens"
is_a: GO:0003674 ! molecular_function

[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: gocheck_do_not_manually_annotate
subset: goslim_pir
subset: goslim_plant
synonym: "ligand" NARROW []
xref: Wikipedia:Binding_(molecular)
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0005496
name: steroid binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene." [GOC:jl, ISBN:0198506732]
subset: goslim_pir
is_a: GO:0008289 ! lipid binding

[Term]
id: GO:0005515
name: protein binding
namespace: molecular_function
alt_id: GO:0001948
alt_id: GO:0045308
def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC:go_curators]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "glycoprotein binding" NARROW []
synonym: "protein amino acid binding" EXACT []
xref: Reactome:REACT_100287 "Formation of the IGF:IGFBP-4 Complex, Canis familiaris"
xref: Reactome:REACT_101129 "Formation of the IGF:IGFBP-3:ALS Complex, Rattus norvegicus"
xref: Reactome:REACT_102084 "Formation of the IGF:IGFBP-5:ALS Complex, Mus musculus"
xref: Reactome:REACT_102457 "An anchoring protein, SARA, recruits SMAD2/3, Canis familiaris"
xref: Reactome:REACT_103972 "Type II receptor recruits type I receptor, Xenopus tropicalis"
xref: Reactome:REACT_104029 "Formation of the IGF:IGFBP-6 Complex, Bos taurus"
xref: Reactome:REACT_104599 "Type II receptor recruits type I receptor, Sus scrofa"
xref: Reactome:REACT_105776 "Formation of the IGF:IGFBP-3:ALS Complex, Danio rerio"
xref: Reactome:REACT_105895 "Formation of the IGF:IGFBP-4 Complex, Bos taurus"
xref: Reactome:REACT_106168 "Formation of the IGF:IGFBP-2 Complex, Bos taurus"
xref: Reactome:REACT_106189 "Formation of the IGF:IGFBP-5:ALS Complex, Gallus gallus"
xref: Reactome:REACT_107402 "Formation of the IGF:IGFBP-4 Complex, Mus musculus"
xref: Reactome:REACT_108283 "Formation of the IGF:IGFBP-4 Complex, Xenopus tropicalis"
xref: Reactome:REACT_109392 "Formation of the IGF:IGFBP-3:ALS Complex, Gallus gallus"
xref: Reactome:REACT_110419 "Type II receptor recruits type I receptor, Bos taurus"
xref: Reactome:REACT_110570 "Formation of the IGF:IGFBP-3:ALS Complex, Sus scrofa"
xref: Reactome:REACT_15321 "Formation of the IGF:IGFBP-1 Complex, Homo sapiens"
xref: Reactome:REACT_15325 "Formation of the IGF:IGFBP-4 Complex, Homo sapiens"
xref: Reactome:REACT_15355 "Formation of the IGF:IGFBP-5:ALS Complex, Homo sapiens"
xref: Reactome:REACT_15417 "Formation of the IGF:IGFBP-3:ALS Complex, Homo sapiens"
xref: Reactome:REACT_15419 "Formation of the IGF:IGFBP-2 Complex, Homo sapiens"
xref: Reactome:REACT_15506 "Formation of the IGF:IGFBP-6 Complex, Homo sapiens"
xref: Reactome:REACT_15541 "Traversal of the cortical actin network and docking at plasma membrane, Homo sapiens"
xref: Reactome:REACT_20509 "Exocytosis of Insulin, Mus musculus"
xref: Reactome:REACT_20539 "Traversal of the cortical actin network., Mus musculus"
xref: Reactome:REACT_28794 "Formation of the IGF:IGFBP-4 Complex, Sus scrofa"
xref: Reactome:REACT_30571 "Formation of the IGF:IGFBP-6 Complex, Danio rerio"
xref: Reactome:REACT_30672 "Formation of the IGF:IGFBP-2 Complex, Taeniopygia guttata"
xref: Reactome:REACT_31305 "Formation of the IGF:IGFBP-3:ALS Complex, Taeniopygia guttata"
xref: Reactome:REACT_31537 "Formation of the IGF:IGFBP-6 Complex, Rattus norvegicus"
xref: Reactome:REACT_31641 "Type II receptor recruits type I receptor, Danio rerio"
xref: Reactome:REACT_31648 "An anchoring protein, SARA, recruits SMAD2/3, Mus musculus"
xref: Reactome:REACT_32973 "Formation of the IGF:IGFBP-1 Complex, Canis familiaris"
xref: Reactome:REACT_33135 "An anchoring protein, SARA, recruits SMAD2/3, Rattus norvegicus"
xref: Reactome:REACT_34719 "Formation of the IGF:IGFBP-1 Complex, Danio rerio"
xref: Reactome:REACT_6923 "An anchoring protein, SARA, recruits SMAD2/3, Homo sapiens"
xref: Reactome:REACT_6945 "Type II receptor recruits type I receptor, Homo sapiens"
xref: Reactome:REACT_78382 "Formation of the IGF:IGFBP-1 Complex, Mus musculus"
xref: Reactome:REACT_78466 "Formation of the IGF:IGFBP-6 Complex, Canis familiaris"
xref: Reactome:REACT_79634 "Formation of the IGF:IGFBP-5:ALS Complex, Canis familiaris"
xref: Reactome:REACT_80470 "Formation of the IGF:IGFBP-1 Complex, Rattus norvegicus"
xref: Reactome:REACT_80778 "Type II receptor recruits type I receptor, Mus musculus"
xref: Reactome:REACT_83147 "Type II receptor recruits type I receptor, Rattus norvegicus"
xref: Reactome:REACT_83165 "Formation of the IGF:IGFBP-5:ALS Complex, Sus scrofa"
xref: Reactome:REACT_83532 "Formation of the IGF:IGFBP-2 Complex, Xenopus tropicalis"
xref: Reactome:REACT_85250 "Formation of the IGF:IGFBP-2 Complex, Canis familiaris"
xref: Reactome:REACT_85858 "Formation of the IGF:IGFBP-2 Complex, Gallus gallus"
xref: Reactome:REACT_85975 "An anchoring protein, SARA, recruits SMAD2/3, Danio rerio"
xref: Reactome:REACT_87187 "An anchoring protein, SARA, recruits SMAD2/3, Xenopus tropicalis"
xref: Reactome:REACT_87374 "Formation of the IGF:IGFBP-6 Complex, Sus scrofa"
xref: Reactome:REACT_87652 "Formation of the IGF:IGFBP-5:ALS Complex, Bos taurus"
xref: Reactome:REACT_88068 "Formation of the IGF:IGFBP-3:ALS Complex, Canis familiaris"
xref: Reactome:REACT_88138 "Formation of the IGF:IGFBP-5:ALS Complex, Danio rerio"
xref: Reactome:REACT_88223 "Formation of the IGF:IGFBP-1 Complex, Sus scrofa"
xref: Reactome:REACT_89261 "Formation of the IGF:IGFBP-4 Complex, Taeniopygia guttata"
xref: Reactome:REACT_90027 "Formation of the IGF:IGFBP-2 Complex, Rattus norvegicus"
xref: Reactome:REACT_90105 "Formation of the IGF:IGFBP-1 Complex, Xenopus tropicalis"
xref: Reactome:REACT_90666 "An anchoring protein, SARA, recruits SMAD2/3, Sus scrofa"
xref: Reactome:REACT_91560 "Type II receptor recruits type I receptor, Canis familiaris"
xref: Reactome:REACT_92029 "Formation of the IGF:IGFBP-4 Complex, Rattus norvegicus"
xref: Reactome:REACT_93175 "Formation of the IGF:IGFBP-1 Complex, Gallus gallus"
xref: Reactome:REACT_93938 "Formation of the IGF:IGFBP-5:ALS Complex, Rattus norvegicus"
xref: Reactome:REACT_94522 "Formation of the IGF:IGFBP-5:ALS Complex, Taeniopygia guttata"
xref: Reactome:REACT_94808 "Formation of the IGF:IGFBP-6 Complex, Mus musculus"
xref: Reactome:REACT_95241 "Formation of the IGF:IGFBP-3:ALS Complex, Mus musculus"
xref: Reactome:REACT_95561 "Formation of the IGF:IGFBP-5:ALS Complex, Xenopus tropicalis"
xref: Reactome:REACT_95647 "Formation of the IGF:IGFBP-3:ALS Complex, Bos taurus"
xref: Reactome:REACT_96236 "Formation of the IGF:IGFBP-2 Complex, Mus musculus"
xref: Reactome:REACT_96264 "Formation of the IGF:IGFBP-2 Complex, Danio rerio"
xref: Reactome:REACT_98028 "Formation of the IGF:IGFBP-1 Complex, Taeniopygia guttata"
xref: Reactome:REACT_98807 "An anchoring protein, SARA, recruits SMAD2/3, Bos taurus"
is_a: GO:0005488 ! binding

[Term]
id: GO:0005549
name: odorant binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell." [GOC:jl, ISBN:0721662544]
subset: goslim_pir
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 when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)." [GOC:pdt, NIF_Subcellular:sao-1337158144]
comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use 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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
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:sao-1337158144
xref: NIF_Subcellular:sao1337158144

[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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
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, http://en.wikipedia.org/wiki/Microbial_cyst, ISBN:0198547684, PMID:15134259]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
xref: Wikipedia:Cell_wall
is_a: GO:0030312 ! external encapsulating structure

[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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
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:0043231 ! intracellular membrane-bounded organelle

[Term]
id: GO:0005643
name: nuclear pore
namespace: cellular_component
alt_id: GO:0005644
def: "Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined." [ISBN:0198547684]
subset: goslim_pir
synonym: "NPC" EXACT []
synonym: "nuclear pore complex" EXACT []
synonym: "nuclear pore membrane protein" NARROW []
synonym: "nucleopore" EXACT [GOC:al, PMID:7603572]
xref: NIF_Subcellular:sao220861693
xref: Wikipedia:Nuclear_pore
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0005663
name: DNA replication factor C complex
namespace: cellular_component
def: "A complex that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. In eukaryotes the complex consists of five polypeptides." [PMID:14614842, PMID:14646196, PMID:16172520]
subset: goslim_pir
synonym: "activator 1 complex" EXACT []
synonym: "RFC complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005694 ! chromosome

[Term]
id: GO:0005667
name: transcription factor complex
namespace: cellular_component
def: "A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription." [GOC:jl]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0005681
name: spliceosomal complex
namespace: cellular_component
def: "Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA." [GOC:editors, GOC:mah, ISBN:0198547684, PMID:19239890]
subset: goslim_pir
synonym: "spliceosome" BROAD []
synonym: "spliceosome complex" EXACT []
xref: Wikipedia:Spliceosome
is_a: GO:0044464 ! cell part
is_a: GO:1990904 ! ribonucleoprotein complex
relationship: part_of GO:0005634 ! nucleus

[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]
comment: Chromosomes include parts that are not part of the chromatin.  Examples include the kinetochore.
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
synonym: "chromatid" RELATED []
synonym: "interphase chromosome" NARROW []
synonym: "prophase chromosome" NARROW []
xref: Wikipedia:Chromosome
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle

[Term]
id: GO:0005697
name: telomerase holoenzyme complex
namespace: cellular_component
def: "Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits." [PMID:11884619]
subset: goslim_pir
is_a: GO:0044464 ! cell part
is_a: GO:1990904 ! ribonucleoprotein complex
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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
xref: NIF_Subcellular:sao1820400233
xref: Wikipedia:Nucleolus
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0005732
name: small nucleolar ribonucleoprotein complex
namespace: cellular_component
def: "A ribonucleoprotein complex that contains an RNA molecule of the small nucleolar RNA (snoRNA) family and associated proteins. Most are involved in a step of processing of rRNA: cleavage, 2'-O-methylation, or pseudouridylation. The majority, though not all, fall into one of two classes, box C/D type or box H/ACA type." [GOC:krc, GOC:mah, ISBN:0879695897]
comment: Note that 'nucleolar' in the term name is part of the RNA family designation 'small nucleolar', and does not necessarily reflect the location of the complex.
subset: goslim_pir
synonym: "small nucleolar ribonucleoprotein" EXACT []
synonym: "snoRNP" EXACT []
is_a: GO:1990904 ! ribonucleoprotein complex

[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_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
xref: Wikipedia:Cytoplasm
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "mitochondria" EXACT []
xref: NIF_Subcellular:sao1860313010
xref: Wikipedia:Mitochondrion
is_a: GO:0043231 ! intracellular membrane-bounded organelle
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0005744
name: TIM23 mitochondrial import inner membrane translocase complex
namespace: cellular_component
def: "The protein transport machinery of the mitochondrial inner membrane that typically transports proteins that possess a matrix-targeting N-terminal presequence. The TIM23 complex contains three essential Tim proteins: Tim17 and Tim23 are thought to build a preprotein translocation channel while Tim44 interacts transiently with the matrix heat-shock protein Hsp70 to form an ATP-driven import motor." [EC:3.6.3.51, PMID:27554484, PMID:8851659]
comment: See also the cellular component term 'mitochondrial inner membrane ; GO:0005743'.
subset: goslim_pir
synonym: "mitochondrial inner membrane pre-sequence translocase complex" EXACT []
synonym: "mitochondrial inner membrane presequence translocase complex" EXACT []
synonym: "mitochondrial inner membrane translocase complex" BROAD []
synonym: "Tim23 complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005739 ! mitochondrion
relationship: part_of GO:0016020 ! membrane

[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_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
xref: NIF_Subcellular:sao1720343330
xref: Wikipedia:Endosome
is_a: GO:0031982 ! vesicle
is_a: GO:0043229 ! intracellular organelle
relationship: part_of GO:0005737 ! cytoplasm

[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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "vacuolar carboxypeptidase Y" RELATED []
xref: Wikipedia:Vacuole
is_a: GO:0043231 ! intracellular membrane-bounded organelle
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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "ER" EXACT []
xref: NIF_Subcellular:sao1036339110
xref: Wikipedia:Endoplasmic_reticulum
is_a: GO:0043231 ! intracellular membrane-bounded organelle

[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_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
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:0043231 ! intracellular membrane-bounded organelle
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0005813
name: centrosome
namespace: cellular_component
def: "A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle." [GOC:mah, ISBN:0198547684]
subset: goslim_pir
xref: Wikipedia:Centrosome
is_a: GO:0044464 ! cell part
relationship: has_part GO:0043232 ! intracellular non-membrane-bounded organelle
relationship: part_of GO:0005856 ! cytoskeleton

[Term]
id: GO:0005835
name: fatty acid synthase complex
namespace: cellular_component
alt_id: GO:0031373
alt_id: GO:0031374
def: "A multienzyme complex that catalyses the synthesis of fatty acids from acetyl CoA." [GOC:pde, GOC:sgd_curators, ISBN:0716746840]
subset: goslim_pir
synonym: "cytosolic FAS complex" EXACT []
synonym: "cytosolic fatty acid synthase complex" EXACT []
synonym: "cytosolic type I FAS complex" EXACT []
synonym: "cytosolic type I fatty acid synthase complex" EXACT []
synonym: "FAS complex" EXACT []
synonym: "fatty acid synthetase complex" EXACT []
synonym: "holo-[acyl-carrier-protein] synthase complex" RELATED []
xref: Wikipedia:Fatty_acid_synthetase_complex
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
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:0043232 ! intracellular non-membrane-bounded organelle
is_a: GO:1990904 ! ribonucleoprotein complex
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0005844
name: polysome
namespace: cellular_component
def: "A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro." [ISBN:0198506732, NIF_Subcellular:sao1038025871]
subset: goslim_pir
synonym: "polyribosome" EXACT [NIF_Subcellular:sao1038025871]
xref: NIF_Subcellular:sao1038025871
xref: Wikipedia:Polysome
is_a: GO:1990904 ! ribonucleoprotein complex

[Term]
id: GO:0005849
name: mRNA cleavage factor complex
namespace: cellular_component
def: "Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules." [GOC:mah, PMID:10357856]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0005856
name: cytoskeleton
namespace: cellular_component
def: "Any of the various filamentous elements that form the internal framework of cells, and typically 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, 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, ISBN:0198547684, PMID:16959967]
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
xref: Wikipedia:Cytoskeleton
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle

[Term]
id: GO:0005891
name: voltage-gated calcium channel complex
namespace: cellular_component
def: "A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential." [GOC:mah]
subset: goslim_pir
synonym: "voltage gated calcium channel complex" EXACT []
synonym: "voltage-dependent calcium channel complex" EXACT []
synonym: "voltage-sensitive calcium channel complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0016020 ! membrane
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0005902
name: microvillus
namespace: cellular_component
def: "Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells." [ISBN:0813516194]
comment: Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta.
subset: goslim_pir
synonym: "microvilli" RELATED [NIF_Subcellular:sao671419673]
xref: NIF_Subcellular:sao671419673
xref: Wikipedia:Microvillus
is_a: GO:0042995 ! cell projection
relationship: has_part GO:0016020 ! membrane
relationship: has_part GO:0044464 ! cell part

[Term]
id: GO:0005903
name: brush border
namespace: cellular_component
def: "The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell." [GOC:sl, ISBN:0815316194]
subset: goslim_pir
xref: Wikipedia:Brush_border
is_a: GO:0044464 ! cell part
relationship: has_part GO:0005902 ! microvillus

[Term]
id: GO:0005929
name: cilium
namespace: cellular_component
alt_id: GO:0072372
def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body." [GOC:cilia, GOC:curators, GOC:kmv, GOC:vw, ISBN:0198547684, PMID:16824949, PMID:17009929, PMID:20144998]
comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms.
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
synonym: "eukaryotic flagellum" EXACT []
synonym: "flagellum" RELATED []
synonym: "microtubule-based flagellum" EXACT []
synonym: "primary cilium" NARROW []
xref: FMA:67181
xref: NIF_Subcellular:sao787716553
xref: Wikipedia:Cilium
is_a: GO:0042995 ! cell projection
is_a: GO:0043226 ! organelle
relationship: has_part GO:0016020 ! membrane
relationship: has_part GO:0030990 ! intraciliary transport particle
relationship: has_part GO:0044464 ! cell part

[Term]
id: GO:0005930
name: axoneme
namespace: cellular_component
alt_id: GO:0035085
alt_id: GO:0035086
def: "The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." [GOC:bf, GOC:cilia, ISBN:0198547684]
comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane.
subset: goslim_pir
synonym: "ciliary axoneme" EXACT []
synonym: "cilium axoneme" EXACT []
synonym: "flagellar axoneme" EXACT []
synonym: "flagellum axoneme" EXACT []
xref: Wikipedia:Axoneme
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm
relationship: part_of GO:0005856 ! cytoskeleton
relationship: part_of GO:0005929 ! cilium

[Term]
id: GO:0005933
name: cellular bud
namespace: cellular_component
def: "A protuberance from a cell of an organism that reproduces by budding, which will grow larger and become a separate daughter cell after nuclear division, cytokinesis, and cell wall formation (when appropriate). The daughter cell may completely separate from the mother cell, or the mother and daughter cells may remain associated." [GOC:sgd_curators]
subset: goslim_candida
subset: goslim_pir
subset: goslim_yeast
is_a: GO:0044464 ! cell part

[Term]
id: GO:0005937
name: mating projection
namespace: cellular_component
def: "The projection formed by unicellular fungi in response to mating pheromone." [GOC:mcc]
subset: goslim_pir
synonym: "conjugation tube" NARROW []
synonym: "shmoo" NARROW []
is_a: GO:0042995 ! cell projection
relationship: has_part GO:0016020 ! membrane
relationship: has_part GO:0044464 ! cell part

[Term]
id: GO:0005942
name: phosphatidylinositol 3-kinase complex
namespace: cellular_component
def: "A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too." [GOC:bf, PMID:24587488]
comment: For discussion of membrane association, please see https://sourceforge.net/p/geneontology/ontology-requests/11559/
subset: goslim_pir
synonym: "1-phosphatidylinositol 3-kinase complex" EXACT []
synonym: "phosphoinositide 3-kinase complex" EXACT [GOC:curators]
synonym: "PI3-kinase p85-subunit alpha- PI3-kinase p110 complex" NARROW [CORUM:2575]
synonym: "PI3K complex" EXACT []
synonym: "PIK3C3-PIK3R4 complex" NARROW [CORUM:429]
synonym: "PIK3CA-PIK3R1 complex" NARROW [CORUM:439]
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0016020 ! membrane

[Term]
id: GO:0005960
name: glycine cleavage complex
namespace: cellular_component
alt_id: GO:0005961
alt_id: GO:0070015
def: "A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T." [GOC:mah, MetaCyc:GCVMULTI-CPLX]
subset: goslim_pir
synonym: "glycine cleavage system" EXACT []
synonym: "glycine decarboxylase complex" EXACT []
synonym: "glycine dehydrogenase (decarboxylating) complex" EXACT []
synonym: "glycine dehydrogenase complex (decarboxylating)" RELATED []
synonym: "glycine synthase complex" EXACT []
xref: Wikipedia:Glycine_decarboxylase_complex
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm

[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. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC:mah, ISBN:0198506732]
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
synonym: "carbohydrate metabolism" EXACT []
synonym: "multicellular organismal carbohydrate metabolic process" NARROW []
synonym: "single-organism carbohydrate metabolic process" RELATED []
xref: Reactome:REACT_102834 "Metabolism of carbohydrates, Mus musculus"
xref: Reactome:REACT_103806 "Metabolism of carbohydrates, Mycobacterium tuberculosis"
xref: Reactome:REACT_104502 "Metabolism of carbohydrates, Gallus gallus"
xref: Reactome:REACT_105321 "Metabolism of carbohydrates, Escherichia coli"
xref: Reactome:REACT_106046 "Metabolism of carbohydrates, Drosophila melanogaster"
xref: Reactome:REACT_107409 "Metabolism of carbohydrates, Caenorhabditis elegans"
xref: Reactome:REACT_115733 "Carbohydrate metabolism, Gallus gallus"
xref: Reactome:REACT_28218 "Metabolism of carbohydrates, Xenopus tropicalis"
xref: Reactome:REACT_32291 "Metabolism of carbohydrates, Staphylococcus aureus N315"
xref: Reactome:REACT_33141 "Metabolism of carbohydrates, Taeniopygia guttata"
xref: Reactome:REACT_33953 "Metabolism of carbohydrates, Rattus norvegicus"
xref: Reactome:REACT_34800 "Metabolism of carbohydrates, Danio rerio"
xref: Reactome:REACT_474 "Metabolism of carbohydrates, Homo sapiens"
xref: Reactome:REACT_77669 "Metabolism of carbohydrates, Plasmodium falciparum"
xref: Reactome:REACT_81945 "Metabolism of carbohydrates, Schizosaccharomyces pombe"
xref: Reactome:REACT_83038 "Metabolism of carbohydrates, Arabidopsis thaliana"
xref: Reactome:REACT_83329 "Metabolism of carbohydrates, Saccharomyces cerevisiae"
xref: Reactome:REACT_88330 "Metabolism of carbohydrates, Bos taurus"
xref: Reactome:REACT_88558 "Metabolism of carbohydrates, Canis familiaris"
xref: Reactome:REACT_90099 "Metabolism of carbohydrates, Sus scrofa"
xref: Reactome:REACT_96375 "Metabolism of carbohydrates, Dictyostelium discoideum"
xref: Reactome:REACT_98394 "Metabolism of carbohydrates, Oryza sativa"
xref: Wikipedia:Carbohydrate_metabolism
is_a: GO:0044238 ! primary metabolic process
created_by: janelomax
creation_date: 2012-10-23T15:40:34Z

[Term]
id: GO:0005976
name: polysaccharide metabolic process
namespace: biological_process
alt_id: GO:0044263
def: "The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [CHEBI:18154, ISBN:0198547684]
subset: goslim_pir
synonym: "glycan metabolic process" NARROW []
synonym: "glycan metabolism" NARROW []
synonym: "multicellular organismal polysaccharide metabolic process" NARROW []
synonym: "polysaccharide metabolism" EXACT []
is_a: GO:0005975 ! carbohydrate metabolic process
is_a: GO:0043170 ! macromolecule metabolic process

[Term]
id: GO:0006066
name: alcohol metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." [CHEBI:30879, ISBN:0198506732]
subset: goslim_pir
synonym: "alcohol metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006081
name: cellular aldehyde metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells." [GOC:go_curators, ISBN:0198506732]
subset: goslim_pir
synonym: "aldehyde metabolism" EXACT []
synonym: "alkanal metabolic process" EXACT []
synonym: "alkanal metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006082
name: organic acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732]
subset: goslim_pir
synonym: "organic acid metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[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_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
synonym: "energy pathways" BROAD []
synonym: "intermediary metabolism" RELATED [GOC:mah]
synonym: "metabolic energy generation" RELATED []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006112
name: energy reserve metabolic process
namespace: biological_process
def: "The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen." [GOC:mah]
subset: goslim_pir
synonym: "energy reserve metabolism" EXACT []
xref: Reactome:REACT_100070 "Integration of energy metabolism, Taeniopygia guttata"
xref: Reactome:REACT_105810 "Integration of energy metabolism, Mus musculus"
xref: Reactome:REACT_108807 "Integration of energy metabolism, Plasmodium falciparum"
xref: Reactome:REACT_109211 "Integration of energy metabolism, Arabidopsis thaliana"
xref: Reactome:REACT_110910 "Integration of energy metabolism, Rattus norvegicus"
xref: Reactome:REACT_1505 "Integration of energy metabolism, Homo sapiens"
xref: Reactome:REACT_28839 "Integration of energy metabolism, Dictyostelium discoideum"
xref: Reactome:REACT_31409 "Integration of energy metabolism, Caenorhabditis elegans"
xref: Reactome:REACT_33977 "Integration of energy metabolism, Xenopus tropicalis"
xref: Reactome:REACT_77410 "Integration of energy metabolism, Bos taurus"
xref: Reactome:REACT_79340 "Integration of energy metabolism, Escherichia coli"
xref: Reactome:REACT_80356 "Integration of energy metabolism, Canis familiaris"
xref: Reactome:REACT_83420 "Integration of energy metabolism, Mycobacterium tuberculosis"
xref: Reactome:REACT_85294 "Integration of energy metabolism, Danio rerio"
xref: Reactome:REACT_87289 "Integration of energy metabolism, Saccharomyces cerevisiae"
xref: Reactome:REACT_88950 "Integration of energy metabolism, Staphylococcus aureus N315"
xref: Reactome:REACT_89538 "Integration of energy metabolism, Drosophila melanogaster"
xref: Reactome:REACT_93425 "Integration of energy metabolism, Oryza sativa"
xref: Reactome:REACT_94255 "Integration of energy metabolism, Gallus gallus"
xref: Reactome:REACT_94635 "Integration of energy metabolism, Schizosaccharomyces pombe"
xref: Reactome:REACT_98844 "Integration of energy metabolism, Sus scrofa"
is_a: GO:0006091 ! generation of precursor metabolites and energy
is_a: GO:0055114 ! oxidation-reduction process

[Term]
id: GO:0006113
name: fermentation
namespace: biological_process
def: "The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP)." [GOC:curators, ISBN:0201090910, ISBN:124925502, MetaCyc:Fermentation]
subset: goslim_pir
xref: MetaCyc:FERMENTATION-PWY
xref: Wikipedia:Fermentation_(biochemistry)
is_a: GO:0006091 ! generation of precursor metabolites and energy
is_a: GO:0055114 ! oxidation-reduction process

[Term]
id: GO:0006119
name: oxidative phosphorylation
namespace: biological_process
def: "The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis." [ISBN:0198506732, ISBN:0471331309]
subset: goslim_pir
synonym: "respiratory-chain phosphorylation" EXACT []
xref: Wikipedia:Oxidative_phosphorylation
is_a: GO:0006091 ! generation of precursor metabolites and energy
is_a: GO:0009117 ! nucleotide metabolic process
is_a: GO:0017144 ! drug metabolic process
relationship: has_part GO:0009117 ! nucleotide metabolic process
relationship: has_part GO:0017144 ! drug metabolic process
relationship: has_part GO:1902600 ! proton transmembrane transport

[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:0006725 ! cellular aromatic compound metabolic process
is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0044238 ! primary metabolic process
is_a: GO:0046483 ! heterocycle 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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "cellular DNA metabolism" EXACT []
synonym: "DNA metabolism" EXACT []
is_a: GO:0006139 ! nucleobase-containing compound metabolic process
is_a: GO:0043170 ! macromolecule metabolic process

[Term]
id: GO:0006260
name: DNA replication
namespace: biological_process
alt_id: GO:0055133
def: "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC:mah]
comment: DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'.
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
xref: Reactome:REACT_100559 "Activation of ATR in response to replication stress, Mus musculus"
xref: Reactome:REACT_101280 "Activation of claspin, Xenopus tropicalis"
xref: Reactome:REACT_101497 "Activation of claspin, Bos taurus"
xref: Reactome:REACT_102679 "Activation of ATR in response to replication stress, Gallus gallus"
xref: Reactome:REACT_103614 "Stalling of DNA replication fork and RPA binding, Taeniopygia guttata"
xref: Reactome:REACT_104547 "Recruitment and activation of Chk1, Gallus gallus"
xref: Reactome:REACT_105292 "Activation of ATR in response to replication stress, Xenopus tropicalis"
xref: Reactome:REACT_105467 "Loading of claspin onto DNA during replication origin firing, Danio rerio"
xref: Reactome:REACT_105835 "Stalling of DNA replication fork and RPA binding, Gallus gallus"
xref: Reactome:REACT_106018 "Recruitment of Rad17-RFC complex to DNA, Gallus gallus"
xref: Reactome:REACT_106104 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Bos taurus"
xref: Reactome:REACT_106382 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Drosophila melanogaster"
xref: Reactome:REACT_106434 "Activation of claspin, Canis familiaris"
xref: Reactome:REACT_106732 "Recruitment and activation of Chk1, Canis familiaris"
xref: Reactome:REACT_107075 "Activation of ATR in response to replication stress, Danio rerio"
xref: Reactome:REACT_107423 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Caenorhabditis elegans"
xref: Reactome:REACT_108461 "Recruitment and activation of Chk1, Bos taurus"
xref: Reactome:REACT_108634 "Loading of claspin onto DNA during replication origin firing, Mus musculus"
xref: Reactome:REACT_108739 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Xenopus tropicalis"
xref: Reactome:REACT_108768 "Activation of ATR in response to replication stress, Bos taurus"
xref: Reactome:REACT_108929 "Activation of ATR in response to replication stress, Drosophila melanogaster"
xref: Reactome:REACT_109137 "Stalling of DNA replication fork and RPA binding, Rattus norvegicus"
xref: Reactome:REACT_112472 "Activation of ATR in response to replication stress, Saccharomyces cerevisiae"
xref: Reactome:REACT_113703 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Gallus gallus"
xref: Reactome:REACT_29423 "Activation of ATR in response to replication stress, Schizosaccharomyces pombe"
xref: Reactome:REACT_29444 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Taeniopygia guttata"
xref: Reactome:REACT_29691 "Activation of ATR in response to replication stress, Rattus norvegicus"
xref: Reactome:REACT_29764 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Taeniopygia guttata"
xref: Reactome:REACT_30149 "Activation of claspin, Rattus norvegicus"
xref: Reactome:REACT_31024 "Recruitment of Rad17-RFC complex to DNA, Xenopus tropicalis"
xref: Reactome:REACT_31919 "Loading of claspin onto DNA during replication origin firing, Rattus norvegicus"
xref: Reactome:REACT_32546 "Recruitment of Rad17-RFC complex to DNA, Mus musculus"
xref: Reactome:REACT_32932 "Recruitment and activation of Chk1, Taeniopygia guttata"
xref: Reactome:REACT_33572 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Dictyostelium discoideum"
xref: Reactome:REACT_33874 "Recruitment and activation of Chk1, Xenopus tropicalis"
xref: Reactome:REACT_50018 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Rattus norvegicus"
xref: Reactome:REACT_53588 "Loading of claspin onto DNA during replication origin firing, Canis familiaris"
xref: Reactome:REACT_6729 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Homo sapiens"
xref: Reactome:REACT_6738 "Loading of claspin onto DNA during replication origin firing, Homo sapiens"
xref: Reactome:REACT_6750 "Activation of claspin, Homo sapiens"
xref: Reactome:REACT_6769 "Activation of ATR in response to replication stress, Homo sapiens"
xref: Reactome:REACT_6798 "Recruitment of Rad17-RFC complex to DNA, Homo sapiens"
xref: Reactome:REACT_6869 "Recruitment and activation of Chk1, Homo sapiens"
xref: Reactome:REACT_6936 "Stalling of DNA replication fork and RPA binding, Homo sapiens"
xref: Reactome:REACT_6939 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Homo sapiens"
xref: Reactome:REACT_77532 "Stalling of DNA replication fork and RPA binding, Canis familiaris"
xref: Reactome:REACT_79188 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Canis familiaris"
xref: Reactome:REACT_79450 "Activation of ATR in response to replication stress, Dictyostelium discoideum"
xref: Reactome:REACT_80432 "Loading of claspin onto DNA during replication origin firing, Taeniopygia guttata"
xref: Reactome:REACT_80571 "Activation of claspin, Mus musculus"
xref: Reactome:REACT_80896 "Recruitment and activation of Chk1, Sus scrofa"
xref: Reactome:REACT_80988 "Loading of claspin onto DNA during replication origin firing, Bos taurus"
xref: Reactome:REACT_81803 "Recruitment of Rad17-RFC complex to DNA, Canis familiaris"
xref: Reactome:REACT_83095 "Recruitment of Rad17-RFC complex to DNA, Danio rerio"
xref: Reactome:REACT_84829 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Danio rerio"
xref: Reactome:REACT_85561 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Rattus norvegicus"
xref: Reactome:REACT_86410 "Stalling of DNA replication fork and RPA binding, Mus musculus"
xref: Reactome:REACT_86739 "Recruitment and activation of Chk1, Rattus norvegicus"
xref: Reactome:REACT_87233 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Canis familiaris"
xref: Reactome:REACT_87449 "Recruitment of Rad17-RFC complex to DNA, Rattus norvegicus"
xref: Reactome:REACT_87590 "Recruitment of Rad17-RFC complex to DNA, Bos taurus"
xref: Reactome:REACT_88085 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Gallus gallus"
xref: Reactome:REACT_88384 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Schizosaccharomyces pombe"
xref: Reactome:REACT_88529 "Activation of claspin, Gallus gallus"
xref: Reactome:REACT_89355 "Activation of claspin, Danio rerio"
xref: Reactome:REACT_89439 "Activation of ATR in response to replication stress, Sus scrofa"
xref: Reactome:REACT_89725 "Loading of claspin onto DNA during replication origin firing, Drosophila melanogaster"
xref: Reactome:REACT_90512 "Stalling of DNA replication fork and RPA binding, Bos taurus"
xref: Reactome:REACT_90809 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Danio rerio"
xref: Reactome:REACT_90838 "Recruitment of Rad17-RFC complex to DNA, Taeniopygia guttata"
xref: Reactome:REACT_91184 "Recruitment and activation of Chk1, Danio rerio"
xref: Reactome:REACT_91302 "Activation of ATR in response to replication stress, Canis familiaris"
xref: Reactome:REACT_92527 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Mus musculus"
xref: Reactome:REACT_92644 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Xenopus tropicalis"
xref: Reactome:REACT_92706 "Stalling of DNA replication fork and RPA binding, Danio rerio"
xref: Reactome:REACT_94983 "Stalling of DNA replication fork and RPA binding, Xenopus tropicalis"
xref: Reactome:REACT_95253 "Activation of ATR in response to replication stress, Taeniopygia guttata"
xref: Reactome:REACT_95329 "Activation of claspin, Taeniopygia guttata"
xref: Reactome:REACT_96115 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Mus musculus"
xref: Reactome:REACT_96804 "Recruitment and activation of Chk1, Mus musculus"
xref: Reactome:REACT_96998 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Bos taurus"
xref: Reactome:REACT_97204 "Loading of claspin onto DNA during replication origin firing, Gallus gallus"
xref: Reactome:REACT_97726 "Activation of ATR in response to replication stress, Caenorhabditis elegans"
xref: Reactome:REACT_99948 "Loading of claspin onto DNA during replication origin firing, Xenopus tropicalis"
xref: Wikipedia:DNA_replication
is_a: GO:0006259 ! DNA metabolic process
is_a: GO:0009059 ! macromolecule biosynthetic process
relationship: has_part GO:0006259 ! DNA metabolic process
relationship: has_part GO:0009059 ! macromolecule biosynthetic process

[Term]
id: GO:0006266
name: DNA ligation
namespace: biological_process
def: "The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase." [ISBN:0815316194]
subset: goslim_pir
is_a: GO:0006259 ! DNA metabolic process

[Term]
id: GO:0006276
name: plasmid maintenance
namespace: biological_process
def: "The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division." [GOC:ai]
subset: goslim_pir
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0006281
name: DNA repair
namespace: biological_process
def: "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID:11563486]
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
xref: Reactome:REACT_102034 "DNA Repair, Staphylococcus aureus N315"
xref: Reactome:REACT_106650 "DNA Damage Reversal, Taeniopygia guttata"
xref: Reactome:REACT_107446 "DNA Repair, Arabidopsis thaliana"
xref: Reactome:REACT_107692 "DNA Damage Reversal, Gallus gallus"
xref: Reactome:REACT_107752 "DNA Repair, Plasmodium falciparum"
xref: Reactome:REACT_108864 "DNA Damage Reversal, Rattus norvegicus"
xref: Reactome:REACT_108881 "DNA Damage Reversal, Bos taurus"
xref: Reactome:REACT_108903 "DNA Repair, Xenopus tropicalis"
xref: Reactome:REACT_109956 "DNA Repair, Gallus gallus"
xref: Reactome:REACT_115642 "DNA repair, Gallus gallus"
xref: Reactome:REACT_115836 "Fanconi Anemia Pathway in DNA repair, Gallus gallus"
xref: Reactome:REACT_127 "DNA Damage Reversal, Homo sapiens"
xref: Reactome:REACT_216 "DNA Repair, Homo sapiens"
xref: Reactome:REACT_29531 "DNA Damage Reversal, Saccharomyces cerevisiae"
xref: Reactome:REACT_29636 "DNA Damage Reversal, Staphylococcus aureus N315"
xref: Reactome:REACT_78051 "DNA Damage Reversal, Canis familiaris"
xref: Reactome:REACT_82907 "DNA Repair, Oryza sativa"
xref: Reactome:REACT_83608 "DNA Damage Reversal, Caenorhabditis elegans"
xref: Reactome:REACT_83660 "DNA Repair, Escherichia coli"
xref: Reactome:REACT_84835 "DNA Damage Reversal, Dictyostelium discoideum"
xref: Reactome:REACT_85522 "DNA Repair, Mus musculus"
xref: Reactome:REACT_86513 "DNA Repair, Mycobacterium tuberculosis"
xref: Reactome:REACT_86902 "DNA Repair, Danio rerio"
xref: Reactome:REACT_88201 "DNA Repair, Drosophila melanogaster"
xref: Reactome:REACT_88946 "DNA Damage Reversal, Mycobacterium tuberculosis"
xref: Reactome:REACT_89524 "DNA Damage Reversal, Drosophila melanogaster"
xref: Reactome:REACT_90385 "DNA Repair, Canis familiaris"
xref: Reactome:REACT_90952 "DNA Damage Reversal, Arabidopsis thaliana"
xref: Reactome:REACT_91094 "DNA Repair, Rattus norvegicus"
xref: Reactome:REACT_91330 "DNA Repair, Bos taurus"
xref: Reactome:REACT_91442 "DNA Repair, Caenorhabditis elegans"
xref: Reactome:REACT_91576 "DNA Damage Reversal, Oryza sativa"
xref: Reactome:REACT_92707 "DNA Repair, Taeniopygia guttata"
xref: Reactome:REACT_93704 "DNA Repair, Saccharomyces cerevisiae"
xref: Reactome:REACT_94204 "DNA Repair, Sus scrofa"
xref: Reactome:REACT_94769 "DNA Repair, Schizosaccharomyces pombe"
xref: Reactome:REACT_95050 "DNA Damage Reversal, Sus scrofa"
xref: Reactome:REACT_95158 "DNA Damage Reversal, Xenopus tropicalis"
xref: Reactome:REACT_96052 "DNA Repair, Dictyostelium discoideum"
xref: Reactome:REACT_96452 "DNA Damage Reversal, Danio rerio"
xref: Reactome:REACT_99277 "DNA Damage Reversal, Mus musculus"
xref: Wikipedia:DNA_repair
is_a: GO:0006259 ! DNA metabolic process
is_a: GO:0050896 ! response to stimulus

[Term]
id: GO:0006304
name: DNA modification
namespace: biological_process
def: "The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties." [GOC:jl, GOC:ma]
subset: goslim_pir
is_a: GO:0006259 ! DNA metabolic process
is_a: GO:0043412 ! macromolecule modification

[Term]
id: GO:0006323
name: DNA packaging
namespace: biological_process
def: "Any process in which DNA and associated proteins are formed into a compact, orderly structure." [GOC:mah, ISBN:0815316194]
subset: goslim_pir
synonym: "DNA condensation" EXACT []
synonym: "DNA organisation" EXACT [GOC:curators]
synonym: "DNA organization" EXACT [GOC:curators]
is_a: GO:0051276 ! chromosome organization
relationship: has_part GO:0003676 ! nucleic acid binding

[Term]
id: GO:0006351
name: transcription, DNA-templated
namespace: biological_process
alt_id: GO:0006350
alt_id: GO:0061018
alt_id: GO:0061022
def: "The cellular synthesis of RNA on a template of DNA." [GOC:jl, GOC:txnOH]
subset: goslim_aspergillus
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
synonym: "cellular transcription" BROAD []
synonym: "cellular transcription, DNA-dependent" EXACT []
synonym: "DNA-dependent transcription" EXACT []
synonym: "transcription" BROAD []
synonym: "transcription regulator activity" RELATED []
synonym: "transcription, DNA-dependent" EXACT [GOC:txnOH]
xref: Wikipedia:Transcription_(genetics)
is_a: GO:0009059 ! macromolecule biosynthetic process
is_a: GO:0016070 ! RNA metabolic process
relationship: part_of GO:0043170 ! macromolecule metabolic process

[Term]
id: GO:0006354
name: DNA-templated transcription, elongation
namespace: biological_process
def: "The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase." [GOC:mah, GOC:txnOH, PMID:15020047, PMID:18280161]
subset: goslim_pir
subset: goslim_yeast
synonym: "DNA-dependent transcription, elongation" EXACT [GOC:txnOH]
synonym: "RNA elongation" BROAD []
synonym: "transcription elongation, DNA-dependent" EXACT [GOC:jh2]
synonym: "transcriptional elongation, DNA-dependent" EXACT []
is_a: GO:0009059 ! macromolecule biosynthetic process
is_a: GO:0016070 ! RNA metabolic process
relationship: part_of GO:0006351 ! transcription, DNA-templated

[Term]
id: GO:0006396
name: RNA processing
namespace: biological_process
alt_id: GO:0006394
def: "Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules." [GOC:mah]
subset: goslim_pir
xref: Wikipedia:Post-transcriptional_modification
is_a: GO:0016070 ! RNA metabolic process
relationship: part_of GO:0043170 ! macromolecule 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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "protein anabolism" EXACT []
synonym: "protein biosynthesis" EXACT []
synonym: "protein biosynthetic process" EXACT [GOC:curators]
synonym: "protein formation" EXACT []
synonym: "protein synthesis" EXACT []
synonym: "protein translation" EXACT []
xref: Reactome:REACT_100338 "Translation, Sus scrofa"
xref: Reactome:REACT_100851 "Translation, Saccharomyces cerevisiae"
xref: Reactome:REACT_101045 "Translation, Dictyostelium discoideum"
xref: Reactome:REACT_101324 "Translation, Canis familiaris"
xref: Reactome:REACT_1014 "Translation, Homo sapiens"
xref: Reactome:REACT_103420 "Translation, Plasmodium falciparum"
xref: Reactome:REACT_105544 "Translation, Arabidopsis thaliana"
xref: Reactome:REACT_29980 "Translation, Bos taurus"
xref: Reactome:REACT_33559 "Translation, Rattus norvegicus"
xref: Reactome:REACT_77710 "Translation, Drosophila melanogaster"
xref: Reactome:REACT_79784 "Translation, Danio rerio"
xref: Reactome:REACT_81734 "Translation, Schizosaccharomyces pombe"
xref: Reactome:REACT_81833 "Translation, Caenorhabditis elegans"
xref: Reactome:REACT_82171 "Translation, Xenopus tropicalis"
xref: Reactome:REACT_83429 "Translation, Taeniopygia guttata"
xref: Reactome:REACT_83530 "Translation, Gallus gallus"
xref: Reactome:REACT_86996 "Translation, Oryza sativa"
xref: Reactome:REACT_95535 "Translation, Mus musculus"
xref: Reactome:REACT_96394 "Translation, Escherichia coli"
xref: Wikipedia:Translation_(genetics)
is_a: GO:0006518 ! peptide metabolic process
is_a: GO:0009059 ! macromolecule biosynthetic process
is_a: GO:0019538 ! protein metabolic process
relationship: has_part GO:0022411 ! cellular component disassembly

[Term]
id: GO:0006457
name: protein folding
namespace: biological_process
alt_id: GO:0007022
alt_id: GO:0007024
alt_id: GO:0007025
def: "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure." [GOC:go_curators, GOC:rb]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
synonym: "alpha-tubulin folding" NARROW [GOC:mah]
synonym: "beta-tubulin folding" NARROW [GOC:mah]
synonym: "chaperone activity" RELATED []
synonym: "chaperonin ATPase activity" RELATED []
synonym: "chaperonin-mediated tubulin folding" NARROW [GOC:mah]
synonym: "co-chaperone activity" RELATED []
synonym: "co-chaperonin activity" RELATED []
synonym: "glycoprotein-specific chaperone activity" RELATED []
synonym: "non-chaperonin molecular chaperone ATPase activity" RELATED []
synonym: "protein complex assembly, multichaperone pathway" RELATED []
xref: Reactome:REACT_100411 "Chaperonin-mediated protein folding, Arabidopsis thaliana"
xref: Reactome:REACT_104912 "Chaperonin-mediated protein folding, Caenorhabditis elegans"
xref: Reactome:REACT_105663 "Chaperonin-mediated protein folding, Rattus norvegicus"
xref: Reactome:REACT_106009 "Chaperonin-mediated protein folding, Canis familiaris"
xref: Reactome:REACT_106427 "Chaperonin-mediated protein folding, Mus musculus"
xref: Reactome:REACT_106894 "Formation of tubulin folding intermediates by CCT/TriC, Canis familiaris"
xref: Reactome:REACT_106927 "Chaperonin-mediated protein folding, Drosophila melanogaster"
xref: Reactome:REACT_107029 "Formation of tubulin folding intermediates by CCT/TriC, Drosophila melanogaster"
xref: Reactome:REACT_108248 "Chaperonin-mediated protein folding, Gallus gallus"
xref: Reactome:REACT_109411 "Formation of tubulin folding intermediates by CCT/TriC, Bos taurus"
xref: Reactome:REACT_110417 "Formation of tubulin folding intermediates by CCT/TriC, Rattus norvegicus"
xref: Reactome:REACT_16956 "Formation of tubulin folding intermediates by CCT/TriC, Homo sapiens"
xref: Reactome:REACT_17001 "Formation of tubulin folding intermediates by CCT/TriC, Mus musculus"
xref: Reactome:REACT_17004 "Chaperonin-mediated protein folding, Homo sapiens"
xref: Reactome:REACT_17056 "Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding, Bos taurus"
xref: Reactome:REACT_23878 "N-glycan trimming in the ER and Calnexin/Calreticulin cycle, Homo sapiens"
xref: Reactome:REACT_30906 "Chaperonin-mediated protein folding, Oryza sativa"
xref: Reactome:REACT_32155 "Chaperonin-mediated protein folding, Saccharomyces cerevisiae"
xref: Reactome:REACT_32255 "Chaperonin-mediated protein folding, Schizosaccharomyces pombe"
xref: Reactome:REACT_33395 "Formation of tubulin folding intermediates by CCT/TriC, Mus musculus"
xref: Reactome:REACT_77627 "Chaperonin-mediated protein folding, Plasmodium falciparum"
xref: Reactome:REACT_77963 "Formation of tubulin folding intermediates by CCT/TriC, Saccharomyces cerevisiae"
xref: Reactome:REACT_78530 "Formation of tubulin folding intermediates by CCT/TriC, Gallus gallus"
xref: Reactome:REACT_81155 "Formation of tubulin folding intermediates by CCT/TriC, Caenorhabditis elegans"
xref: Reactome:REACT_83906 "Chaperonin-mediated protein folding, Dictyostelium discoideum"
xref: Reactome:REACT_85492 "Formation of tubulin folding intermediates by CCT/TriC, Sus scrofa"
xref: Reactome:REACT_85496 "Formation of tubulin folding intermediates by CCT/TriC, Plasmodium falciparum"
xref: Reactome:REACT_86318 "Formation of tubulin folding intermediates by CCT/TriC, Arabidopsis thaliana"
xref: Reactome:REACT_91676 "Formation of tubulin folding intermediates by CCT/TriC, Schizosaccharomyces pombe"
xref: Reactome:REACT_92785 "Formation of tubulin folding intermediates by CCT/TriC, Dictyostelium discoideum"
xref: Reactome:REACT_92961 "Chaperonin-mediated protein folding, Xenopus tropicalis"
xref: Reactome:REACT_92981 "Chaperonin-mediated protein folding, Taeniopygia guttata"
xref: Reactome:REACT_94123 "Formation of tubulin folding intermediates by CCT/TriC, Taeniopygia guttata"
xref: Reactome:REACT_94443 "Formation of tubulin folding intermediates by CCT/TriC, Danio rerio"
xref: Reactome:REACT_94772 "Chaperonin-mediated protein folding, Sus scrofa"
xref: Reactome:REACT_96773 "Chaperonin-mediated protein folding, Danio rerio"
xref: Reactome:REACT_97016 "Chaperonin-mediated protein folding, Bos taurus"
xref: Reactome:REACT_97220 "Formation of tubulin folding intermediates by CCT/TriC, Xenopus tropicalis"
xref: Reactome:REACT_98132 "Formation of tubulin folding intermediates by CCT/TriC, Oryza sativa"
xref: Wikipedia:Protein_folding
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0006464
name: cellular protein modification process
namespace: biological_process
def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:go_curators]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
synonym: "process resulting in protein modification" RELATED []
synonym: "protein modification process" BROAD [GOC:bf, GOC:jl]
synonym: "protein tagging activity" RELATED []
is_a: GO:0019538 ! protein metabolic process
is_a: GO:0043412 ! macromolecule modification

[Term]
id: GO:0006508
name: proteolysis
namespace: biological_process
def: "The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds." [GOC:bf, GOC:mah]
comment: This term was intentionally placed under 'protein metabolic process ; GO:0019538' rather than 'protein catabolic process ; GO:0030163' to cover all processes centered on breaking peptide bonds, including those involved in protein processing.
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
synonym: "ATP-dependent proteolysis" NARROW [GOC:mah]
synonym: "peptidolysis" EXACT []
xref: Reactome:REACT_105459 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Gallus gallus"
xref: Reactome:REACT_106013 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Canis familiaris"
xref: Reactome:REACT_106377 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Mus musculus"
xref: Reactome:REACT_107219 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Danio rerio"
xref: Reactome:REACT_110326 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Bos taurus"
xref: Reactome:REACT_733 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Homo sapiens"
xref: Reactome:REACT_84556 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Xenopus tropicalis"
xref: Reactome:REACT_92566 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Sus scrofa"
xref: Reactome:REACT_95969 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Taeniopygia guttata"
xref: Reactome:REACT_98959 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Rattus norvegicus"
xref: Wikipedia:Proteolysis
is_a: GO:0019538 ! protein metabolic process

[Term]
id: GO:0006518
name: peptide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." [CHEBI:16670, GOC:go_curators]
subset: goslim_pir
synonym: "peptide metabolism" EXACT []
is_a: GO:0043603 ! cellular amide metabolic process

[Term]
id: GO:0006520
name: cellular amino acid metabolic process
namespace: biological_process
alt_id: GO:0006519
def: "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells." [CHEBI:33709, GOC:curators, ISBN:0198506732]
subset: goslim_aspergillus
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
synonym: "amino acid and derivative metabolism" EXACT [GOC:curators]
synonym: "amino acid metabolic process" EXACT [GOC:curators]
synonym: "cellular amino acid and derivative metabolic process" EXACT []
synonym: "cellular amino acid metabolism" EXACT []
xref: Reactome:REACT_116093 "Amino acid metabolism, Gallus gallus"
is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0044238 ! primary metabolic 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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
synonym: "lipid metabolism" EXACT []
xref: Reactome:REACT_104930 "Lipid digestion, mobilization, and transport, Drosophila melanogaster"
xref: Reactome:REACT_107479 "Lipid digestion, mobilization, and transport, Xenopus tropicalis"
xref: Reactome:REACT_108775 "Lipid digestion, mobilization, and transport, Canis familiaris"
xref: Reactome:REACT_114669 "Lipid digestion, mobilization, and transport, Staphylococcus aureus N315"
xref: Reactome:REACT_115652 "Lipid metabolism, Gallus gallus"
xref: Reactome:REACT_28745 "Lipid digestion, mobilization, and transport, Saccharomyces cerevisiae"
xref: Reactome:REACT_31395 "Lipid digestion, mobilization, and transport, Sus scrofa"
xref: Reactome:REACT_32539 "Lipid digestion, mobilization, and transport, Bos taurus"
xref: Reactome:REACT_33836 "Lipid digestion, mobilization, and transport, Rattus norvegicus"
xref: Reactome:REACT_602 "Lipid digestion, mobilization, and transport, Homo sapiens"
xref: Reactome:REACT_77176 "Lipid digestion, mobilization, and transport, Danio rerio"
xref: Reactome:REACT_77191 "Lipid digestion, mobilization, and transport, Arabidopsis thaliana"
xref: Reactome:REACT_79244 "Lipid digestion, mobilization, and transport, Plasmodium falciparum"
xref: Reactome:REACT_81778 "Lipid digestion, mobilization, and transport, Oryza sativa"
xref: Reactome:REACT_82512 "Lipid digestion, mobilization, and transport, Taeniopygia guttata"
xref: Reactome:REACT_82723 "Lipid digestion, mobilization, and transport, Escherichia coli"
xref: Reactome:REACT_87884 "Lipid digestion, mobilization, and transport, Caenorhabditis elegans"
xref: Reactome:REACT_90757 "Lipid digestion, mobilization, and transport, Mus musculus"
xref: Reactome:REACT_94607 "Lipid digestion, mobilization, and transport, Mycobacterium tuberculosis"
xref: Reactome:REACT_97906 "Lipid digestion, mobilization, and transport, Gallus gallus"
xref: Reactome:REACT_98129 "Lipid digestion, mobilization, and transport, Schizosaccharomyces pombe"
xref: Reactome:REACT_99706 "Lipid digestion, mobilization, and transport, Dictyostelium discoideum"
xref: Wikipedia:Lipid_metabolism
is_a: GO:0044238 ! primary metabolic process

[Term]
id: GO:0006662
name: glycerol ether metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol." [GOC:ai, ISBN:0198506732]
subset: goslim_pir
synonym: "glycerol ether metabolism" EXACT []
is_a: GO:0018904 ! ether metabolic process

[Term]
id: GO:0006725
name: cellular aromatic compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells." [GOC:ai, ISBN:0198506732]
subset: goslim_pir
synonym: "aromatic compound metabolism" EXACT []
synonym: "aromatic hydrocarbon metabolic process" NARROW []
synonym: "aromatic hydrocarbon metabolism" NARROW []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006730
name: one-carbon metabolic process
namespace: biological_process
alt_id: GO:0019753
alt_id: GO:0019754
def: "The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states." [GOC:hjd, GOC:mah, GOC:pde]
subset: goslim_pir
synonym: "one carbon metabolic process" EXACT [GOC:mah]
synonym: "one carbon metabolism" EXACT [GOC:mah]
synonym: "one-carbon metabolism" EXACT [GOC:mah]
synonym: "one-carbon transfer metabolic process" EXACT [GOC:mah]
synonym: "one-carbon transfer metabolism" EXACT [GOC:mah]
xref: UM-BBD_pathwayID:C1cyc
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006766
name: vitamin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems." [GOC:ai]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
synonym: "vitamin metabolism" EXACT []
xref: Reactome:REACT_101808 "Metabolism of vitamins and cofactors, Bos taurus"
xref: Reactome:REACT_101968 "Metabolism of vitamins and cofactors, Saccharomyces cerevisiae"
xref: Reactome:REACT_102472 "Vitamins, Xenopus tropicalis"
xref: Reactome:REACT_103646 "Metabolism of vitamins and cofactors, Staphylococcus aureus N315"
xref: Reactome:REACT_104403 "Vitamins, Bos taurus"
xref: Reactome:REACT_105907 "Metabolism of vitamins and cofactors, Danio rerio"
xref: Reactome:REACT_106152 "Metabolism of vitamins and cofactors, Xenopus tropicalis"
xref: Reactome:REACT_108558 "Metabolism of vitamins and cofactors, Rattus norvegicus"
xref: Reactome:REACT_110948 "Metabolism of vitamins and cofactors, Sus scrofa"
xref: Reactome:REACT_11193 "Metabolism of vitamins and cofactors, Homo sapiens"
xref: Reactome:REACT_13450 "Vitamins, Homo sapiens"
xref: Reactome:REACT_30091 "Metabolism of vitamins and cofactors, Oryza sativa"
xref: Reactome:REACT_31562 "Vitamins, Sus scrofa"
xref: Reactome:REACT_33241 "Vitamins, Oryza sativa"
xref: Reactome:REACT_33738 "Metabolism of vitamins and cofactors, Mycobacterium tuberculosis"
xref: Reactome:REACT_34161 "Metabolism of vitamins and cofactors, Mus musculus"
xref: Reactome:REACT_34372 "Vitamins, Taeniopygia guttata"
xref: Reactome:REACT_36524 "Vitamins, Gallus gallus"
xref: Reactome:REACT_78899 "Metabolism of vitamins and cofactors, Caenorhabditis elegans"
xref: Reactome:REACT_79004 "Vitamins, Danio rerio"
xref: Reactome:REACT_80415 "Vitamins, Rattus norvegicus"
xref: Reactome:REACT_81509 "Metabolism of vitamins and cofactors, Gallus gallus"
xref: Reactome:REACT_82129 "Metabolism of vitamins and cofactors, Taeniopygia guttata"
xref: Reactome:REACT_82903 "Vitamins, Canis familiaris"
xref: Reactome:REACT_83508 "Metabolism of vitamins and cofactors, Arabidopsis thaliana"
xref: Reactome:REACT_84128 "Vitamins, Drosophila melanogaster"
xref: Reactome:REACT_87513 "Metabolism of vitamins and cofactors, Schizosaccharomyces pombe"
xref: Reactome:REACT_88847 "Vitamins, Mus musculus"
xref: Reactome:REACT_88850 "Metabolism of vitamins and cofactors, Dictyostelium discoideum"
xref: Reactome:REACT_90099 "Vitamins, Arabidopsis thaliana"
xref: Reactome:REACT_96278 "Metabolism of vitamins and cofactors, Plasmodium falciparum"
xref: Reactome:REACT_96904 "Metabolism of vitamins and cofactors, Drosophila melanogaster"
xref: Reactome:REACT_97734 "Metabolism of vitamins and cofactors, Escherichia coli"
xref: Reactome:REACT_97893 "Metabolism of vitamins and cofactors, Canis familiaris"
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006790
name: sulfur compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione." [GOC:ai]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
synonym: "sulfur metabolism" EXACT []
synonym: "sulphur metabolic process" EXACT []
synonym: "sulphur metabolism" EXACT []
xref: Reactome:REACT_27247 "Sulfur compound metabolism, Mycobacterium tuberculosis"
xref: Wikipedia:Sulfur_metabolism
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006793
name: phosphorus metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4)." [GOC:ai]
subset: goslim_pir
synonym: "phosphorus metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006805
name: xenobiotic metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide." [GOC:cab2]
subset: goslim_chembl
subset: goslim_pir
synonym: "xenobiotic metabolism" EXACT []
xref: Reactome:REACT_100124 "Conjugation of benzoate with glycine, Mus musculus"
xref: Reactome:REACT_100325 "Conjugation of phenylacetate with glutamine, Mus musculus"
xref: Reactome:REACT_100603 "Biological oxidations, Arabidopsis thaliana"
xref: Reactome:REACT_101131 "Phase 1 - Functionalization of compounds, Dictyostelium discoideum"
xref: Reactome:REACT_101207 "Phase II conjugation, Bos taurus"
xref: Reactome:REACT_101609 "Conjugation of benzoate with glycine, Staphylococcus aureus N315"
xref: Reactome:REACT_102115 "Phase 1 - Functionalization of compounds, Schizosaccharomyces pombe"
xref: Reactome:REACT_102424 "Phase 1 - Functionalization of compounds, Danio rerio"
xref: Reactome:REACT_102433 "Conjugation of salicylate with glycine, Sus scrofa"
xref: Reactome:REACT_102710 "Phase II conjugation, Drosophila melanogaster"
xref: Reactome:REACT_102875 "Conjugation of phenylacetate with glutamine, Bos taurus"
xref: Reactome:REACT_103896 "Phase 1 - Functionalization of compounds, Saccharomyces cerevisiae"
xref: Reactome:REACT_104199 "Phase II conjugation, Staphylococcus aureus N315"
xref: Reactome:REACT_104666 "Phase 1 - Functionalization of compounds, Arabidopsis thaliana"
xref: Reactome:REACT_104877 "Conjugation of carboxylic acids, Canis familiaris"
xref: Reactome:REACT_105707 "Phase 1 - Functionalization of compounds, Canis familiaris"
xref: Reactome:REACT_106111 "Phase II conjugation, Schizosaccharomyces pombe"
xref: Reactome:REACT_106484 "Conjugation of salicylate with glycine, Danio rerio"
xref: Reactome:REACT_106812 "Biological oxidations, Staphylococcus aureus N315"
xref: Reactome:REACT_108383 "Phase 1 - Functionalization of compounds, Gallus gallus"
xref: Reactome:REACT_110034 "Biological oxidations, Saccharomyces cerevisiae"
xref: Reactome:REACT_110188 "Conjugation of phenylacetate with glutamine, Rattus norvegicus"
xref: Reactome:REACT_110735 "Conjugation of salicylate with glycine, Canis familiaris"
xref: Reactome:REACT_110771 "Phase II conjugation, Saccharomyces cerevisiae"
xref: Reactome:REACT_110976 "Biological oxidations, Sus scrofa"
xref: Reactome:REACT_112180 "Conjugation of phenylacetate with glutamine, Dictyostelium discoideum"
xref: Reactome:REACT_112300 "Amino Acid conjugation, Dictyostelium discoideum"
xref: Reactome:REACT_112424 "Conjugation of salicylate with glycine, Dictyostelium discoideum"
xref: Reactome:REACT_114132 "Conjugation of benzoate with glycine, Dictyostelium discoideum"
xref: Reactome:REACT_115263 "Phase 1 - Functionalization of compounds, Escherichia coli"
xref: Reactome:REACT_115368 "Conjugation of carboxylic acids, Dictyostelium discoideum"
xref: Reactome:REACT_13433 "Biological oxidations, Homo sapiens"
xref: Reactome:REACT_13705 "Phase 1 - Functionalization of compounds, Homo sapiens"
xref: Reactome:REACT_30367 "Conjugation of carboxylic acids, Danio rerio"
xref: Reactome:REACT_30613 "Amino Acid conjugation, Canis familiaris"
xref: Reactome:REACT_31665 "Phase II conjugation, Caenorhabditis elegans"
xref: Reactome:REACT_32556 "Biological oxidations, Escherichia coli"
xref: Reactome:REACT_32957 "Conjugation of phenylacetate with glutamine, Sus scrofa"
xref: Reactome:REACT_33042 "Phase II conjugation, Xenopus tropicalis"
xref: Reactome:REACT_33621 "Biological oxidations, Canis familiaris"
xref: Reactome:REACT_33687 "Phase 1 - Functionalization of compounds, Drosophila melanogaster"
xref: Reactome:REACT_34424 "Biological oxidations, Plasmodium falciparum"
xref: Reactome:REACT_43989 "Phase II conjugation, Gallus gallus"
xref: Reactome:REACT_6800 "Conjugation of phenylacetate with glutamine, Homo sapiens"
xref: Reactome:REACT_6812 "Conjugation of salicylate with glycine, Homo sapiens"
xref: Reactome:REACT_6889 "Conjugation of carboxylic acids, Homo sapiens"
xref: Reactome:REACT_6933 "Conjugation of benzoate with glycine, Homo sapiens"
xref: Reactome:REACT_6959 "Phase II conjugation, Homo sapiens"
xref: Reactome:REACT_6971 "Amino Acid conjugation, Homo sapiens"
xref: Reactome:REACT_76924 "Biological oxidations, Bos taurus"
xref: Reactome:REACT_76938 "Phase II conjugation, Canis familiaris"
xref: Reactome:REACT_77460 "Phase II conjugation, Danio rerio"
xref: Reactome:REACT_77547 "Phase 1 - Functionalization of compounds, Oryza sativa"
xref: Reactome:REACT_77582 "Biological oxidations, Taeniopygia guttata"
xref: Reactome:REACT_77645 "Phase 1 - Functionalization of compounds, Mus musculus"
xref: Reactome:REACT_78106 "Biological oxidations, Drosophila melanogaster"
xref: Reactome:REACT_78563 "Phase 1 - Functionalization of compounds, Sus scrofa"
xref: Reactome:REACT_78673 "Amino Acid conjugation, Staphylococcus aureus N315"
xref: Reactome:REACT_78750 "Phase 1 - Functionalization of compounds, Taeniopygia guttata"
xref: Reactome:REACT_79195 "Conjugation of salicylate with glycine, Mus musculus"
xref: Reactome:REACT_80247 "Biological oxidations, Dictyostelium discoideum"
xref: Reactome:REACT_80647 "Biological oxidations, Xenopus tropicalis"
xref: Reactome:REACT_81143 "Biological oxidations, Mus musculus"
xref: Reactome:REACT_81813 "Amino Acid conjugation, Mus musculus"
xref: Reactome:REACT_82058 "Phase II conjugation, Escherichia coli"
xref: Reactome:REACT_82657 "Biological oxidations, Rattus norvegicus"
xref: Reactome:REACT_82846 "Phase II conjugation, Plasmodium falciparum"
xref: Reactome:REACT_83594 "Phase II conjugation, Taeniopygia guttata"
xref: Reactome:REACT_83912 "Amino Acid conjugation, Bos taurus"
xref: Reactome:REACT_83999 "Biological oxidations, Oryza sativa"
xref: Reactome:REACT_84336 "Phase 1 - Functionalization of compounds, Caenorhabditis elegans"
xref: Reactome:REACT_84559 "Phase 1 - Functionalization of compounds, Xenopus tropicalis"
xref: Reactome:REACT_84880 "Conjugation of carboxylic acids, Sus scrofa"
xref: Reactome:REACT_86049 "Conjugation of carboxylic acids, Bos taurus"
xref: Reactome:REACT_87255 "Phase II conjugation, Oryza sativa"
xref: Reactome:REACT_87382 "Phase II conjugation, Mycobacterium tuberculosis"
xref: Reactome:REACT_87394 "Amino Acid conjugation, Sus scrofa"
xref: Reactome:REACT_87515 "Phase 1 - Functionalization of compounds, Bos taurus"
xref: Reactome:REACT_87608 "Phase II conjugation, Mus musculus"
xref: Reactome:REACT_88305 "Amino Acid conjugation, Danio rerio"
xref: Reactome:REACT_88538 "Conjugation of salicylate with glycine, Rattus norvegicus"
xref: Reactome:REACT_89162 "Biological oxidations, Gallus gallus"
xref: Reactome:REACT_89167 "Phase II conjugation, Sus scrofa"
xref: Reactome:REACT_89372 "Biological oxidations, Danio rerio"
xref: Reactome:REACT_89381 "Conjugation of benzoate with glycine, Sus scrofa"
xref: Reactome:REACT_89411 "Phase II conjugation, Arabidopsis thaliana"
xref: Reactome:REACT_89902 "Biological oxidations, Mycobacterium tuberculosis"
xref: Reactome:REACT_89981 "Conjugation of benzoate with glycine, Danio rerio"
xref: Reactome:REACT_90526 "Biological oxidations, Caenorhabditis elegans"
xref: Reactome:REACT_90693 "Conjugation of phenylacetate with glutamine, Canis familiaris"
xref: Reactome:REACT_93150 "Amino Acid conjugation, Rattus norvegicus"
xref: Reactome:REACT_93320 "Biological oxidations, Schizosaccharomyces pombe"
xref: Reactome:REACT_93377 "Conjugation of carboxylic acids, Rattus norvegicus"
xref: Reactome:REACT_94407 "Phase 1 - Functionalization of compounds, Mycobacterium tuberculosis"
xref: Reactome:REACT_94419 "Conjugation of carboxylic acids, Staphylococcus aureus N315"
xref: Reactome:REACT_95660 "Phase II conjugation, Rattus norvegicus"
xref: Reactome:REACT_96794 "Phase II conjugation, Dictyostelium discoideum"
xref: Reactome:REACT_96971 "Conjugation of carboxylic acids, Mus musculus"
xref: Reactome:REACT_97920 "Conjugation of salicylate with glycine, Bos taurus"
xref: Reactome:REACT_98166 "Conjugation of benzoate with glycine, Canis familiaris"
xref: Reactome:REACT_98222 "Conjugation of benzoate with glycine, Rattus norvegicus"
xref: Reactome:REACT_98651 "Conjugation of benzoate with glycine, Bos taurus"
xref: Reactome:REACT_99593 "Conjugation of salicylate with glycine, Staphylococcus aureus N315"
xref: Reactome:REACT_99671 "Conjugation of phenylacetate with glutamine, Staphylococcus aureus N315"
xref: Reactome:REACT_99818 "Phase 1 - Functionalization of compounds, Rattus norvegicus"
xref: Wikipedia:Xenobiotic_metabolism
is_a: GO:0008152 ! metabolic process
relationship: part_of GO:0050896 ! response to stimulus

[Term]
id: GO:0006807
name: nitrogen compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen." [CHEBI:51143, GOC:go_curators, GOC:jl, ISBN:0198506732]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "nitrogen compound metabolism" EXACT []
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, pore or 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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "single-organism transport" RELATED []
synonym: "small molecule transport" NARROW []
synonym: "solute:solute exchange" NARROW []
is_a: GO:0051234 ! establishment of localization
created_by: janelomax
creation_date: 2012-12-13T16:25:32Z

[Term]
id: GO:0006811
name: ion transport
namespace: biological_process
def: "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
subset: goslim_yeast
xref: Reactome:REACT_102356 "Transport of inorganic cations/anions and amino acids/oligopeptides, Xenopus tropicalis"
xref: Reactome:REACT_102895 "Transport of inorganic cations/anions and amino acids/oligopeptides, Staphylococcus aureus N315"
xref: Reactome:REACT_106972 "Transport of inorganic cations/anions and amino acids/oligopeptides, Sus scrofa"
xref: Reactome:REACT_109067 "Transport of inorganic cations/anions and amino acids/oligopeptides, Saccharomyces cerevisiae"
xref: Reactome:REACT_110862 "Transport of inorganic cations/anions and amino acids/oligopeptides, Arabidopsis thaliana"
xref: Reactome:REACT_19397 "Transport of inorganic cations/anions and amino acids/oligopeptides, Homo sapiens"
xref: Reactome:REACT_29110 "Transport of inorganic cations/anions and amino acids/oligopeptides, Oryza sativa"
xref: Reactome:REACT_31978 "Transport of inorganic cations/anions and amino acids/oligopeptides, Mus musculus"
xref: Reactome:REACT_33992 "Transport of inorganic cations/anions and amino acids/oligopeptides, Danio rerio"
xref: Reactome:REACT_34201 "Transport of inorganic cations/anions and amino acids/oligopeptides, Gallus gallus"
xref: Reactome:REACT_79109 "Transport of inorganic cations/anions and amino acids/oligopeptides, Caenorhabditis elegans"
xref: Reactome:REACT_82618 "Transport of inorganic cations/anions and amino acids/oligopeptides, Escherichia coli"
xref: Reactome:REACT_87822 "Transport of inorganic cations/anions and amino acids/oligopeptides, Bos taurus"
xref: Reactome:REACT_91472 "Transport of inorganic cations/anions and amino acids/oligopeptides, Dictyostelium discoideum"
xref: Reactome:REACT_91958 "Transport of inorganic cations/anions and amino acids/oligopeptides, Drosophila melanogaster"
xref: Reactome:REACT_92903 "Transport of inorganic cations/anions and amino acids/oligopeptides, Mycobacterium tuberculosis"
xref: Reactome:REACT_93485 "Transport of inorganic cations/anions and amino acids/oligopeptides, Canis familiaris"
xref: Reactome:REACT_94357 "Transport of inorganic cations/anions and amino acids/oligopeptides, Rattus norvegicus"
xref: Reactome:REACT_96078 "Transport of inorganic cations/anions and amino acids/oligopeptides, Plasmodium falciparum"
xref: Reactome:REACT_96919 "Transport of inorganic cations/anions and amino acids/oligopeptides, Taeniopygia guttata"
xref: Reactome:REACT_98077 "Transport of inorganic cations/anions and amino acids/oligopeptides, Schizosaccharomyces pombe"
is_a: GO:0006810 ! transport

[Term]
id: GO:0006836
name: neurotransmitter transport
namespace: biological_process
def: "The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. 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]
subset: goslim_pir
synonym: "sodium:neurotransmitter transport" NARROW []
is_a: GO:0006810 ! transport

[Term]
id: GO:0006865
name: amino acid transport
namespace: biological_process
alt_id: GO:0006866
def: "The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
subset: goslim_yeast
xref: Reactome:REACT_104605 "Amino acid transport across the plasma membrane, Rattus norvegicus"
xref: Reactome:REACT_105142 "Amino acid transport across the plasma membrane, Mus musculus"
xref: Reactome:REACT_105179 "Amino acid transport across the plasma membrane, Caenorhabditis elegans"
xref: Reactome:REACT_106669 "Amino acid transport across the plasma membrane, Dictyostelium discoideum"
xref: Reactome:REACT_107151 "Amino acid transport across the plasma membrane, Arabidopsis thaliana"
xref: Reactome:REACT_107366 "Amino acid transport across the plasma membrane, Gallus gallus"
xref: Reactome:REACT_107449 "Amino acid transport across the plasma membrane, Escherichia coli"
xref: Reactome:REACT_112073 "Amino acid transport across the plasma membrane, Mycobacterium tuberculosis"
xref: Reactome:REACT_115423 "Amino acid transport across the plasma membrane, Saccharomyces cerevisiae"
xref: Reactome:REACT_13796 "Amino acid transport across the plasma membrane, Homo sapiens"
xref: Reactome:REACT_29020 "Amino acid transport across the plasma membrane, Staphylococcus aureus N315"
xref: Reactome:REACT_81602 "Amino acid transport across the plasma membrane, Oryza sativa"
xref: Reactome:REACT_81848 "Amino acid transport across the plasma membrane, Danio rerio"
xref: Reactome:REACT_83425 "Amino acid transport across the plasma membrane, Bos taurus"
xref: Reactome:REACT_90553 "Amino acid transport across the plasma membrane, Drosophila melanogaster"
xref: Reactome:REACT_95755 "Amino acid transport across the plasma membrane, Taeniopygia guttata"
xref: Reactome:REACT_96944 "Amino acid transport across the plasma membrane, Sus scrofa"
xref: Reactome:REACT_98408 "Amino acid transport across the plasma membrane, Xenopus tropicalis"
xref: Reactome:REACT_99072 "Amino acid transport across the plasma membrane, Canis familiaris"
is_a: GO:0006811 ! ion transport
is_a: GO:0015849 ! organic acid transport

[Term]
id: GO:0006869
name: lipid transport
namespace: biological_process
def: "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [ISBN:0198506732]
subset: goslim_pir
subset: goslim_yeast
is_a: GO:0006810 ! transport
relationship: part_of GO:0051179 ! localization

[Term]
id: GO:0006914
name: autophagy
namespace: biological_process
alt_id: GO:0016238
def: "The cellular catabolic process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation." [GOC:autophagy, ISBN:0198547684, PMID:11099404, PMID:9412464]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
xref: Wikipedia:Autophagy_(cellular)
is_a: GO:0008152 ! metabolic process
relationship: has_part GO:0006810 ! transport

[Term]
id: GO:0006928
name: movement of cell or subcellular component
namespace: biological_process
def: "The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore." [GOC:dgh, GOC:dph, GOC:jl, GOC:mlg]
comment: Note that in GO cellular components include whole cells (cell is_a cellular component).
subset: gocheck_do_not_annotate
subset: goslim_pir
synonym: "cell movement" RELATED []
synonym: "cellular component motion" EXACT [GOC:dph, GOC:jl]
synonym: "cellular component movement" EXACT []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0006936
name: muscle contraction
namespace: biological_process
def: "A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis." [GOC:ef, GOC:mtg_muscle, ISBN:0198506732]
subset: goslim_pir
xref: Reactome:REACT_100109 "Smooth Muscle Contraction, Canis familiaris"
xref: Reactome:REACT_102067 "Smooth Muscle Contraction, Taeniopygia guttata"
xref: Reactome:REACT_20558 "Smooth Muscle Contraction, Homo sapiens"
xref: Reactome:REACT_29015 "Smooth Muscle Contraction, Danio rerio"
xref: Reactome:REACT_77478 "Smooth Muscle Contraction, Xenopus tropicalis"
xref: Reactome:REACT_81255 "Smooth Muscle Contraction, Mus musculus"
xref: Reactome:REACT_83607 "Smooth Muscle Contraction, Bos taurus"
xref: Reactome:REACT_85440 "Smooth Muscle Contraction, Gallus gallus"
xref: Reactome:REACT_87764 "Smooth Muscle Contraction, Sus scrofa"
xref: Reactome:REACT_88232 "Smooth Muscle Contraction, Rattus norvegicus"
xref: Reactome:REACT_92442 "Smooth Muscle Contraction, Dictyostelium discoideum"
xref: Wikipedia:Muscle_contraction
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0006949
name: syncytium formation
namespace: biological_process
def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division." [ISBN:0198506732]
subset: goslim_pir
is_a: GO:0032502 ! developmental process
relationship: part_of GO:0032502 ! developmental process

[Term]
id: GO:0006996
name: organelle organization
namespace: biological_process
alt_id: GO:1902589
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
synonym: "organelle organisation" EXACT [GOC:curators]
synonym: "organelle organization and biogenesis" RELATED [GOC:dph, GOC:jl, GOC:mah]
synonym: "single organism organelle organization" EXACT [GOC:TermGenie]
synonym: "single-organism organelle organization" RELATED []
is_a: GO:0016043 ! cellular component organization
created_by: jl
creation_date: 2013-12-19T15:25:51Z

[Term]
id: GO:0006997
name: nucleus organization
namespace: biological_process
alt_id: GO:0048287
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus." [GOC:dph, GOC:ems, GOC:jl, GOC:mah]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
subset: goslim_yeast
synonym: "nuclear morphology" RELATED []
synonym: "nuclear organisation" EXACT [GOC:curators]
synonym: "nuclear organization" EXACT [GOC:curators]
synonym: "nuclear organization and biogenesis" RELATED [GOC:mah]
synonym: "nucleus organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0006996 ! organelle organization

[Term]
id: GO:0007005
name: mitochondrion organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components." [GOC:dph, GOC:jl, GOC:mah, GOC:sgd_curators, PMID:9786946]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
synonym: "mitochondria organization" EXACT [GOC:mah]
synonym: "mitochondrion organisation" EXACT [GOC:mah]
synonym: "mitochondrion organization and biogenesis" RELATED [GOC:curators]
is_a: GO:0006996 ! organelle organization

[Term]
id: GO:0007028
name: cytoplasm organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [GOC:curators, GOC:dph, GOC:jl, GOC:mah]
subset: goslim_pir
synonym: "cytoplasm organisation" EXACT [GOC:curators]
synonym: "cytoplasm organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0016043 ! cellular component organization

[Term]
id: GO:0007029
name: endoplasmic reticulum organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum." [GOC:dph, GOC:jl, GOC:mah]
subset: goslim_pir
synonym: "endoplasmic reticulum morphology" RELATED []
synonym: "endoplasmic reticulum organisation" EXACT [GOC:curators]
synonym: "endoplasmic reticulum organization and biogenesis" RELATED [GOC:mah]
synonym: "ER organisation" EXACT [GOC:curators]
synonym: "ER organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0006996 ! organelle organization
relationship: part_of GO:0016043 ! cellular component organization

[Term]
id: GO:0007030
name: Golgi organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus." [GOC:dph, GOC:jl, GOC:mah]
subset: goslim_pir
synonym: "Golgi organisation" EXACT [GOC:curators]
synonym: "Golgi organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0006996 ! organelle organization
relationship: part_of GO:0016043 ! cellular component organization

[Term]
id: GO:0007031
name: peroxisome organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules." [GOC:mah]
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
synonym: "peroxisome organisation" EXACT [GOC:curators]
synonym: "peroxisome organization and biogenesis" RELATED [GOC:mah]
synonym: "peroxisome-assembly ATPase activity" RELATED []
is_a: GO:0006996 ! organelle organization

[Term]
id: GO:0007032
name: endosome organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes." [GOC:dph, GOC:jl, GOC:mah]
subset: goslim_pir
synonym: "endosome organisation" EXACT [GOC:curators]
synonym: "endosome organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0016050 ! vesicle organization
relationship: part_of GO:0016043 ! cellular component organization

[Term]
id: GO:0007033
name: vacuole organization
namespace: biological_process
alt_id: GO:0044086
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole." [GOC:mah]
subset: goslim_pir
subset: goslim_yeast
synonym: "vacuolar assembly" NARROW [GOC:mah]
synonym: "vacuole biogenesis" RELATED [GOC:mah]
synonym: "vacuole organisation" EXACT [GOC:curators]
synonym: "vacuole organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0006996 ! organelle organization

[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_manually_annotate
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
synonym: "cell-division cycle" EXACT []
xref: Wikipedia:Cell_cycle
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0007059
name: chromosome segregation
namespace: biological_process
def: "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." [GOC:jl, GOC:mah, GOC:mtg_cell_cycle, GOC:vw]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_yeast
synonym: "chromosome division" EXACT []
synonym: "chromosome transmission" RELATED []
xref: Wikipedia:Chromosome_segregation
is_a: GO:0008150 ! biological_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:0008150 ! biological_process

[Term]
id: GO:0007155
name: cell adhesion
namespace: biological_process
alt_id: GO:0098602
def: "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules." [GOC:hb, GOC:pf]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
synonym: "cell adhesion molecule activity" RELATED []
synonym: "single organism cell adhesion" RELATED []
xref: Wikipedia:Cell_adhesion
is_a: GO:0022610 ! biological adhesion
created_by: davidos
creation_date: 2014-04-15T15:59:10Z

[Term]
id: GO:0007586
name: digestion
namespace: biological_process
def: "The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [GOC:isa_complete, ISBN:0198506732]
subset: goslim_chembl
subset: goslim_pir
xref: Wikipedia:Digestion
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0007588
name: excretion
namespace: biological_process
def: "The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds." [ISBN:0192801023]
subset: goslim_pir
xref: Wikipedia:Excretion
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0008015
name: blood circulation
namespace: biological_process
alt_id: GO:0070261
def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825]
subset: goslim_pir
synonym: "hemolymph circulation" RELATED []
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0008023
name: transcription elongation factor complex
namespace: cellular_component
def: "Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation." [GOC:jl]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0008037
name: cell recognition
namespace: biological_process
def: "The process in which a cell in an organism interprets its surroundings." [GOC:go_curators]
subset: goslim_pir
synonym: "recognition of surroundings by cell" EXACT [GOC:curators]
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0008144
name: drug binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease." [GOC:jl, ISBN:0198506732]
subset: goslim_pir
is_a: GO:0005488 ! binding

[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 represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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 use 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_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
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
created_by: janelomax
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_manually_annotate
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
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
created_by: janelomax
creation_date: 2012-10-17T15:46:40Z

[Term]
id: GO:0008233
name: peptidase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid." [GOC:jl, ISBN:0815332181]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
synonym: "hydrolase, acting on peptide bonds" EXACT []
synonym: "peptide hydrolase activity" EXACT []
synonym: "protease activity" EXACT []
synonym: "proteinase activity" NARROW []
xref: EC:3.4
xref: Reactome:REACT_106748 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Rattus norvegicus"
xref: Reactome:REACT_110349 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Mus musculus"
xref: Reactome:REACT_13710 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Homo sapiens"
xref: Reactome:REACT_19284 "Proteolytic processing of Slit, Homo sapiens"
xref: Reactome:REACT_93020 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Bos taurus"
xref: Reactome:REACT_99630 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Gallus gallus"
is_a: GO:0016787 ! hydrolase activity
relationship: part_of GO:0006508 ! proteolysis

[Term]
id: GO:0008278
name: cohesin complex
namespace: cellular_component
alt_id: GO:0008279
alt_id: GO:0008280
alt_id: GO:0043222
def: "A protein complex that is required for sister chromatid cohesion in eukaryotes. The cohesin complex forms a molecular ring complex, and is composed of structural maintenance of chromosomes (SMC) and kleisin proteins. For example, in yeast, the complex is composed of the SMC proteins Smc1p and Smc3p, and the kleisin protein Scc1p. In vertebrates, the complex is composed of the SMC1 (SMC1A or SMC1B) and SMC3 heterodimer attached via their hinge domains to a kleisin (RAD21, REC8 or RAD21L) which links them, and one STAG protein (STAG1, STAG2 or STAG3)." [GOC:jl, GOC:sp, GOC:vw, PMID:9887095]
subset: goslim_pir
synonym: "14S cohesin" NARROW []
synonym: "9S cohesin" NARROW []
synonym: "cohesin core heterodimer" RELATED []
synonym: "SMC complex" RELATED []
synonym: "SMC/kleisin ring complex" EXACT []
synonym: "Smc1-Smc3 complex" NARROW []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005694 ! chromosome

[Term]
id: GO:0008283
name: cell proliferation
namespace: biological_process
def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [GOC:mah, GOC:mb]
comment: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.
subset: goslim_agr
subset: goslim_chembl
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0008287
name: protein serine/threonine phosphatase complex
namespace: cellular_component
def: "A complex, normally consisting of a catalytic and a regulatory subunit, which catalyzes the removal of a phosphate group from a serine or threonine residue of a protein." [GOC:bf]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part

[Term]
id: GO:0008289
name: lipid binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a lipid." [GOC:ai]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
is_a: GO:0005488 ! binding

[Term]
id: GO:0008290
name: F-actin capping protein complex
namespace: cellular_component
def: "A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, thereby regulating the polymerization of actin monomers but not severing actin filaments." [GOC:go_curators, ISBN:0198599560]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005856 ! cytoskeleton

[Term]
id: GO:0008641
name: ubiquitin-like modifier activating enzyme activity
namespace: molecular_function
alt_id: GO:0008642
def: "Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond." [GOC:jl, GOC:mah]
comment: Discussion of class label in this ticket: https://github.com/geneontology/go-ontology/issues/14208
subset: goslim_pir
synonym: "small protein activating enzyme activity" NARROW []
is_a: GO:0016874 ! ligase activity

[Term]
id: GO:0008643
name: carbohydrate transport
namespace: biological_process
alt_id: GO:0006861
alt_id: GO:0008644
def: "The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC:ai]
subset: goslim_pir
subset: goslim_yeast
synonym: "sugar transport" NARROW []
is_a: GO:0006810 ! transport

[Term]
id: GO:0008655
name: pyrimidine-containing compound salvage
namespace: biological_process
def: "Any process that generates a pyrimidine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis." [CHEBI:39447, GOC:jl]
subset: goslim_pir
synonym: "pyrimidine salvage" RELATED [GOC:curators]
is_a: GO:0006139 ! nucleobase-containing compound metabolic process
is_a: GO:0043094 ! cellular metabolic compound salvage

[Term]
id: GO:0008907
name: integrase activity
namespace: molecular_function
def: "Catalysis of the integration of one segment of DNA into another." [GOC:mah]
subset: goslim_pir
is_a: GO:0003824 ! catalytic activity
relationship: part_of GO:0015074 ! DNA integration

[Term]
id: GO:0009009
name: site-specific recombinase activity
namespace: molecular_function
def: "Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences." [GOC:elh]
comment: Note that this term is not a child of 'recombinase activity ; GO:0000150' because the latter represents activities that do not break or form phosphodiester bonds.
subset: goslim_pir
is_a: GO:0003824 ! catalytic activity
relationship: part_of GO:0006259 ! DNA metabolic process

[Term]
id: GO:0009055
name: electron transfer activity
namespace: molecular_function
alt_id: GO:0009053
alt_id: GO:0009054
def: "Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient." [ISBN:0198506732]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "electron acceptor activity" NARROW []
synonym: "electron carrier" RELATED []
synonym: "electron donor activity" NARROW []
synonym: "electron transporter activity" RELATED []
xref: Reactome:REACT_100606 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Caenorhabditis elegans"
xref: Reactome:REACT_107372 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Xenopus tropicalis"
xref: Reactome:REACT_107740 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Mus musculus"
xref: Reactome:REACT_107845 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Rattus norvegicus"
xref: Reactome:REACT_108215 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Saccharomyces cerevisiae"
xref: Reactome:REACT_109222 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Danio rerio"
xref: Reactome:REACT_28440 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Escherichia coli"
xref: Reactome:REACT_29712 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Bos taurus"
xref: Reactome:REACT_31774 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Dictyostelium discoideum"
xref: Reactome:REACT_6154 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Homo sapiens"
xref: Reactome:REACT_78399 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Sus scrofa"
xref: Reactome:REACT_81671 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Arabidopsis thaliana"
xref: Reactome:REACT_89868 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Taeniopygia guttata"
xref: Reactome:REACT_94498 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Drosophila melanogaster"
xref: Reactome:REACT_98413 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Canis familiaris"
xref: Reactome:REACT_98930 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Schizosaccharomyces pombe"
xref: Reactome:REACT_99683 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Mycobacterium tuberculosis"
xref: Reactome:REACT_99848 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF, Oryza sativa"
is_a: GO:0016491 ! oxidoreductase activity
intersection_of: GO:0016491 ! oxidoreductase activity
intersection_of: part_of GO:0022900 ! electron transport chain
relationship: part_of GO:0022900 ! electron transport chain

[Term]
id: GO:0009057
name: macromolecule catabolic process
namespace: biological_process
alt_id: GO:0043285
alt_id: GO:0044266
def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah]
subset: goslim_pir
synonym: "biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09]
synonym: "macromolecule breakdown" EXACT []
synonym: "macromolecule catabolism" EXACT []
synonym: "macromolecule degradation" EXACT []
synonym: "multicellular organismal macromolecule catabolic process" NARROW []
is_a: GO:0043170 ! macromolecule metabolic process

[Term]
id: GO:0009059
name: macromolecule biosynthetic process
namespace: biological_process
alt_id: GO:0043284
def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah]
subset: goslim_pir
synonym: "biopolymer biosynthetic process" EXACT [GOC:mtg_chebi_dec09]
synonym: "macromolecule anabolism" EXACT []
synonym: "macromolecule biosynthesis" EXACT []
synonym: "macromolecule formation" EXACT []
synonym: "macromolecule synthesis" EXACT []
is_a: GO:0043170 ! macromolecule metabolic process

[Term]
id: GO:0009116
name: nucleoside metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine)." [GOC:ma]
subset: goslim_pir
synonym: "nucleoside metabolism" EXACT []
is_a: GO:0006139 ! nucleobase-containing compound metabolic process

[Term]
id: GO:0009117
name: nucleotide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates)." [GOC:ma]
subset: goslim_pir
synonym: "nucleotide metabolism" EXACT []
is_a: GO:0006139 ! nucleobase-containing compound metabolic process
is_a: GO:0006793 ! phosphorus metabolic process

[Term]
id: GO:0009225
name: nucleotide-sugar metabolic process
namespace: biological_process
def: "The cellular chemical reactions and pathways involving nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative." [ISBN:0198506732]
comment: Added parent as requested here https://github.com/geneontology/go-ontology/issues/14587
subset: goslim_pir
synonym: "nucleotide-sugar metabolism" EXACT []
is_a: GO:0006139 ! nucleobase-containing compound metabolic process

[Term]
id: GO:0009288
name: bacterial-type flagellum
namespace: cellular_component
def: "A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope." [GOC:cilia, GOC:jh2, GOC:krc, GOC:mtg_sensu, http:en.wikipedia.org/wiki/Flagellum#Bacterial, PMID:7787060]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "flagellin-based flagellum" EXACT []
is_a: GO:0042995 ! cell projection
is_a: GO:0043226 ! organelle

[Term]
id: GO:0009289
name: pilus
namespace: cellular_component
def: "A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter." [GOC:pamgo_curators]
subset: goslim_pir
synonym: "fimbria" EXACT []
synonym: "fimbriae" EXACT []
synonym: "fimbrium" EXACT []
synonym: "pili" EXACT []
xref: Wikipedia:Pilus
is_a: GO:0042995 ! cell projection

[Term]
id: GO:0009292
name: genetic transfer
namespace: biological_process
def: "In the absence of a sexual life cycle, the process involved in the introduction of genetic information to create a genetically different individual." [GOC:clt]
comment: GO:0009292 should not be used for annotation of phage lysogeny (integration of the bacteriophage nucleic acid into the host bacterium's genome).
subset: goslim_pir
synonym: "genetic exchange" BROAD []
is_a: GO:0051704 ! multi-organism process

[Term]
id: GO:0009308
name: amine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." [GOC:jl, ISBN:0198506732]
subset: goslim_chembl
subset: goslim_pir
synonym: "amine metabolism" EXACT []
is_a: GO:0006807 ! nitrogen compound metabolic process

[Term]
id: GO:0009317
name: acetyl-CoA carboxylase complex
namespace: cellular_component
def: "A protein complex that catalyzes the first step in long-chain fatty acid biosynthesis. For example, in E. coli the complex is heterohexameric and composed of biotin carbonyl carrier protein, biotin carboxylase and the acetate CoA-transferase complex." [GOC:jl, GOC:mah, PMID:12121720]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "ACCase complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0009368
name: endopeptidase Clp complex
namespace: cellular_component
def: "A protein complex comprised of members of the ClpX, ClpC, ClpD, ClpP or ClpR protein families. ClpPs are the proteolytic subunit of active complexes, and ClpA and ClpX form the regulatory subunits. Enzymatically active and inactive complexes can form." [GOC:mah, PMID:11352464]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0009372
name: quorum sensing
namespace: biological_process
def: "The process in which single-celled organisms monitor their population density by detecting the concentration of small, diffusible signal molecules produced by the cells themselves." [PMID:15716452, PMID:8288518]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "quorum sensing system" EXACT []
xref: Wikipedia:Quorum_sensing
is_a: GO:0051704 ! multi-organism process

[Term]
id: GO:0009404
name: toxin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving a toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism." [GOC:cab2]
subset: goslim_aspergillus
subset: goslim_pir
synonym: "toxin metabolism" EXACT []
is_a: GO:0019748 ! secondary metabolic process

[Term]
id: GO:0009521
name: photosystem
namespace: cellular_component
alt_id: GO:0030090
def: "A complex located in a photosynthetic membrane that consists of a photoreaction center associated with accessory pigments and electron carriers. Examples of this component are found in Arabidopsis thaliana and in photosynthetic bacterial and archaeal species." [GOC:ds, GOC:mah, ISBN:0140514031, PMID:9821949]
subset: goslim_pir
synonym: "reaction center" NARROW []
synonym: "reaction centre" NARROW []
xref: Wikipedia:Photosystem
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0009579 ! thylakoid
relationship: part_of GO:0016020 ! membrane

[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
xref: Wikipedia:Plastid
is_a: GO:0043231 ! intracellular membrane-bounded organelle
relationship: part_of GO:0005737 ! cytoplasm

[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
synonym: "photosynthetic membrane" RELATED []
xref: Wikipedia:Thylakoid
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0009657
name: plastid organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plastid." [GOC:mah]
subset: goslim_pir
synonym: "plastid organisation" EXACT [GOC:curators]
synonym: "plastid organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0006996 ! organelle organization

[Term]
id: GO:0009914
name: hormone transport
namespace: biological_process
def: "The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:tb]
subset: goslim_pir
is_a: GO:0006810 ! transport
is_a: GO:0065008 ! regulation of biological quality

[Term]
id: GO:0009975
name: cyclase activity
namespace: molecular_function
def: "Catalysis of a ring closure reaction." [ISBN:0198547684]
subset: goslim_pir
is_a: GO:0003824 ! catalytic activity

[Term]
id: GO:0009986
name: cell surface
namespace: cellular_component
alt_id: GO:0009928
alt_id: GO:0009929
def: "The external part of the cell wall and/or plasma membrane." [GOC:jl, GOC:mtg_sensu, GOC:sm]
comment: Note that this term is intended to annotate gene products that are attached (integrated or loosely bound) to the plasma membrane or cell wall.
subset: goslim_pir
synonym: "cell associated" EXACT []
synonym: "cell bound" EXACT []
is_a: GO:0044464 ! cell part

[Term]
id: GO:0010118
name: stomatal movement
namespace: biological_process
def: "The process of opening or closing of stomata, which is directly related to the stomatal conductance (measuring rate of passage of either water vapor or carbon dioxide (CO2) through stomata)." [GOC:sm]
subset: goslim_pir
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0010191
name: mucilage metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving mucilage, a gelatinous substance secreted by plants." [GOC:sm]
subset: goslim_pir
synonym: "mucilage metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0010316
name: pyrophosphate-dependent phosphofructokinase complex
namespace: cellular_component
def: "Heterodimeric complex that catalyzes the pyrophosphate-dependent phosphorylation of D-fructose 6-phosphate into D-fructose 1,6-bisphosphate." [PMID:2170409]
subset: goslim_pir
synonym: "PFK complex" RELATED []
is_a: GO:0032991 ! protein-containing complex

[Term]
id: GO:0015031
name: protein transport
namespace: biological_process
alt_id: GO:0015831
def: "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
synonym: "enzyme transport" NARROW []
is_a: GO:0015833 ! peptide transport

[Term]
id: GO:0015074
name: DNA integration
namespace: biological_process
def: "The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome." [GOC:mah]
subset: goslim_pir
is_a: GO:0006259 ! DNA metabolic process

[Term]
id: GO:0015669
name: gas transport
namespace: biological_process
def: "The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
is_a: GO:0006810 ! transport

[Term]
id: GO:0015791
name: polyol transport
namespace: biological_process
def: "The directed movement of polyols, any polyhydric alcohol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
is_a: GO:0006810 ! transport

[Term]
id: GO:0015833
name: peptide transport
namespace: biological_process
def: "The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
is_a: GO:0042886 ! amide transport

[Term]
id: GO:0015835
name: peptidoglycan transport
namespace: biological_process
def: "The directed movement of peptidoglycans, a class of glycoconjugates found in bacterial cell walls, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
synonym: "murein transport" EXACT []
is_a: GO:0006810 ! transport

[Term]
id: GO:0015837
name: amine transport
namespace: biological_process
def: "The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai, ISBN:0198506732]
subset: goslim_pir
synonym: "amine/polyamine transport" RELATED []
is_a: GO:0006810 ! transport

[Term]
id: GO:0015849
name: organic acid transport
namespace: biological_process
def: "The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [ISBN:0198506732]
subset: goslim_pir
is_a: GO:0006810 ! transport

[Term]
id: GO:0015891
name: siderophore transport
namespace: biological_process
alt_id: GO:0015892
def: "The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
synonym: "iron-siderochrome transport" NARROW []
synonym: "iron-siderophore transport" EXACT []
synonym: "siderochrome transport" NARROW []
synonym: "siderophore-iron transport" EXACT []
is_a: GO:0051181 ! cofactor transport

[Term]
id: GO:0015893
name: drug transport
namespace: biological_process
def: "The directed movement of a drug, a substance used in the diagnosis, treatment or prevention of a disease, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
is_a: GO:0006810 ! transport
relationship: part_of GO:0050896 ! response to stimulus

[Term]
id: GO:0015920
name: lipopolysaccharide transport
namespace: biological_process
def: "The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide." [GOC:ai]
subset: goslim_pir
synonym: "LPS transport" EXACT []
is_a: GO:0006869 ! lipid transport

[Term]
id: GO:0015931
name: nucleobase-containing compound transport
namespace: biological_process
def: "The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
subset: goslim_yeast
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid transport" RELATED [GOC:dph, GOC:tb]
is_a: GO:0006810 ! transport

[Term]
id: GO:0015935
name: small ribosomal subunit
namespace: cellular_component
def: "The smaller of the two subunits of a ribosome." [GOC:mah]
subset: goslim_pir
synonym: "ribosomal small subunit" EXACT []
is_a: GO:0044464 ! cell part
is_a: GO:1990904 ! ribonucleoprotein complex
relationship: part_of GO:0005840 ! ribosome

[Term]
id: GO:0015948
name: methanogenesis
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes." [GOC:ai]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "methane biosynthesis" EXACT []
synonym: "methane biosynthetic process" EXACT []
xref: UM-BBD_pathwayID:meth
xref: Wikipedia:Methanogenesis
is_a: GO:0043446 ! cellular alkane metabolic process
is_a: GO:0045333 ! cellular respiration

[Term]
id: GO:0015949
name: nucleobase-containing small molecule interconversion
namespace: biological_process
def: "The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule." [GOC:mah, ISBN:0306444747, ISBN:0471394831]
subset: goslim_pir
xref: MetaCyc:P1-PWY
xref: Reactome:REACT_102506 "Synthesis and interconversion of nucleotide di- and triphosphates, Oryza sativa"
xref: Reactome:REACT_107209 "Synthesis and interconversion of nucleotide di- and triphosphates, Drosophila melanogaster"
xref: Reactome:REACT_108426 "Synthesis and interconversion of nucleotide di- and triphosphates, Danio rerio"
xref: Reactome:REACT_109014 "Synthesis and interconversion of nucleotide di- and triphosphates, Saccharomyces cerevisiae"
xref: Reactome:REACT_109980 "Synthesis and interconversion of nucleotide di- and triphosphates, Gallus gallus"
xref: Reactome:REACT_110584 "Synthesis and interconversion of nucleotide di- and triphosphates, Escherichia coli"
xref: Reactome:REACT_21330 "Synthesis and interconversion of nucleotide di- and triphosphates, Homo sapiens"
xref: Reactome:REACT_29794 "Synthesis and interconversion of nucleotide di- and triphosphates, Caenorhabditis elegans"
xref: Reactome:REACT_41788 "Synthesis and interconversion of nucleotide di- and triphosphates, Canis familiaris"
xref: Reactome:REACT_77249 "Synthesis and interconversion of nucleotide di- and triphosphates, Arabidopsis thaliana"
xref: Reactome:REACT_77992 "Synthesis and interconversion of nucleotide di- and triphosphates, Xenopus tropicalis"
xref: Reactome:REACT_80972 "Synthesis and interconversion of nucleotide di- and triphosphates, Taeniopygia guttata"
xref: Reactome:REACT_82335 "Synthesis and interconversion of nucleotide di- and triphosphates, Mus musculus"
xref: Reactome:REACT_82859 "Synthesis and interconversion of nucleotide di- and triphosphates, Bos taurus"
xref: Reactome:REACT_86356 "Synthesis and interconversion of nucleotide di- and triphosphates, Schizosaccharomyces pombe"
xref: Reactome:REACT_89651 "Synthesis and interconversion of nucleotide di- and triphosphates, Mycobacterium tuberculosis"
xref: Reactome:REACT_90295 "Synthesis and interconversion of nucleotide di- and triphosphates, Plasmodium falciparum"
xref: Reactome:REACT_95252 "Synthesis and interconversion of nucleotide di- and triphosphates, Rattus norvegicus"
xref: Reactome:REACT_96776 "Synthesis and interconversion of nucleotide di- and triphosphates, Sus scrofa"
xref: Reactome:REACT_97285 "Synthesis and interconversion of nucleotide di- and triphosphates, Dictyostelium discoideum"
is_a: GO:0006139 ! nucleobase-containing compound metabolic process

[Term]
id: GO:0015976
name: carbon utilization
namespace: biological_process
alt_id: GO:0015978
def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbon sources and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize alternative carbon sources such as carbon dioxide or carbonic acid. The utilization process begins when the cell or organism detects carbon levels, includes the activation of genes whose products detect, transport or metabolize carbon-containing substances, and ends when carbon is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg]
subset: goslim_chembl
subset: goslim_pir
synonym: "carbon utilization by utilization of organic compounds" EXACT [GOC:mah]
synonym: "heterotrophy" EXACT []
xref: Wikipedia:Heterotroph
is_a: GO:0008150 ! biological_process
relationship: has_part GO:0006810 ! transport
relationship: has_part GO:0008152 ! metabolic process
relationship: has_part GO:0051606 ! detection of stimulus

[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
xref: Wikipedia:Photosynthesis
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0016010
name: dystrophin-associated glycoprotein complex
namespace: cellular_component
def: "A multiprotein complex that forms a strong mechanical link between the cytoskeleton and extracellular matrix; typical of, but not confined to, muscle cells. The complex is composed of transmembrane, cytoplasmic, and extracellular proteins, including dystrophin, sarcoglycans, dystroglycan, dystrobrevins, syntrophins, sarcospan, caveolin-3, and NO synthase." [PMID:15117830, PMID:16710609]
subset: goslim_pir
synonym: "DGC" EXACT []
synonym: "dystrophin glycoprotein complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0016020 ! membrane
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0016020
name: membrane
namespace: cellular_component
def: "A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it." [GOC:dos, GOC:mah, ISBN:0815316194]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
xref: Wikipedia:Biological_membrane
is_a: GO:0005575 ! cellular_component

[Term]
id: GO:0016028
name: rhabdomere
namespace: cellular_component
def: "The specialized microvilli-containing organelle on the apical surfaces of a photoreceptor cell containing the visual pigment rhodopsin and most of the proteins involved in phototransduction." [GOC:hb, GOC:sart, PMID:8646774]
subset: goslim_pir
is_a: GO:0042995 ! cell projection
relationship: has_part GO:0016020 ! membrane
relationship: has_part GO:0044464 ! cell part

[Term]
id: GO:0016032
name: viral process
namespace: biological_process
alt_id: GO:0022415
def: "A multi-organism process in which a virus is a participant. The other participant is the host. Includes 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:bf, GOC:jl, GOC:mah]
comment: See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'.
subset: goslim_metagenomics
subset: goslim_pir
synonym: "viral infection" RELATED []
synonym: "virulence" RELATED []
synonym: "virus process" EXACT [GOC:bf, GOC:jl]
xref: Reactome:REACT_6145 "Influenza Life Cycle, Homo sapiens"
xref: Reactome:REACT_6185 "HIV Infection, Homo sapiens"
xref: Reactome:REACT_6256 "HIV Life Cycle, Homo sapiens"
xref: Wikipedia:Viral_life_cycle
is_a: GO:0044419 ! interspecies interaction between organisms

[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: goslim_agr
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
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:0008150 ! biological_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_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:0040007 ! growth

[Term]
id: GO:0016050
name: vesicle organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle." [GOC:mah]
subset: goslim_pir
subset: goslim_yeast
synonym: "vesicle organisation" EXACT [GOC:curators]
synonym: "vesicle organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0006996 ! organelle organization

[Term]
id: GO:0016070
name: RNA metabolic process
namespace: biological_process
def: "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732]
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_metagenomics
subset: goslim_pir
synonym: "RNA metabolism" EXACT []
xref: Reactome:REACT_107259 "Metabolism of RNA, Sus scrofa"
xref: Reactome:REACT_107652 "Metabolism of RNA, Schizosaccharomyces pombe"
xref: Reactome:REACT_110289 "Metabolism of RNA, Danio rerio"
xref: Reactome:REACT_21257 "Metabolism of RNA, Homo sapiens"
xref: Reactome:REACT_30579 "Metabolism of RNA, Xenopus tropicalis"
xref: Reactome:REACT_31367 "Metabolism of RNA, Dictyostelium discoideum"
xref: Reactome:REACT_33720 "Metabolism of RNA, Plasmodium falciparum"
xref: Reactome:REACT_80071 "Metabolism of RNA, Caenorhabditis elegans"
xref: Reactome:REACT_83630 "Metabolism of RNA, Taeniopygia guttata"
xref: Reactome:REACT_84169 "Metabolism of RNA, Canis familiaris"
xref: Reactome:REACT_85788 "Metabolism of RNA, Oryza sativa"
xref: Reactome:REACT_88316 "Metabolism of RNA, Mus musculus"
xref: Reactome:REACT_89992 "Metabolism of RNA, Saccharomyces cerevisiae"
xref: Reactome:REACT_91556 "Metabolism of RNA, Bos taurus"
xref: Reactome:REACT_92152 "Metabolism of RNA, Drosophila melanogaster"
xref: Reactome:REACT_94876 "Metabolism of RNA, Arabidopsis thaliana"
xref: Reactome:REACT_99403 "Metabolism of RNA, Rattus norvegicus"
xref: Reactome:REACT_99885 "Metabolism of RNA, Gallus gallus"
is_a: GO:0006139 ! nucleobase-containing compound metabolic process
is_a: GO:0043170 ! macromolecule metabolic process

[Term]
id: GO:0016192
name: vesicle-mediated transport
namespace: biological_process
alt_id: GO:0006899
def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
synonym: "nonselective vesicle transport" NARROW []
synonym: "protein sorting along secretory pathway" RELATED []
synonym: "vesicle trafficking" RELATED []
synonym: "vesicle transport" EXACT []
synonym: "vesicular transport" EXACT [GOC:mah]
is_a: GO:0006810 ! transport

[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_metagenomics
subset: goslim_pir
is_a: GO:0003674 ! molecular_function
relationship: part_of GO:0050896 ! response to stimulus

[Term]
id: GO:0016458
name: gene silencing
namespace: biological_process
def: "Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression." [GOC:dos, GOC:dph, GOC:jid, GOC:tb]
comment: This is a rather broad grouping term.  While it was originally defined for long-term, heritable, epigenetic effects, short term effects on expression mediated by RNA are also frequently referred to as gene silencing, and are grouped under this class.
subset: goslim_pir
synonym: "long-term maintenance of gene inactivation" NARROW []
xref: Wikipedia:Gene_silencing
is_a: GO:0050789 ! regulation of biological process
relationship: negatively_regulates GO:0043170 ! macromolecule metabolic process
relationship: regulates GO:0043170 ! macromolecule metabolic process

[Term]
id: GO:0016469
name: proton-transporting two-sector ATPase complex
namespace: cellular_component
def: "A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of protons across a membrane. The complex comprises a membrane sector (F0, V0, or A0) that carries out proton transport and a cytoplasmic compartment sector (F1, V1, or A1) that catalyzes ATP synthesis or hydrolysis. Two major types have been characterized: V-type ATPases couple ATP hydrolysis to the transport of protons across a concentration gradient, whereas F-type ATPases, also known as ATP synthases, normally run in the reverse direction to utilize energy from a proton concentration or electrochemical gradient to synthesize ATP. A third type, A-type ATPases have been found in archaea, and are closely related to eukaryotic V-type ATPases but are reversible." [GOC:mah, ISBN:0716743663, PMID:16691483]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "hydrogen-transporting two-sector ATPase complex" EXACT []
synonym: "vacuolar hydrogen-transporting ATPase" RELATED []
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0016020 ! membrane

[Term]
id: GO:0016472
name: sodium ion-transporting two-sector ATPase complex
namespace: cellular_component
def: "A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of sodium ions across a membrane. The complex comprises a membrane sector (F0 or V0) that carries out ion transport and a cytoplasmic compartment sector (F1 or V1) that catalyzes ATP synthesis or hydrolysis." [GOC:mah, PMID:14656431]
subset: goslim_pir
synonym: "sodium-transporting two-sector ATPase complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0016020 ! membrane

[Term]
id: GO:0016491
name: oxidoreductase activity
namespace: molecular_function
def: "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC:go_curators]
comment: Note that enzymes of class EC:1.97.-.- should also be annotated to this term.
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_yeast
synonym: "oxidoreductase activity, acting on other substrates" NARROW []
synonym: "redox activity" EXACT []
xref: EC:1
xref: Reactome:REACT_102858 "Diiodinated tyrosine can be deiodinated, Mus musculus"
xref: Reactome:REACT_102973 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Canis familiaris"
xref: Reactome:REACT_103874 "Monoiodinated tyrosine can be deiodinated, Canis familiaris"
xref: Reactome:REACT_104604 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Danio rerio"
xref: Reactome:REACT_105062 "Monoiodinated tyrosine can be deiodinated, Danio rerio"
xref: Reactome:REACT_105121 "Monoiodinated tyrosine can be deiodinated, Caenorhabditis elegans"
xref: Reactome:REACT_106088 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Rattus norvegicus"
xref: Reactome:REACT_106276 "Monoiodinated tyrosine can be deiodinated, Rattus norvegicus"
xref: Reactome:REACT_107002 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Sus scrofa"
xref: Reactome:REACT_107467 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Rattus norvegicus"
xref: Reactome:REACT_108745 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Taeniopygia guttata"
xref: Reactome:REACT_109500 "Monoiodinated tyrosine can be deiodinated, Bos taurus"
xref: Reactome:REACT_110582 "Diiodinated tyrosine can be deiodinated, Rattus norvegicus"
xref: Reactome:REACT_115316 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Drosophila melanogaster"
xref: Reactome:REACT_15389 "Monoiodinated tyrosine can be deiodinated, Homo sapiens"
xref: Reactome:REACT_15410 "Diiodinated tyrosine can be deiodinated, Homo sapiens"
xref: Reactome:REACT_17006 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Homo sapiens"
xref: Reactome:REACT_17042 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Homo sapiens"
xref: Reactome:REACT_29212 "Diiodinated tyrosine can be deiodinated, Canis familiaris"
xref: Reactome:REACT_30160 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Mus musculus"
xref: Reactome:REACT_31762 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Gallus gallus"
xref: Reactome:REACT_32960 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Bos taurus"
xref: Reactome:REACT_34705 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Mus musculus"
xref: Reactome:REACT_44470 "Monoiodinated tyrosine can be deiodinated, Mus musculus"
xref: Reactome:REACT_78923 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Taeniopygia guttata"
xref: Reactome:REACT_84842 "Diiodinated tyrosine can be deiodinated, Gallus gallus"
xref: Reactome:REACT_86178 "Monoiodinated tyrosine can be deiodinated, Xenopus tropicalis"
xref: Reactome:REACT_88304 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Bos taurus"
xref: Reactome:REACT_89057 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Gallus gallus"
xref: Reactome:REACT_90394 "Diiodinated tyrosine can be deiodinated, Xenopus tropicalis"
xref: Reactome:REACT_91638 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Arabidopsis thaliana"
xref: Reactome:REACT_91952 "Monoiodinated tyrosine can be deiodinated, Gallus gallus"
xref: Reactome:REACT_92075 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Xenopus tropicalis"
xref: Reactome:REACT_92434 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Canis familiaris"
xref: Reactome:REACT_93539 "Diiodinated tyrosine can be deiodinated, Drosophila melanogaster"
xref: Reactome:REACT_93974 "Diiodinated tyrosine can be deiodinated, Taeniopygia guttata"
xref: Reactome:REACT_95169 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Danio rerio"
xref: Reactome:REACT_95558 "Monoiodinated tyrosine can be deiodinated, Sus scrofa"
xref: Reactome:REACT_95573 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Caenorhabditis elegans"
xref: Reactome:REACT_97234 "Diiodinated tyrosine can be deiodinated, Caenorhabditis elegans"
xref: Reactome:REACT_97568 "Diiodinated tyrosine can be deiodinated, Sus scrofa"
xref: Reactome:REACT_97851 "Diiodinated tyrosine can be deiodinated, Bos taurus"
xref: Reactome:REACT_98022 "Monoiodinated tyrosine can be deiodinated, Drosophila melanogaster"
xref: Reactome:REACT_99085 "palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Oryza sativa"
xref: Reactome:REACT_99794 "Diiodinated tyrosine can be deiodinated, Danio rerio"
xref: Reactome:REACT_99989 "Monoiodinated tyrosine can be deiodinated, Taeniopygia guttata"
is_a: GO:0003824 ! catalytic activity
relationship: part_of GO:0055114 ! oxidation-reduction process

[Term]
id: GO:0016530
name: metallochaperone activity
namespace: molecular_function
def: "Directly binding to and delivering metal ions to a target protein." [PMID:11739376]
subset: goslim_pir
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0016591
name: RNA polymerase II, holoenzyme
namespace: cellular_component
def: "A nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters." [GOC:jl, GOC:krc, PMID:16858867, Wikipedia:Rna_polymerase_ii]
subset: goslim_pir
synonym: "DNA-directed RNA polymerase II, holoenzyme" EXACT []
is_a: GO:0030880 ! RNA polymerase complex
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0016597
name: amino acid binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents." [GOC:ai]
subset: goslim_metagenomics
subset: goslim_pir
is_a: GO:0031406 ! carboxylic acid binding

[Term]
id: GO:0016610
name: nitrogenase complex
namespace: cellular_component
def: "An enzyme complex composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase is tetrameric with an alpha2-beta2 structure and nitrogenase reductase is a homodimer, and both are associated with metal ions, which differ between species. Both proteins are required for the enzyme activity of the complex, the formation of oxidized ferredoxin and ammonia from reduced ferredoxin and nitrogen." [EC:1.18.6.1, MetaCyc:CPLX-186, MetaCyc:CPLX-525]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[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_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
xref: EC:2
xref: Reactome:REACT_25050 "Molybdenum ion transfer onto molybdopterin, Homo sapiens"
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. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732]
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
xref: EC:3
xref: Reactome:REACT_110436 "Hydrolysis of phosphatidylcholine, Bos taurus"
xref: Reactome:REACT_111159 "Partial proteolysis of antigen in phagolysosomes, Homo sapiens"
xref: Reactome:REACT_15331 "Hydrolysis of phosphatidylcholine, Homo sapiens"
xref: Reactome:REACT_83734 "Hydrolysis of phosphatidylcholine, Danio rerio"
xref: Reactome:REACT_84047 "Hydrolysis of phosphatidylcholine, Xenopus tropicalis"
xref: Reactome:REACT_87959 "Hydrolysis of phosphatidylcholine, Gallus gallus"
xref: Reactome:REACT_88159 "Hydrolysis of phosphatidylcholine, Canis familiaris"
xref: Reactome:REACT_90118 "Hydrolysis of phosphatidylcholine, Mus musculus"
xref: Reactome:REACT_91045 "Hydrolysis of phosphatidylcholine, Taeniopygia guttata"
xref: Reactome:REACT_98572 "Hydrolysis of phosphatidylcholine, Rattus norvegicus"
is_a: GO:0003824 ! catalytic activity

[Term]
id: GO:0016829
name: lyase activity
namespace: molecular_function
def: "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC:4.-.-.-, ISBN:0198547684]
comment: Note that enzymes of class EC:4.99.-.- should also be annotated to this term.
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
synonym: "other lyase activity" NARROW []
xref: EC:4
is_a: GO:0003824 ! catalytic activity

[Term]
id: GO:0016853
name: isomerase activity
namespace: molecular_function
def: "Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5." [ISBN:0198506732]
comment: Note that enzymes of class EC:5.99.-.- should also be annotated to this term.
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
synonym: "other isomerase activity" NARROW []
xref: EC:5
is_a: GO:0003824 ! catalytic activity

[Term]
id: GO:0016874
name: ligase activity
namespace: molecular_function
def: "Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC:6, GOC:mah]
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_yeast
synonym: "synthetase activity" EXACT [GOC:jh2]
xref: EC:6
xref: Reactome:REACT_115603 "Ligation of DNA at sites of patch replacement, Gallus gallus"
xref: Reactome:REACT_116018 "Ligation of newly synthesized repair patch to incised DNA in GG-NER, Gallus gallus"
is_a: GO:0003824 ! catalytic activity

[Term]
id: GO:0016942
name: insulin-like growth factor binding protein complex
namespace: cellular_component
def: "A complex of proteins which includes the insulin-like growth factor (IGF) and a number of IGF-binding proteins. The complex plays a role in growth and development." [GOC:jl]
subset: goslim_pir
synonym: "IGF binding protein complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0005576 ! extracellular region

[Term]
id: GO:0017053
name: transcriptional repressor complex
namespace: cellular_component
def: "A protein complex that possesses activity that prevents or downregulates transcription." [GOC:mah]
subset: goslim_pir
synonym: "transcription factor inhibitor complex" EXACT [GOC:bhm]
is_a: GO:0032991 ! protein-containing complex

[Term]
id: GO:0017144
name: drug metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice." [GOC:cab2]
subset: goslim_chembl
subset: goslim_pir
synonym: "drug metabolism" EXACT []
xref: Reactome:REACT_100188 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Danio rerio"
xref: Reactome:REACT_106588 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Canis familiaris"
xref: Reactome:REACT_109592 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Taeniopygia guttata"
xref: Reactome:REACT_110347 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Gallus gallus"
xref: Reactome:REACT_163 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Homo sapiens"
xref: Reactome:REACT_54870 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Bos taurus"
xref: Reactome:REACT_85142 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Mus musculus"
xref: Reactome:REACT_88376 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Rattus norvegicus"
xref: Reactome:REACT_92052 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Sus scrofa"
xref: Wikipedia:Drug_metabolism
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0018904
name: ether metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving organic ethers, any anhydride of the general formula R1-O-R2, formed between two identical or nonidentical organic hydroxy compounds." [GOC:pr, ISBN:0198506732]
subset: goslim_pir
synonym: "ether metabolism" EXACT []
synonym: "organic ether metabolic process" EXACT []
synonym: "organic ether metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0018942
name: organometal metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving organometals, any metal-containing organic compound, especially one in which the metal atom is linked directly to one of more carbon atoms." [ISBN:0198506732]
subset: goslim_pir
synonym: "organometal metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0019012
name: virion
namespace: cellular_component
def: "The complete fully infectious extracellular virus particle." [ISBN:0781718325]
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
synonym: "complete virus particle" EXACT []
xref: Wikipedia:Virus
is_a: GO:0005575 ! cellular_component

[Term]
id: GO:0019213
name: deacetylase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule." [GOC:jl]
subset: goslim_pir
is_a: GO:0016787 ! hydrolase activity

[Term]
id: GO:0019239
name: deaminase activity
namespace: molecular_function
def: "Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3)." [GOC:jl]
subset: goslim_pir
is_a: GO:0016787 ! hydrolase activity

[Term]
id: GO:0019538
name: protein metabolic process
namespace: biological_process
alt_id: GO:0006411
alt_id: GO:0044268
def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma]
subset: goslim_agr
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
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:0006807 ! nitrogen compound metabolic process
is_a: GO:0043170 ! macromolecule metabolic process
is_a: GO:0044238 ! primary metabolic 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_aspergillus
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
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:0019787
name: ubiquitin-like protein transferase activity
namespace: molecular_function
alt_id: GO:0008639
alt_id: GO:0008640
def: "Catalysis of the transfer of a ubiquitin-like from one protein to another via the reaction X-ULP + Y --> Y-ULP + X, where both X-ULP and Y-ULP are covalent linkages. ULP represents a ubiquitin-like protein." [GOC:mah, GOC:rn, PMID:10806345, PMID:10884686]
subset: goslim_pir
synonym: "E2" RELATED []
synonym: "E3" RELATED [dph:GOC]
synonym: "small conjugating protein ligase activity" NARROW [GOC:dph]
synonym: "small conjugating protein transferase activity" EXACT [GOC:dph]
synonym: "small protein conjugating enzyme activity" NARROW []
synonym: "ubiquitin-like conjugating enzyme activity" NARROW []
synonym: "ubiquitin-like-protein ligase activity" NARROW []
xref: Reactome:REACT_75843 "RIP2 is K63 polyubiquitinated, Homo sapiens"
is_a: GO:0016740 ! transferase activity

[Term]
id: GO:0019814
name: immunoglobulin complex
namespace: cellular_component
def: "A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, GOC:jl, ISBN:0781765196]
comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
subset: goslim_pir
synonym: "antibody" NARROW []
is_a: GO:0032991 ! protein-containing complex

[Term]
id: GO:0019825
name: oxygen binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with oxygen (O2)." [GOC:jl]
subset: goslim_pir
subset: goslim_plant
synonym: "cytochrome P450" NARROW []
synonym: "cytochrome P450 activity" RELATED []
xref: Reactome:REACT_100179 "Cyclophosphamide is 4-hydroxylated by CYP2B6, Mus musculus"
xref: Reactome:REACT_100188 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Danio rerio"
xref: Reactome:REACT_100232 "CYP4B1 can 12-hydroxylate arachidonic acid, Xenopus tropicalis"
xref: Reactome:REACT_100276 "Dehalogenation of carbon tetrachloride to form a free radical, Mus musculus"
xref: Reactome:REACT_100352 "CYP2F1 dehydrogenates 3-methylindole, Sus scrofa"
xref: Reactome:REACT_100647 "N-atom dealkylation of caffeine, Bos taurus"
xref: Reactome:REACT_100686 "CYP4B1 can 12-hydroxylate arachidonic acid, Gallus gallus"
xref: Reactome:REACT_100861 "CYP4B1 can 12-hydroxylate arachidonic acid, Sus scrofa"
xref: Reactome:REACT_100981 "N-hydroxylation of 4-aminobiphenyl, Taeniopygia guttata"
xref: Reactome:REACT_101073 "N-atom dealkylation of caffeine, Taeniopygia guttata"
xref: Reactome:REACT_101109 "CYP1B1 4-hydroxylates estradiol-17beta, Canis familiaris"
xref: Reactome:REACT_101424 "MEOS oxidizes ethanol to acetaldehyde, Bos taurus"
xref: Reactome:REACT_101610 "CYP2C19 5-hydroxylates omeprazole, Rattus norvegicus"
xref: Reactome:REACT_101735 "CYP2C18 initiates bioactivation of phenytoin by 4-hydroxylation, Taeniopygia guttata"
xref: Reactome:REACT_102272 "CYP2C9 inactivates tolbutamide by 4methyl-hydroxylation, Bos taurus"
xref: Reactome:REACT_102377 "Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide, Sus scrofa"
xref: Reactome:REACT_102634 "Cyclophosphamide is 4-hydroxylated by CYP2B6, Sus scrofa"
xref: Reactome:REACT_102704 "CYP2C8 inactivates paclitaxel by 6alpha-hydroxylation, Mus musculus"
xref: Reactome:REACT_102736 "S-atom dealkylation of 6-methylmercaptopurine, Sus scrofa"
xref: Reactome:REACT_103035 "Ethylene is oxidized to Ethylene oxide by CYP1A1, Canis familiaris"
xref: Reactome:REACT_103579 "Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide, Rattus norvegicus"
xref: Reactome:REACT_103850 "CYP2C18 initiates bioactivation of phenytoin by 4-hydroxylation, Sus scrofa"
xref: Reactome:REACT_103936 "CYP4F12 hydroxylates arachidonic acid, Taeniopygia guttata"
xref: Reactome:REACT_104062 "Vinyl chloride is oxidized to 2-Chloroethylene oxide, Rattus norvegicus"
xref: Reactome:REACT_104186 "Cyclophosphamide is 4-hydroxylated by CYP2B6, Xenopus tropicalis"
xref: Reactome:REACT_104401 "CYP4B1 can 12-hydroxylate arachidonic acid, Danio rerio"
xref: Reactome:REACT_104682 "CYP4F12 hydroxylates arachidonic acid, Mus musculus"
xref: Reactome:REACT_104739 "Cyclophosphamide is 4-hydroxylated by CYP2B6, Danio rerio"
xref: Reactome:REACT_105445 "CYP3A4 can N-demethylate loperaminde, Drosophila melanogaster"
xref: Reactome:REACT_105726 "Benzene is hydroxylated to phenol, Taeniopygia guttata"
xref: Reactome:REACT_106173 "N-atom dealkylation of caffeine, Sus scrofa"
xref: Reactome:REACT_106332 "CYP2U1 can omega-hydroxylate arachidonate, Rattus norvegicus"
xref: Reactome:REACT_106588 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Canis familiaris"
xref: Reactome:REACT_106593 "CYP4F8 hydroxylates prostaglandin H2, Danio rerio"
xref: Reactome:REACT_106741 "CYP2C19 5-hydroxylates omeprazole, Mus musculus"
xref: Reactome:REACT_106777 "Cyclophosphamide is 4-hydroxylated by CYP2B6, Canis familiaris"
xref: Reactome:REACT_106979 "Ethylene is oxidized to Ethylene oxide by CYP1A1, Taeniopygia guttata"
xref: Reactome:REACT_107183 "CYP2U1 can omega-hydroxylate arachidonate, Canis familiaris"
xref: Reactome:REACT_107350 "CYP2C9 inactivates tolbutamide by 4methyl-hydroxylation, Taeniopygia guttata"
xref: Reactome:REACT_107408 "CYP2C19 5-hydroxylates omeprazole, Sus scrofa"
xref: Reactome:REACT_107478 "MEOS oxidizes ethanol to acetaldehyde, Danio rerio"
xref: Reactome:REACT_107548 "N-hydroxylation of 4-aminobiphenyl, Rattus norvegicus"
xref: Reactome:REACT_107861 "CYP2U1 can omega-hydroxylate arachidonate, Taeniopygia guttata"
xref: Reactome:REACT_107973 "CYP2C19 5-hydroxylates omeprazole, Gallus gallus"
xref: Reactome:REACT_108050 "Benzene is hydroxylated to phenol, Gallus gallus"
xref: Reactome:REACT_108219 "N-hydroxylation of 4-aminobiphenyl, Mus musculus"
xref: Reactome:REACT_108341 "N-atom dealkylation of caffeine, Mus musculus"
xref: Reactome:REACT_108385 "Dehalogenation of carbon tetrachloride to form a free radical, Danio rerio"
xref: Reactome:REACT_108547 "Vinyl chloride is oxidized to 2-Chloroethylene oxide, Danio rerio"
xref: Reactome:REACT_108912 "Benzene is hydroxylated to phenol, Canis familiaris"
xref: Reactome:REACT_108924 "Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide, Gallus gallus"
xref: Reactome:REACT_109005 "CYP2F1 dehydrogenates 3-methylindole, Danio rerio"
xref: Reactome:REACT_109209 "MEOS oxidizes ethanol to acetaldehyde, Gallus gallus"
xref: Reactome:REACT_109592 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Taeniopygia guttata"
xref: Reactome:REACT_109788 "CYP2C18 initiates bioactivation of phenytoin by 4-hydroxylation, Rattus norvegicus"
xref: Reactome:REACT_110347 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Gallus gallus"
xref: Reactome:REACT_110759 "CYP3A5 oxidises aflatoxin B1 to aflatoxin-8,9-oxide, Mus musculus"
xref: Reactome:REACT_112032 "CYP3A4 can N-demethylate loperaminde, Taeniopygia guttata"
xref: Reactome:REACT_112331 "S-atom dealkylation of 6-methylmercaptopurine, Danio rerio"
xref: Reactome:REACT_112347 "N-atom dealkylation of caffeine, Danio rerio"
xref: Reactome:REACT_112584 "S-atom dealkylation of 6-methylmercaptopurine, Gallus gallus"
xref: Reactome:REACT_112653 "Ethylene is oxidized to Ethylene oxide by CYP1A1, Gallus gallus"
xref: Reactome:REACT_112751 "CYP1B1 4-hydroxylates estradiol-17beta, Danio rerio"
xref: Reactome:REACT_112900 "N-atom dealkylation of caffeine, Gallus gallus"
xref: Reactome:REACT_113220 "CYP3A5 oxidises aflatoxin B1 to aflatoxin-8,9-oxide, Taeniopygia guttata"
xref: Reactome:REACT_113292 "N-hydroxylation of 4-aminobiphenyl, Danio rerio"
xref: Reactome:REACT_113841 "Ethylene is oxidized to Ethylene oxide by CYP1A1, Danio rerio"
xref: Reactome:REACT_114039 "N-hydroxylation of 4-aminobiphenyl, Gallus gallus"
xref: Reactome:REACT_114317 "CYP3A7 can 6beta-hydroxylate testosterone, Taeniopygia guttata"
xref: Reactome:REACT_1165 "N-atom dealkylation of caffeine, Homo sapiens"
xref: Reactome:REACT_122 "Dehalogenation of carbon tetrachloride to form a free radical, Homo sapiens"
xref: Reactome:REACT_13412 "CYP2U1 can omega-hydroxylate arachidonate, Homo sapiens"
xref: Reactome:REACT_13485 "CYP4F12 hydroxylates arachidonic acid, Homo sapiens"
xref: Reactome:REACT_13515 "Cyclophosphamide is 4-hydroxylated by CYP2B6, Homo sapiens"
xref: Reactome:REACT_13607 "CYP2C9 inactivates tolbutamide by 4methyl-hydroxylation, Homo sapiens"
xref: Reactome:REACT_13614 "CYP4F3 omega-hydroxylates leukotriene B4, thus inactivating it, Homo sapiens"
xref: Reactome:REACT_13615 "CYP4B1 can 12-hydroxylate arachidonic acid, Homo sapiens"
xref: Reactome:REACT_13624 "CYP4F8 hydroxylates prostaglandin H2, Homo sapiens"
xref: Reactome:REACT_13651 "CYP2C8 inactivates paclitaxel by 6alpha-hydroxylation, Homo sapiens"
xref: Reactome:REACT_13668 "CYP1B1 4-hydroxylates estradiol-17beta, Homo sapiens"
xref: Reactome:REACT_13670 "CYP3A7 can 6beta-hydroxylate testosterone, Homo sapiens"
xref: Reactome:REACT_13671 "CYP2F1 dehydrogenates 3-methylindole, Homo sapiens"
xref: Reactome:REACT_13729 "CYP2C18 initiates bioactivation of phenytoin by 4-hydroxylation, Homo sapiens"
xref: Reactome:REACT_13734 "CYP3A5 oxidises aflatoxin B1 to aflatoxin-8,9-oxide, Homo sapiens"
xref: Reactome:REACT_13738 "CYP4F2 omega-hydroxylates leukotriene B4, thus inactivating it, Homo sapiens"
xref: Reactome:REACT_13761 "CYP2C19 5-hydroxylates omeprazole, Homo sapiens"
xref: Reactome:REACT_13765 "CYP3A4 can N-demethylate loperaminde, Homo sapiens"
xref: Reactome:REACT_1437 "N-hydroxylation of 4-aminobiphenyl, Homo sapiens"
xref: Reactome:REACT_1447 "Ethylene is oxidized to Ethylene oxide by CYP1A1, Homo sapiens"
xref: Reactome:REACT_163 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Homo sapiens"
xref: Reactome:REACT_1750 "Vinyl chloride is oxidized to 2-Chloroethylene oxide, Homo sapiens"
xref: Reactome:REACT_1995 "S-atom dealkylation of 6-methylmercaptopurine, Homo sapiens"
xref: Reactome:REACT_228 "Benzene is hydroxylated to phenol, Homo sapiens"
xref: Reactome:REACT_28287 "CYP4B1 can 12-hydroxylate arachidonic acid, Rattus norvegicus"
xref: Reactome:REACT_28569 "Cyclophosphamide is 4-hydroxylated by CYP2B6, Rattus norvegicus"
xref: Reactome:REACT_29648 "CYP4F2 omega-hydroxylates leukotriene B4, thus inactivating it, Danio rerio"
xref: Reactome:REACT_30083 "O-atom dealkylation of dextromethorphan, Taeniopygia guttata"
xref: Reactome:REACT_30413 "S-atom dealkylation of 6-methylmercaptopurine, Taeniopygia guttata"
xref: Reactome:REACT_305 "Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide, Homo sapiens"
xref: Reactome:REACT_30596 "N-atom dealkylation of caffeine, Xenopus tropicalis"
xref: Reactome:REACT_30757 "CYP3A5 oxidises aflatoxin B1 to aflatoxin-8,9-oxide, Danio rerio"
xref: Reactome:REACT_31096 "CYP3A7 can 6beta-hydroxylate testosterone, Drosophila melanogaster"
xref: Reactome:REACT_31117 "CYP2C9 inactivates tolbutamide by 4methyl-hydroxylation, Sus scrofa"
xref: Reactome:REACT_31871 "Benzene is hydroxylated to phenol, Sus scrofa"
xref: Reactome:REACT_323 "O-atom dealkylation of dextromethorphan, Homo sapiens"
xref: Reactome:REACT_32309 "CYP4A11 omega-hydroxylates laurate, Danio rerio"
xref: Reactome:REACT_32769 "Dehalogenation of carbon tetrachloride to form a free radical, Sus scrofa"
xref: Reactome:REACT_32803 "Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide, Mus musculus"
xref: Reactome:REACT_33304 "CYP4F3 omega-hydroxylates leukotriene B4, thus inactivating it, Bos taurus"
xref: Reactome:REACT_33556 "CYP2U1 can omega-hydroxylate arachidonate, Bos taurus"
xref: Reactome:REACT_33790 "Ethylene is oxidized to Ethylene oxide by CYP1A1, Rattus norvegicus"
xref: Reactome:REACT_33813 "CYP2C9 inactivates tolbutamide by 4methyl-hydroxylation, Rattus norvegicus"
xref: Reactome:REACT_33859 "Ethylene is oxidized to Ethylene oxide by CYP1A1, Sus scrofa"
xref: Reactome:REACT_33898 "Vinyl chloride is oxidized to 2-Chloroethylene oxide, Mus musculus"
xref: Reactome:REACT_33922 "CYP1B1 4-hydroxylates estradiol-17beta, Xenopus tropicalis"
xref: Reactome:REACT_34265 "CYP2C18 initiates bioactivation of phenytoin by 4-hydroxylation, Danio rerio"
xref: Reactome:REACT_34271 "Benzene is hydroxylated to phenol, Mus musculus"
xref: Reactome:REACT_34597 "Dehalogenation of carbon tetrachloride to form a free radical, Canis familiaris"
xref: Reactome:REACT_44575 "O-atom dealkylation of dextromethorphan, Rattus norvegicus"
xref: Reactome:REACT_49029 "Ethylene is oxidized to Ethylene oxide by CYP1A1, Bos taurus"
xref: Reactome:REACT_499 "MEOS oxidizes ethanol to acetaldehyde, Homo sapiens"
xref: Reactome:REACT_54870 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Bos taurus"
xref: Reactome:REACT_58290 "CYP1B1 4-hydroxylates estradiol-17beta, Mus musculus"
xref: Reactome:REACT_58734 "CYP4A11 omega-hydroxylates laurate, Bos taurus"
xref: Reactome:REACT_75504 "Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide, Bos taurus"
xref: Reactome:REACT_77501 "CYP4F2 omega-hydroxylates leukotriene B4, thus inactivating it, Mus musculus"
xref: Reactome:REACT_77895 "Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide, Taeniopygia guttata"
xref: Reactome:REACT_77958 "O-atom dealkylation of dextromethorphan, Sus scrofa"
xref: Reactome:REACT_78242 "Dehalogenation of carbon tetrachloride to form a free radical, Bos taurus"
xref: Reactome:REACT_78392 "N-hydroxylation of 4-aminobiphenyl, Canis familiaris"
xref: Reactome:REACT_78439 "CYP2C18 initiates bioactivation of phenytoin by 4-hydroxylation, Mus musculus"
xref: Reactome:REACT_79087 "N-hydroxylation of 4-aminobiphenyl, Bos taurus"
xref: Reactome:REACT_79814 "Benzene is hydroxylated to phenol, Rattus norvegicus"
xref: Reactome:REACT_80448 "CYP2C8 inactivates paclitaxel by 6alpha-hydroxylation, Taeniopygia guttata"
xref: Reactome:REACT_80600 "Vinyl chloride is oxidized to 2-Chloroethylene oxide, Gallus gallus"
xref: Reactome:REACT_80785 "MEOS oxidizes ethanol to acetaldehyde, Canis familiaris"
xref: Reactome:REACT_81228 "CYP2U1 can omega-hydroxylate arachidonate, Mus musculus"
xref: Reactome:REACT_81599 "Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide, Canis familiaris"
xref: Reactome:REACT_81769 "S-atom dealkylation of 6-methylmercaptopurine, Canis familiaris"
xref: Reactome:REACT_82090 "CYP2C8 inactivates paclitaxel by 6alpha-hydroxylation, Gallus gallus"
xref: Reactome:REACT_82546 "CYP4F8 hydroxylates prostaglandin H2, Xenopus tropicalis"
xref: Reactome:REACT_82713 "CYP2C9 inactivates tolbutamide by 4methyl-hydroxylation, Gallus gallus"
xref: Reactome:REACT_82917 "CYP4A11 omega-hydroxylates laurate, Sus scrofa"
xref: Reactome:REACT_83225 "CYP1B1 4-hydroxylates estradiol-17beta, Rattus norvegicus"
xref: Reactome:REACT_83236 "CYP2C8 inactivates paclitaxel by 6alpha-hydroxylation, Danio rerio"
xref: Reactome:REACT_83558 "N-atom dealkylation of caffeine, Canis familiaris"
xref: Reactome:REACT_83900 "Dehalogenation of carbon tetrachloride to form a free radical, Rattus norvegicus"
xref: Reactome:REACT_83932 "O-atom dealkylation of dextromethorphan, Xenopus tropicalis"
xref: Reactome:REACT_83946 "Vinyl chloride is oxidized to 2-Chloroethylene oxide, Bos taurus"
xref: Reactome:REACT_83985 "MEOS oxidizes ethanol to acetaldehyde, Rattus norvegicus"
xref: Reactome:REACT_84011 "CYP2C18 initiates bioactivation of phenytoin by 4-hydroxylation, Bos taurus"
xref: Reactome:REACT_84240 "CYP4A11 omega-hydroxylates laurate, Mus musculus"
xref: Reactome:REACT_84540 "CYP3A5 oxidises aflatoxin B1 to aflatoxin-8,9-oxide, Gallus gallus"
xref: Reactome:REACT_84651 "Ethylene is oxidized to Ethylene oxide by CYP1A1, Mus musculus"
xref: Reactome:REACT_84804 "CYP4B1 can 12-hydroxylate arachidonic acid, Mus musculus"
xref: Reactome:REACT_85142 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Mus musculus"
xref: Reactome:REACT_85617 "CYP2C19 5-hydroxylates omeprazole, Danio rerio"
xref: Reactome:REACT_85789 "CYP3A7 can 6beta-hydroxylate testosterone, Danio rerio"
xref: Reactome:REACT_86584 "CYP2F1 dehydrogenates 3-methylindole, Canis familiaris"
xref: Reactome:REACT_86609 "Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide, Danio rerio"
xref: Reactome:REACT_87066 "CYP2U1 can omega-hydroxylate arachidonate, Xenopus tropicalis"
xref: Reactome:REACT_87553 "CYP1B1 4-hydroxylates estradiol-17beta, Taeniopygia guttata"
xref: Reactome:REACT_87557 "MEOS oxidizes ethanol to acetaldehyde, Taeniopygia guttata"
xref: Reactome:REACT_87585 "CYP2C9 inactivates tolbutamide by 4methyl-hydroxylation, Mus musculus"
xref: Reactome:REACT_88131 "CYP4B1 can 12-hydroxylate arachidonic acid, Bos taurus"
xref: Reactome:REACT_88365 "S-atom dealkylation of 6-methylmercaptopurine, Xenopus tropicalis"
xref: Reactome:REACT_88376 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Rattus norvegicus"
xref: Reactome:REACT_88388 "CYP1B1 4-hydroxylates estradiol-17beta, Sus scrofa"
xref: Reactome:REACT_88780 "N-hydroxylation of 4-aminobiphenyl, Xenopus tropicalis"
xref: Reactome:REACT_89077 "Benzene is hydroxylated to phenol, Bos taurus"
xref: Reactome:REACT_89132 "Ethylene is oxidized to Ethylene oxide by CYP1A1, Xenopus tropicalis"
xref: Reactome:REACT_89288 "MEOS oxidizes ethanol to acetaldehyde, Sus scrofa"
xref: Reactome:REACT_89918 "CYP4A11 omega-hydroxylates laurate, Xenopus tropicalis"
xref: Reactome:REACT_90187 "Cyclophosphamide is 4-hydroxylated by CYP2B6, Bos taurus"
xref: Reactome:REACT_90287 "CYP4F2 omega-hydroxylates leukotriene B4, thus inactivating it, Xenopus tropicalis"
xref: Reactome:REACT_90452 "CYP2C19 5-hydroxylates omeprazole, Taeniopygia guttata"
xref: Reactome:REACT_90650 "N-atom dealkylation of caffeine, Rattus norvegicus"
xref: Reactome:REACT_90911 "CYP4F8 hydroxylates prostaglandin H2, Mus musculus"
xref: Reactome:REACT_91080 "CYP3A4 can N-demethylate loperaminde, Danio rerio"
xref: Reactome:REACT_91491 "CYP3A4 can N-demethylate loperaminde, Gallus gallus"
xref: Reactome:REACT_91742 "CYP4F3 omega-hydroxylates leukotriene B4, thus inactivating it, Rattus norvegicus"
xref: Reactome:REACT_91815 "O-atom dealkylation of dextromethorphan, Gallus gallus"
xref: Reactome:REACT_92052 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI), Sus scrofa"
xref: Reactome:REACT_92115 "N-hydroxylation of 4-aminobiphenyl, Sus scrofa"
xref: Reactome:REACT_92163 "CYP4A11 omega-hydroxylates laurate, Gallus gallus"
xref: Reactome:REACT_92564 "O-atom dealkylation of dextromethorphan, Mus musculus"
xref: Reactome:REACT_92660 "CYP3A7 can 6beta-hydroxylate testosterone, Mus musculus"
xref: Reactome:REACT_92678 "CYP4F2 omega-hydroxylates leukotriene B4, thus inactivating it, Taeniopygia guttata"
xref: Reactome:REACT_92793 "CYP2U1 can omega-hydroxylate arachidonate, Sus scrofa"
xref: Reactome:REACT_92798 "CYP2C8 inactivates paclitaxel by 6alpha-hydroxylation, Bos taurus"
xref: Reactome:REACT_93025 "CYP3A5 oxidises aflatoxin B1 to aflatoxin-8,9-oxide, Drosophila melanogaster"
xref: Reactome:REACT_93071 "CYP2F1 dehydrogenates 3-methylindole, Rattus norvegicus"
xref: Reactome:REACT_93076 "Vinyl chloride is oxidized to 2-Chloroethylene oxide, Sus scrofa"
xref: Reactome:REACT_93786 "CYP3A4 can N-demethylate loperaminde, Mus musculus"
xref: Reactome:REACT_94252 "CYP2F1 dehydrogenates 3-methylindole, Mus musculus"
xref: Reactome:REACT_94389 "CYP1B1 4-hydroxylates estradiol-17beta, Gallus gallus"
xref: Reactome:REACT_95074 "CYP2U1 can omega-hydroxylate arachidonate, Danio rerio"
xref: Reactome:REACT_95175 "CYP4B1 can 12-hydroxylate arachidonic acid, Canis familiaris"
xref: Reactome:REACT_95629 "CYP2F1 dehydrogenates 3-methylindole, Xenopus tropicalis"
xref: Reactome:REACT_95768 "CYP4F8 hydroxylates prostaglandin H2, Taeniopygia guttata"
xref: Reactome:REACT_95891 "O-atom dealkylation of dextromethorphan, Canis familiaris"
xref: Reactome:REACT_96007 "CYP2C9 inactivates tolbutamide by 4methyl-hydroxylation, Danio rerio"
xref: Reactome:REACT_96630 "O-atom dealkylation of dextromethorphan, Bos taurus"
xref: Reactome:REACT_97001 "Vinyl chloride is oxidized to 2-Chloroethylene oxide, Canis familiaris"
xref: Reactome:REACT_97031 "S-atom dealkylation of 6-methylmercaptopurine, Mus musculus"
xref: Reactome:REACT_97724 "S-atom dealkylation of 6-methylmercaptopurine, Bos taurus"
xref: Reactome:REACT_97732 "Benzene is hydroxylated to phenol, Danio rerio"
xref: Reactome:REACT_97964 "CYP4F12 hydroxylates arachidonic acid, Xenopus tropicalis"
xref: Reactome:REACT_97980 "CYP4F12 hydroxylates arachidonic acid, Danio rerio"
xref: Reactome:REACT_98 "CYP4A11 omega-hydroxylates laurate, Homo sapiens"
xref: Reactome:REACT_98236 "CYP1B1 4-hydroxylates estradiol-17beta, Bos taurus"
xref: Reactome:REACT_98427 "CYP2C19 5-hydroxylates omeprazole, Bos taurus"
xref: Reactome:REACT_98774 "CYP2C8 inactivates paclitaxel by 6alpha-hydroxylation, Sus scrofa"
xref: Reactome:REACT_98874 "MEOS oxidizes ethanol to acetaldehyde, Mus musculus"
xref: Reactome:REACT_98906 "S-atom dealkylation of 6-methylmercaptopurine, Rattus norvegicus"
xref: Reactome:REACT_98989 "CYP2C18 initiates bioactivation of phenytoin by 4-hydroxylation, Gallus gallus"
xref: Reactome:REACT_99056 "CYP3A7 can 6beta-hydroxylate testosterone, Gallus gallus"
xref: Reactome:REACT_99083 "CYP2C8 inactivates paclitaxel by 6alpha-hydroxylation, Rattus norvegicus"
xref: Reactome:REACT_99093 "Dehalogenation of carbon tetrachloride to form a free radical, Gallus gallus"
xref: Reactome:REACT_99244 "Vinyl chloride is oxidized to 2-Chloroethylene oxide, Taeniopygia guttata"
xref: Reactome:REACT_99362 "Dehalogenation of carbon tetrachloride to form a free radical, Taeniopygia guttata"
xref: Reactome:REACT_99726 "CYP4A11 omega-hydroxylates laurate, Canis familiaris"
is_a: GO:0008144 ! drug binding

[Term]
id: GO:0019840
name: isoprenoid binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [GOC:jl]
subset: goslim_pir
is_a: GO:0008289 ! lipid binding

[Term]
id: GO:0019842
name: vitamin binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body." [GOC:ai]
subset: goslim_metagenomics
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0020015
name: glycosome
namespace: cellular_component
def: "A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis." [GOC:mb]
subset: goslim_pir
xref: Wikipedia:Glycosome
is_a: GO:0042579 ! microbody

[Term]
id: GO:0020022
name: acidocalcisome
namespace: cellular_component
def: "An electron-dense acidic membrane-bounded organelle which contains a matrix of pyrophosphate and polyphosphates with bound calcium and other cations." [GOC:mb]
subset: goslim_pir
synonym: "metachromatic granule" EXACT [PMID:15738951]
synonym: "polyphosphate vacuole" RELATED [PMID:15738951]
synonym: "volutin granule" EXACT [PMID:15738951]
is_a: GO:0043231 ! intracellular membrane-bounded organelle
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0022406
name: membrane docking
namespace: biological_process
def: "The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere." [GOC:isa_complete, PMID:27875684]
subset: goslim_pir
synonym: "membrane docking" EXACT []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0022411
name: cellular component disassembly
namespace: biological_process
alt_id: GO:0071845
def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete]
subset: goslim_pir
synonym: "cell structure disassembly" EXACT []
synonym: "cellular component disassembly at cellular level" EXACT []
is_a: GO:0016043 ! cellular component organization

[Term]
id: GO:0022607
name: cellular component assembly
namespace: biological_process
alt_id: GO:0071844
def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
synonym: "cell structure assembly" EXACT []
synonym: "cellular component assembly at cellular level" EXACT []
is_a: GO:0016043 ! cellular component organization
relationship: part_of GO:0044085 ! cellular component biogenesis

[Term]
id: GO:0022610
name: biological adhesion
namespace: biological_process
def: "The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions." [GOC:isa_complete]
subset: goslim_pir
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0022900
name: electron transport chain
namespace: biological_process
def: "A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient." [GOC:mtg_electron_transport]
subset: goslim_pir
xref: Wikipedia:Electron_transport_chain
is_a: GO:0006091 ! generation of precursor metabolites and energy
is_a: GO:0055114 ! oxidation-reduction process

[Term]
id: GO:0030076
name: light-harvesting complex
namespace: cellular_component
def: "A protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center." [GOC:lr]
subset: goslim_pir
synonym: "antenna complex" RELATED []
xref: Wikipedia:Light-harvesting_complex
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0030112
name: glycocalyx
namespace: cellular_component
def: "A viscous, carbohydrate rich layer at the outermost periphery of a cell." [GOC:mlg, ISBN:0815316208]
subset: goslim_pir
synonym: "cell capsule" EXACT [VZ:3896]
xref: Wikipedia:Glycocalyx
is_a: GO:0030312 ! external encapsulating structure
relationship: part_of GO:0030313 ! cell envelope

[Term]
id: GO:0030115
name: S-layer
namespace: cellular_component
def: "A crystalline protein layer surrounding some bacteria." [GOC:mlg, ISBN:0815108893]
subset: goslim_pir
xref: Wikipedia:S-layer
is_a: GO:0030312 ! external encapsulating structure

[Term]
id: GO:0030119
name: AP-type membrane coat adaptor complex
namespace: cellular_component
def: "Any of several heterotetrameric complexes that link clathrin (or another coat-forming molecule, as hypothesized for AP-3 and AP-4) to a membrane surface; they are found on coated pits and coated vesicles, and mediate sorting of cargo proteins into vesicles. Each AP complex contains two large (a beta and one of either an alpha, gamma, delta, or epsilon) subunits (110-130 kDa), a medium (mu) subunit (approximately 50 kDa), and a small (sigma) subunit (15-20 kDa)." [GOC:mah, PMID:10611976, PMID:15473838]
subset: goslim_pir
synonym: "clathrin adaptor" RELATED []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm
relationship: part_of GO:0016020 ! membrane
relationship: part_of GO:0032991 ! protein-containing complex

[Term]
id: GO:0030175
name: filopodium
namespace: cellular_component
alt_id: GO:0030028
def: "Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft." [GOC:mah, GOC:pr, ISBN:0815316194]
comment: A filopodium may be approximately 0.1 um wide, 5-10 um long, and up to 50 um long in axon growth cones; contain a loose bundle of about 20 actin filaments oriented with their plus ends pointing outward. Note that filopodia on dendritic shafts are distinct from other types of filopodia (even those found in dendritic growth cones) and may react differently to stimuli, as shown in PMID:12904473.
subset: goslim_pir
xref: NIF_Subcellular:sao-1046371754
xref: Wikipedia:Filopodia
is_a: GO:0042995 ! cell projection
relationship: has_part GO:0016020 ! membrane
relationship: has_part GO:0044464 ! cell part

[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: GO:0030234 is reserved for cases when the regulator directly interacts with the enzyme. When regulation of enzyme activity is achieved without enzyme binding, or when the mechanism of regulation is unknown, instead annotate to 'regulation of catalytic activity ; GO:0050790'.
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
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: part_of GO:0065009 ! regulation of molecular function
relationship: regulates GO:0003824 ! catalytic activity

[Term]
id: GO:0030246
name: carbohydrate binding
namespace: molecular_function
alt_id: GO:0005529
def: "Interacting selectively and non-covalently with any 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." [CHEBI:16646, GOC:mah]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
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_generic
subset: goslim_pir
subset: goslim_plant
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0030313
name: cell envelope
namespace: cellular_component
def: "An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present." [GOC:ds, GOC:mlg, http://pathmicro.med.sc.edu/fox/cell_envelope.htm]
subset: goslim_pir
xref: Wikipedia:Cell_envelope
is_a: GO:0044464 ! cell part
relationship: has_part GO:0016020 ! membrane
relationship: has_part GO:0044464 ! cell part

[Term]
id: GO:0030427
name: site of polarized growth
namespace: cellular_component
alt_id: GO:0000134
alt_id: GO:0030483
def: "Any part of a cell where non-isotropic growth takes place." [GOC:mah]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
subset: goslim_yeast
is_a: GO:0044464 ! cell part

[Term]
id: GO:0030428
name: cell septum
namespace: cellular_component
def: "A structure composed of peptidoglycan and often chitin in addition to other materials. It usually forms perpendicular to the long axis of a cell or hypha and grows centripetally from the cell wall to the center of the cell and often functions in the compartmentalization of a cell into two daughter cells." [GOC:clt, ISBN:0471940526]
subset: goslim_pir
synonym: "cross wall" EXACT []
synonym: "septum" BROAD []
is_a: GO:0044464 ! cell part

[Term]
id: GO:0030431
name: sleep
namespace: biological_process
def: "Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain." [ISBN:0192800981]
subset: goslim_pir
synonym: "diapause" RELATED []
synonym: "dormancy" RELATED []
synonym: "lethargus" RELATED []
xref: Wikipedia:Sleep
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0030496
name: midbody
namespace: cellular_component
def: "A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis." [ISBN:0815316194]
subset: goslim_pir
xref: Wikipedia:Midbody_(cell_biology)
is_a: GO:0044464 ! cell part

[Term]
id: GO:0030532
name: small nuclear ribonucleoprotein complex
namespace: cellular_component
def: "A complex composed of RNA of the small nuclear RNA (snRNA) class and protein, found in the nucleus of a eukaryotic cell. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP or U4/U6 snRNP. Many, but not all, of these complexes are involved in splicing of nuclear mRNAs." [GOC:krc, GOC:mah, ISBN:0879695897]
subset: goslim_pir
synonym: "small nuclear ribonucleoprotein" EXACT []
synonym: "snRNP" EXACT []
xref: Wikipedia:SnRNP
is_a: GO:0044464 ! cell part
is_a: GO:1990904 ! ribonucleoprotein complex
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0030677
name: ribonuclease P complex
namespace: cellular_component
def: "A ribonucleoprotein complex that catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs." [GOC:mah, PMID:12045094]
comment: Note that chloroplasts possess a complex that is called 'RNase P' because it catalyzes pre-tRNA cleavage, but the chloroplast complex appears not to contain RNA.
subset: goslim_pir
synonym: "RNase P complex" EXACT []
is_a: GO:1990904 ! ribonucleoprotein complex

[Term]
id: GO:0030684
name: preribosome
namespace: cellular_component
def: "Any complex of pre-rRNAs, ribosomal proteins, and associated proteins formed during ribosome biogenesis." [PMID:10567516]
subset: goslim_pir
is_a: GO:1990904 ! ribonucleoprotein complex

[Term]
id: GO:0030689
name: Noc complex
namespace: cellular_component
def: "Any of several heterodimers containing one or two Noc proteins, associated with preribosomal complexes; involved in ribosome biogenesis." [PMID:12446671]
comment: Noc complexes exhibit a dynamic intranuclear location; consider also annotating to 'nucleolus ; GO:0005730' and/or 'nucleoplasm ; GO:0005654'. Note that the definition uses Saccharomyces gene product names because this complex has only been described in Saccharomyces cerevisiae and no other names have yet arisen; the term nevertheless can be used for analogous complexes in other eukaryotes, and the definition can be changed if better wording is found.
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0030880
name: RNA polymerase complex
namespace: cellular_component
def: "Any complex that possesses RNA polymerase activity; generally comprises a catalytic subunit and one or more additional subunits." [GOC:mah]
subset: goslim_pir
synonym: "multisubunit RNA polymerase" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0030894
name: replisome
namespace: cellular_component
def: "A multi-component enzymatic machine at the replication fork which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins." [GOC:mah, GOC:vw]
subset: goslim_pir
synonym: "DNA synthesome complex" RELATED [CORUM:1001]
synonym: "RC complex" RELATED [CORUM:309, PMID:12006500]
synonym: "replication-competent complex" RELATED [CORUM:309, PMID:12006500]
xref: Wikipedia:Replisome
is_a: GO:0032993 ! protein-DNA complex
is_a: GO:0044464 ! cell part
relationship: has_part GO:0033202 ! DNA helicase complex
relationship: has_part GO:0042575 ! DNA polymerase complex
relationship: part_of GO:0005694 ! chromosome

[Term]
id: GO:0030904
name: retromer complex
namespace: cellular_component
def: "A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35." [GOC:bf, PMID:26220253, PMID:27385586, PMID:9700157]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0016020 ! membrane
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0030929
name: ADPG pyrophosphorylase complex
namespace: cellular_component
def: "Complex that possesses ADPG pyrophosphorylase activity. In all organisms where it has been found, the complex is a tetramer. In bacteria, it is a homotetramer. In plants, the complex is a heterotetramer composed small and large subunits." [GOC:tb, PMID:9680965]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0030964
name: NADH dehydrogenase complex
namespace: cellular_component
alt_id: GO:0030025
alt_id: GO:0030966
alt_id: GO:0031675
alt_id: GO:0031677
alt_id: GO:0031678
alt_id: GO:0045280
def: "An integral membrane complex that possesses NADH oxidoreductase activity. The complex is one of the components of the electron transport chain. It catalyzes the transfer of a pair of electrons from NADH to a quinone." [GOC:mah]
comment: Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function possessed by this complex is represented by the molecular function term 'NADH dehydrogenase (quinone) activity ; GO:0050136'.
subset: goslim_pir
synonym: "Complex I" EXACT []
synonym: "NADH dehydrogenase complex (plastoquinone)" NARROW []
synonym: "NADH dehydrogenase complex (quinone)" NARROW []
synonym: "NADH dehydrogenase complex (ubiquinone)" NARROW []
synonym: "NADH:plastoquinone reductase complex" NARROW []
synonym: "plastid NADH dehydrogenase complex (plastoquinone)" NARROW []
xref: Wikipedia:NADH_dehydrogenase
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0016020 ! membrane

[Term]
id: GO:0030990
name: intraciliary transport particle
namespace: cellular_component
def: "A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules." [GOC:cilia, GOC:kmv, PMID:14570576, PMID:22118932, PMID:23945166]
comment: Note that we deem cilia and microtubule-based flagella to be equivalent.
subset: goslim_pir
synonym: "IFT complex" RELATED []
synonym: "intraflagellar transport complex" EXACT []
synonym: "intraflagellar transport particle" EXACT []
is_a: GO:0032991 ! protein-containing complex

[Term]
id: GO:0031012
name: extracellular matrix
namespace: cellular_component
alt_id: GO:0005578
def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GOC:BHF, GOC:mah, GOC:rph, NIF_Subcellular:nlx_subcell_20090513, PMID:21123617, PMID:28089324]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
synonym: "proteinaceous extracellular matrix" EXACT []
xref: NIF_Subcellular:nlx_subcell_20090513
xref: Wikipedia:Extracellular_matrix
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005576 ! extracellular region

[Term]
id: GO:0031023
name: microtubule organizing center organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microtubule organizing center, a structure from which microtubules grow." [GOC:dph, GOC:jl, GOC:mah]
subset: goslim_pir
synonym: "microtubule organising center organisation" EXACT [GOC:curators]
synonym: "microtubule organizing center organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0016043 ! cellular component organization
relationship: part_of GO:0006996 ! organelle organization

[Term]
id: GO:0031026
name: glutamate synthase complex
namespace: cellular_component
def: "A complex that possesses glutamate synthase activity." [GOC:mah]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0031049
name: programmed DNA elimination
namespace: biological_process
def: "The DNA metabolic process in which micronuclear-limited sequences, internal eliminated sequences (IES) and breakage eliminated sequences (BES) are removed from the developing macronucleus (anlage) of a ciliate." [GOC:mah, GOC:ns]
subset: goslim_pir
is_a: GO:0006259 ! DNA metabolic process

[Term]
id: GO:0031074
name: nucleocytoplasmic transport complex
namespace: cellular_component
def: "Any complex that acts to move proteins or RNAs into or out of the nucleus through nuclear pores." [GOC:mah]
subset: gocheck_do_not_annotate
subset: goslim_pir
synonym: "nucleocytoplasmic shuttling complex" NARROW []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0031082
name: BLOC complex
namespace: cellular_component
def: "Any of several protein complexes required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes, platelet dense granules, and other related organelles; acronym for biogenesis of lysosomal-related organelles complex." [PMID:15102850, PMID:15261680]
subset: goslim_pir
synonym: "BLOC-1 related complex" EXACT [PMID:25898167]
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0031094
name: platelet dense tubular network
namespace: cellular_component
def: "A network of membrane-bounded compartments found in blood platelets, where they regulate platelet activation by sequestering or releasing calcium. The dense tubular network exists as thin elongated membranes in resting platelets, and undergoes a major ultrastructural change, to a rounded vesicular form, upon addition of thrombin." [PMID:1322202]
subset: goslim_pir
is_a: GO:0043231 ! intracellular membrane-bounded organelle

[Term]
id: GO:0031105
name: septin complex
namespace: cellular_component
def: "A protein complex containing septins.  Typically, these complexes contain multiple septins and are oligomeric." [GOC:mah, PMID:15385632]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm
relationship: part_of GO:0005856 ! cytoskeleton

[Term]
id: GO:0031143
name: pseudopodium
namespace: cellular_component
def: "A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding." [ISBN:0198506732]
subset: goslim_pir
synonym: "pseudopod" EXACT []
xref: Wikipedia:Pseudopod
is_a: GO:0042995 ! cell projection
relationship: has_part GO:0016020 ! membrane
relationship: has_part GO:0044464 ! cell part

[Term]
id: GO:0031205
name: endoplasmic reticulum Sec complex
namespace: cellular_component
def: "An endoplasmic reticulum membrane-associated complex involved in the translocation of proteins that are targeted to the ER. In yeast, this complex consists of two subcomplexes, namely, the Sec61 complex and the Sec62/Sec63 complex." [GOC:mtg_sensu, PMID:12158317, PMID:14617809]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: has_part GO:0071256 ! translocon complex

[Term]
id: GO:0031248
name: protein acetyltransferase complex
namespace: cellular_component
def: "A complex that catalyzes the transfer of an acetyl group to a protein acceptor molecule." [GOC:bf]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0031252
name: cell leading edge
namespace: cellular_component
def: "The area of a motile cell closest to the direction of movement." [GOC:pg]
subset: goslim_pir
synonym: "front of cell" EXACT []
synonym: "leading edge of cell" EXACT []
is_a: GO:0044464 ! cell part

[Term]
id: GO:0031254
name: cell trailing edge
namespace: cellular_component
def: "The area of a motile cell opposite to the direction of movement." [GOC:pg]
subset: goslim_pir
synonym: "back of cell" EXACT []
synonym: "trailing edge" EXACT []
is_a: GO:0044464 ! cell part

[Term]
id: GO:0031264
name: death-inducing signaling complex
namespace: cellular_component
def: "A protein complex formed by the association of signaling proteins with a death receptor upon ligand binding. The complex includes procaspases and death domain-containing proteins in addition to the ligand-bound receptor, and may control the activation of caspases 8 and 10." [GOC:mtg_apoptosis, PMID:12628743, PMID:12655293, PMID:8521815]
comment: Gene products that may be annotated to this term include: 1) ligand-bound receptors such as FAS/CD95 (though care should be taken because FAS can also act as a non-apoptotic signal transducer); 2) signaling molecules such as FADD (FAS-associated protein with a death domain), cIAPs (cellular inhibitor of apoptosis proteins), c-FLIPs and caspases 8 and 10.
subset: goslim_pir
synonym: "death receptor-induced signaling complex" EXACT []
synonym: "death receptor-induced signalling complex" EXACT []
synonym: "death-inducing signalling complex" EXACT []
synonym: "DISC" EXACT []
synonym: "DISC protein complex" EXACT []
xref: Wikipedia:Death-inducing_signaling_complex
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0016020 ! membrane
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0031332
name: RNAi effector complex
namespace: cellular_component
def: "Any protein complex that mediates the effects of small interfering RNAs on gene expression. Most known examples contain one or more members of the Argonaute family of proteins." [GOC:mah, PMID:14704433]
subset: goslim_pir
is_a: GO:1990904 ! ribonucleoprotein complex

[Term]
id: GO:0031371
name: ubiquitin conjugating enzyme complex
namespace: cellular_component
def: "Any complex that possesses ubiquitin conjugating enzyme activity." [GOC:mah]
subset: goslim_pir
synonym: "E2 complex" RELATED []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0031386
name: protein tag
namespace: molecular_function
def: "A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation." [GOC:dos, GOC:go_curators, PMID:19028679, PMID:20054389, PMID:6305978]
comment: Use this term to annotate conjugated tags, not for conjugating enzymes. At the time of writing, all known gene products with this activity are ubiquitin-like, either based on overall sequence similarity or the presence of common motifs and structures.
subset: goslim_pir
synonym: "covalent modifier" RELATED [GOC:vw]
synonym: "protein tagging activity" RELATED []
synonym: "ubiquitin" RELATED []
synonym: "ubiquitin-like protein modifier" EXACT []
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0031406
name: carboxylic acid binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:mah, ISBN:0198506732]
subset: goslim_pir
is_a: GO:0043167 ! ion binding

[Term]
id: GO:0031409
name: pigment binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a pigment, any general or particular coloring matter in living organisms, e.g. melanin." [GOC:mah]
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0031469
name: polyhedral organelle
namespace: cellular_component
def: "An organelle found in bacteria consisting of a proteinaceous coat containing metabolic enzymes whose purpose is the sequestration or concentration of metabolites and which has the appearance of a polygonal granule by electron microscopy." [GOC:js, PMID:10498708, PMID:11844753, PMID:12923081]
subset: goslim_pir
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle

[Term]
id: GO:0031501
name: mannosyltransferase complex
namespace: cellular_component
def: "A complex that posseses mannosyltransferase activity." [GOC:mah]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0031519
name: PcG protein complex
namespace: cellular_component
def: "A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure." [PMID:9372908]
subset: goslim_pir
synonym: "Polycomb Group protein complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0031640
name: killing of cells of other organism
namespace: biological_process
alt_id: GO:0001908
def: "Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions." [GOC:add]
subset: goslim_pir
synonym: "killing of cells of another organism" EXACT [GOC:bf]
synonym: "killing of cells of another, non-host, organism" NARROW []
is_a: GO:0001906 ! cell killing
is_a: GO:0044419 ! interspecies interaction between organisms

[Term]
id: GO:0031647
name: regulation of protein stability
namespace: biological_process
def: "Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation." [GOC:dph, GOC:mah, GOC:tb]
subset: goslim_pir
is_a: GO:0065008 ! regulation of biological quality

[Term]
id: GO:0031982
name: vesicle
namespace: cellular_component
alt_id: GO:0031988
def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles]
subset: goslim_pir
synonym: "membrane-bounded vesicle" RELATED []
synonym: "membrane-enclosed vesicle" RELATED []
xref: NIF_Subcellular:sao221389602
xref: Wikipedia:Vesicle_(biology)
is_a: GO:0043226 ! organelle

[Term]
id: GO:0031992
name: energy transducer activity
namespace: molecular_function
def: "The biological transducer activity that accepts energy and converts it to another form, often by transfer to another molecule within the cell." [GOC:go_curators]
subset: goslim_pir
synonym: "light harvesting activity" RELATED []
synonym: "photon capture" RELATED []
is_a: GO:0060089 ! molecular transducer activity

[Term]
id: GO:0032059
name: bleb
namespace: cellular_component
def: "A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses." [GOC:mtg_apoptosis, http://en.wikipedia.org/wiki/Bleb_(cell_biology), PMID:12083798, PMID:16624291]
subset: goslim_pir
synonym: "plasma membrane bleb" EXACT [GOC:pr]
xref: Wikipedia:Bleb_(cell_biology)
is_a: GO:0042995 ! cell projection
relationship: has_part GO:0016020 ! membrane
relationship: has_part GO:0044464 ! cell part

[Term]
id: GO:0032153
name: cell division site
namespace: cellular_component
def: "The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles." [GOC:bf, GOC:imk, GOC:krc, GOC:ns, PMID:12101122, PMID:15380095, PMID:16983191, PMID:18165305]
comment: Note that this term refers to the future site of division in a cell that has not yet divided.
subset: goslim_pir
synonym: "cell division plane" EXACT []
is_a: GO:0044464 ! cell part

[Term]
id: GO:0032179
name: germ tube
namespace: cellular_component
def: "The slender tubular outgrowth first produced by most spores in germination." [ISBN:0877799148]
subset: goslim_pir
xref: Wikipedia:Germ_tube
is_a: GO:0044464 ! cell part

[Term]
id: GO:0032196
name: transposition
namespace: biological_process
def: "Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites." [GOC:jp, ISBN:1555812090]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_yeast
xref: Wikipedia:Transposon
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0032300
name: mismatch repair complex
namespace: cellular_component
def: "Any complex formed of proteins that act in mismatch repair." [GOC:mah]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0032392
name: DNA geometric change
namespace: biological_process
def: "The process in which a transformation is induced in the geometry of a DNA double helix, resulting in a change in twist, writhe, or both, but with no change in linking number. Includes the unwinding of double-stranded DNA by helicases." [GOC:mah]
comment: Note that DNA geometric change and DNA topological change (GO:0006265) are distinct, but are usually coupled in vivo.
subset: goslim_pir
is_a: GO:0051276 ! chromosome organization

[Term]
id: GO:0032421
name: stereocilium bundle
namespace: cellular_component
def: "A bundle of cross-linked stereocilia, arranged around a kinocilium on the apical surface of a sensory hair cell (e.g. a neuromast, auditory or vestibular hair cell). Stereocilium bundles act as mechanosensory organelles by responding to fluid motion or fluid pressure changes." [GOC:ecd, PMID:15661519, PMID:7840137]
subset: goslim_pir
synonym: "stereocilia bundle" EXACT []
is_a: GO:0044464 ! cell part
relationship: has_part GO:0043005 ! neuron projection

[Term]
id: GO:0032451
name: demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a substrate." [GOC:mah]
subset: goslim_pir
is_a: GO:0003824 ! catalytic activity
relationship: part_of GO:0008152 ! metabolic process

[Term]
id: GO:0032476
name: decaprenyl diphosphate synthase complex
namespace: cellular_component
def: "A complex that possesses di-trans,poly-cis-decaprenylcistransferase activity; involved in ubiquinone biosynthesis." [GOC:mah, PMID:14519123]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex

[Term]
id: GO:0032501
name: multicellular organismal process
namespace: biological_process
alt_id: GO:0044707
alt_id: GO:0050874
def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb]
subset: goslim_pir
synonym: "organismal physiological process" EXACT []
synonym: "single-multicellular organism process" RELATED []
is_a: GO:0008150 ! biological_process
created_by: janelomax
creation_date: 2012-09-19T16:07:47Z

[Term]
id: GO:0032502
name: developmental process
namespace: biological_process
alt_id: GO:0044767
def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete]
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_pir
synonym: "development" NARROW []
synonym: "single-organism developmental process" RELATED []
is_a: GO:0008150 ! biological_process
created_by: janelomax
creation_date: 2012-12-19T12:21:31Z

[Term]
id: GO:0032989
name: cellular component morphogenesis
namespace: biological_process
def: "The process in which cellular structures, including whole cells or cell parts, are generated and organized." [GOC:dph, GOC:mah, GOC:tb]
subset: goslim_pir
synonym: "cellular structure morphogenesis" EXACT [GOC:dph, GOC:tb]
is_a: GO:0016043 ! cellular component organization
is_a: GO:0032502 ! developmental process
relationship: part_of GO:0032502 ! developmental process

[Term]
id: GO:0032991
name: protein-containing complex
namespace: cellular_component
alt_id: GO:0043234
def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah]
comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
subset: goslim_agr
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
synonym: "macromolecular complex" EXACT []
synonym: "macromolecule complex" EXACT []
synonym: "protein complex" NARROW []
synonym: "protein containing complex" EXACT []
synonym: "protein-protein complex" NARROW []
is_a: GO:0005575 ! cellular_component

[Term]
id: GO:0032993
name: protein-DNA complex
namespace: cellular_component
def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah]
comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here.
subset: goslim_pir
synonym: "DNA-protein complex" EXACT [GOC:mah]
is_a: GO:0032991 ! protein-containing complex

[Term]
id: GO:0032997
name: Fc receptor complex
namespace: cellular_component
def: "A protein complex composed of a subunit or subunits capable of binding the Fc portion of an immunoglobulin with additional signaling components. The complex functions as a receptor for immunoglobulin." [GOC:add, ISBN:0781735149]
subset: goslim_pir
synonym: "Fc-receptor complex" EXACT []
synonym: "FcR complex" EXACT []
synonym: "immunoglobulin receptor complex" BROAD []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0016020 ! membrane
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0033061
name: DNA recombinase mediator complex
namespace: cellular_component
def: "A protein complex containing accessory proteins which bind a recombinase (e.g. Rad51) and bind single-stranded DNA (ssDNA), and promote nucleation of the recombinase onto ssDNA." [GOC:elh, GOC:mah, GOC:vw, InterPro:IPR003488, PMID:12912992]
comment: Many paralogs of Rad51 act as recombinase mediators. These paralogs dimerize (or occasionally form tetramers) amongst themselves to form complexes with ssDNA-binding activity, and which act as mediators of Rad51 presynaptic filament assembly.
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex

[Term]
id: GO:0033099
name: attachment organelle
namespace: cellular_component
def: "A membrane-bounded extension of the cell, originally characterized in Mycoplasma species, that contains an electron-dense core that is part of the cytoskeleton and is oriented lengthwise and ends distally in a bulbous knob (terminal button). Required for adherence to host cells and involved in gliding motility and cell division." [http://authors.library.caltech.edu/3529/, PMID:11325545, PMID:12003948]
subset: goslim_pir
is_a: GO:0043231 ! intracellular membrane-bounded organelle

[Term]
id: GO:0033202
name: DNA helicase complex
namespace: cellular_component
def: "A protein complex that possesses DNA helicase activity." [GOC:mah]
subset: goslim_metagenomics
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0033218
name: amide binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [CHEBI:32988, GOC:mah]
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0033256
name: I-kappaB/NF-kappaB complex
namespace: cellular_component
def: "A protein complex containing an inhibitory-kappaB (I-kappaB/IKB) protein and one or more copies of an NF-kappaB protein. In the resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm." [GOC:bf, GOC:mah, PMID:9407099]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0035097
name: histone methyltransferase complex
namespace: cellular_component
def: "A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins." [GOC:bf]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005634 ! nucleus

[Term]
id: GO:0035230
name: cytoneme
namespace: cellular_component
def: "A long, thin, polarized cell projection that contains actin and can extend for distances many times the diameter of the cell. Cytonemes represent extensions of cell cytoplasm and typically have a diameter of approximately 0.2um." [PMID:10367889, PMID:10675901]
subset: goslim_pir
synonym: "membrane nanotube" EXACT [Wikipedia:Membrane_nanotube]
xref: Wikipedia:Membrane_nanotube
is_a: GO:0042995 ! cell projection
relationship: has_part GO:0016020 ! membrane
relationship: has_part GO:0044464 ! cell part

[Term]
id: GO:0035273
name: phthalate binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a phthalate, any ester or salt of phthalic acid." [http://umbbd.ahc.umn.edu/pth/pth_map.html]
subset: goslim_pir
is_a: GO:0031406 ! carboxylic acid binding

[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_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
synonym: "receptor activity" BROAD []
synonym: "receptor activity involved in signal transduction" EXACT [GOC:bf]
is_a: GO:0060089 ! molecular transducer activity
created_by: rfoulger
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_generic
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:0040011
name: locomotion
namespace: biological_process
def: "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0042044
name: fluid transport
namespace: biological_process
def: "The directed movement of substances that are in liquid form in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
is_a: GO:0006810 ! transport

[Term]
id: GO:0042056
name: chemoattractant activity
namespace: molecular_function
def: "Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal." [GOC:go_curators, ISBN:0198506732]
subset: goslim_chembl
subset: goslim_pir
synonym: "attractant" BROAD []
is_a: GO:0005515 ! protein binding
relationship: part_of GO:0040011 ! locomotion
relationship: part_of GO:0050789 ! regulation of biological process
relationship: part_of GO:0050896 ! response to stimulus
relationship: part_of GO:0065009 ! regulation of molecular function
relationship: regulates GO:0038023 ! signaling receptor activity

[Term]
id: GO:0042133
name: neurotransmitter metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving neurotransmitters, any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell." [CHEBI:25512, GOC:jl]
subset: goslim_pir
synonym: "neurotransmitter metabolism" EXACT []
xref: Reactome:REACT_100207 "Metabolism of Noradrenaline, Danio rerio"
xref: Reactome:REACT_101077 "Metabolism of Noradrenaline, Taeniopygia guttata"
xref: Reactome:REACT_103666 "Metabolism of Noradrenaline, Rattus norvegicus"
xref: Reactome:REACT_104729 "Metabolism of Noradrenaline, Xenopus tropicalis"
xref: Reactome:REACT_108898 "Metabolism of Noradrenaline, Canis familiaris"
xref: Reactome:REACT_115498 "Metabolism of Noradrenaline, Dictyostelium discoideum"
xref: Reactome:REACT_15390 "Metabolism of Noradrenaline, Homo sapiens"
xref: Reactome:REACT_57518 "Metabolism of Noradrenaline, Gallus gallus"
xref: Reactome:REACT_87838 "Metabolism of Noradrenaline, Bos taurus"
xref: Reactome:REACT_90506 "Metabolism of Noradrenaline, Mycobacterium tuberculosis"
xref: Reactome:REACT_94583 "Metabolism of Noradrenaline, Sus scrofa"
xref: Reactome:REACT_99002 "Metabolism of Noradrenaline, Mus musculus"
is_a: GO:0008152 ! metabolic process
is_a: GO:0065008 ! regulation of biological quality

[Term]
id: GO:0042165
name: neurotransmitter binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a neurotransmitter, any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [ISBN:0198506732]
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0042180
name: cellular ketone metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:jl, ISBN:0787650153]
subset: goslim_pir
synonym: "ketone metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0042254
name: ribosome biogenesis
namespace: biological_process
alt_id: GO:0007046
def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis." [GOC:ma, PMID:26404467, Wikipedia:Ribosome_biogenesis]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
synonym: "ribosome biogenesis and assembly" EXACT []
is_a: GO:0044085 ! cellular component biogenesis

[Term]
id: GO:0042277
name: peptide binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds." [GOC:jl]
subset: goslim_chembl
subset: goslim_pir
is_a: GO:0033218 ! amide binding

[Term]
id: GO:0042303
name: molting cycle
namespace: biological_process
def: "The periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin, etc." [GOC:jl, ISBN:0198506732]
subset: goslim_pir
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0042440
name: pigment metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving pigment, any general or particular coloring matter in living organisms, e.g. melanin." [GOC:jl, ISBN:0198506732]
subset: goslim_pir
synonym: "pigment metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0042445
name: hormone metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." [CHEBI:24621, GOC:jl]
subset: goslim_pir
synonym: "hormone metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
is_a: GO:0065008 ! regulation of biological quality

[Term]
id: GO:0042562
name: hormone binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with any hormone, naturally occurring substances secreted by specialized cells that affect the metabolism or behavior of other cells possessing functional receptors for the hormone." [CHEBI:24621, GOC:jl]
subset: goslim_chembl
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0042566
name: hydrogenosome
namespace: cellular_component
def: "A spherical, membrane-bounded organelle found in some anaerobic protozoa, which participates in ATP and molecular hydrogen formation." [GOC:jl, PMID:11197234, PMID:11293569]
subset: goslim_pir
xref: Wikipedia:Hydrogenosome
is_a: GO:0043231 ! intracellular membrane-bounded organelle
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0042575
name: DNA polymerase complex
namespace: cellular_component
def: "A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA." [GOC:jl, PMID:12045093]
subset: goslim_metagenomics
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0042579
name: microbody
namespace: cellular_component
def: "Cytoplasmic organelles, spherical or oval in shape, that are bounded by a single membrane and contain oxidative enzymes, especially those utilizing hydrogen peroxide (H2O2)." [ISBN:0198506732]
subset: goslim_pir
xref: Wikipedia:Microbody
is_a: GO:0043231 ! intracellular membrane-bounded organelle
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0042597
name: periplasmic space
namespace: cellular_component
alt_id: GO:0005620
def: "The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria)." [GOC:go_curators, GOC:md]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "periplasm" EXACT []
is_a: GO:0044464 ! cell part

[Term]
id: GO:0042600
name: chorion
namespace: cellular_component
def: "A protective, noncellular membrane that surrounds the eggs of various animals including insects and fish." [GOC:jl, ISBN:0721662544]
comment: Note that this term does not refer to the extraembryonic membrane surrounding the embryo of amniote vertebrates as this is an anatomical structure and is therefore not covered by GO.
subset: goslim_pir
is_a: GO:0030312 ! external encapsulating structure

[Term]
id: GO:0042611
name: MHC protein complex
namespace: cellular_component
def: "A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen." [GOC:add, GOC:jl, ISBN:0781735149, PMID:15928678, PMID:16153240]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0016020 ! membrane
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0042620
name: poly(3-hydroxyalkanoate) metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving poly(3-hydroxyalkanoates), polyesters of 3-hydroxyacids produced as intracellular granules by a large variety of bacteria." [GOC:jl, PMID:9925580]
subset: goslim_pir
synonym: "PHA metabolic process" BROAD []
synonym: "PHA metabolism" BROAD []
synonym: "poly(3-hydroxyalkanoate) metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0042710
name: biofilm formation
namespace: biological_process
def: "A process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription." [GOC:di, PMID:11932229]
subset: gocheck_do_not_annotate
subset: gocheck_do_not_manually_annotate
subset: goslim_candida
subset: goslim_pir
is_a: GO:0051704 ! multi-organism process

[Term]
id: GO:0042810
name: pheromone metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving pheromones, a substance that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process." [ISBN:0198506732]
subset: goslim_pir
synonym: "pheromone metabolism" EXACT []
is_a: GO:0019748 ! secondary metabolic process
is_a: GO:0042445 ! hormone metabolic process

[Term]
id: GO:0042824
name: MHC class I peptide loading complex
namespace: cellular_component
def: "A large, multisubunit complex which consists of the MHC class I-beta 2 microglobulin dimer, the transporter associated with antigen presentation (TAP), tapasin (an MHC-encoded membrane protein), the chaperone calreticulin and the thiol oxidoreductase ERp57. Functions in the assembly of peptides with newly synthesized MHC class I molecules." [GOC:jl, PMID:10631934]
comment: Note that although this complex is located in the endoplasmic reticulum, there is some evidence that it may also be found in the Golgi.
subset: goslim_pir
synonym: "peptide-loading complex" EXACT [GOC:bhm]
synonym: "PLC" RELATED [GOC:bhm]
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005783 ! endoplasmic reticulum
relationship: part_of GO:0016020 ! membrane

[Term]
id: GO:0042886
name: amide transport
namespace: biological_process
def: "The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, ISBN:0198506732]
subset: goslim_pir
is_a: GO:0006810 ! transport

[Term]
id: GO:0042908
name: xenobiotic transport
namespace: biological_process
def: "The directed movement of a xenobiotic, a compound foreign to living organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators]
subset: goslim_pir
is_a: GO:0006810 ! transport

[Term]
id: GO:0042995
name: cell projection
namespace: cellular_component
def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
subset: goslim_agr
subset: goslim_mouse
subset: goslim_pir
synonym: "cell process" BROAD []
synonym: "cellular process" BROAD []
synonym: "cellular projection" EXACT []
is_a: GO:0044464 ! cell part

[Term]
id: GO:0043005
name: neuron projection
namespace: cellular_component
def: "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
subset: goslim_pir
synonym: "nerve fiber" RELATED [GOC:dph]
synonym: "neurite" NARROW []
synonym: "neuron process" EXACT []
synonym: "neuron protrusion" EXACT [NIF_Subcellular:sao-250931889]
synonym: "neuronal cell projection" EXACT []
xref: NIF_Subcellular:sao-867568886
is_a: GO:0042995 ! cell projection
relationship: has_part GO:0016020 ! membrane
relationship: has_part GO:0044464 ! cell part

[Term]
id: GO:0043021
name: ribonucleoprotein complex binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with any complex of RNA and protein." [GOC:bf, GOC:go_curators, GOC:vk]
subset: goslim_pir
synonym: "protein-RNA complex binding" EXACT [GOC:bf, GOC:vk]
synonym: "ribonucleoprotein binding" EXACT [GOC:bf, GOC:vk]
synonym: "RNP binding" EXACT []
is_a: GO:0005488 ! binding

[Term]
id: GO:0043025
name: neuronal cell body
namespace: cellular_component
def: "The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites." [GOC:go_curators]
comment: Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections.
subset: goslim_pir
synonym: "neuron cell body" EXACT []
synonym: "neuronal cell soma" EXACT []
xref: NIF_Subcellular:sao1044911821
xref: Wikipedia:Soma_(biology)
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0043033
name: isoamylase complex
namespace: cellular_component
def: "A protein complex whose composition varies amongst species; in rice it probably exists in a homo-tetramer to homo-hexamer form and in Gram-negative bacteria as a dimer. Functions in the hydrolysis of alpha-(1,6)-D-glucosidic branch linkages." [GOC:jl, PMID:10333591]
subset: goslim_pir
synonym: "debranching enzyme complex" BROAD []
is_a: GO:0032991 ! protein-containing complex

[Term]
id: GO:0043062
name: extracellular structure organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in 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, and also covers the host cell environment outside an intracellular parasite." [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
subset: goslim_pir
synonym: "extracellular structure organisation" EXACT [GOC:curators]
synonym: "extracellular structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah]
is_a: GO:0016043 ! cellular component organization

[Term]
id: GO:0043094
name: cellular metabolic compound salvage
namespace: biological_process
def: "Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells." [GOC:mlg]
subset: goslim_pir
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0043101
name: purine-containing compound salvage
namespace: biological_process
def: "Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis." [CHEBI:26401, GOC:jl]
subset: goslim_pir
synonym: "purine salvage" RELATED [GOC:curators]
xref: Reactome:REACT_101336 "Purine salvage, Schizosaccharomyces pombe"
xref: Reactome:REACT_101369 "Purine salvage, Danio rerio"
xref: Reactome:REACT_103526 "Purine salvage, Plasmodium falciparum"
xref: Reactome:REACT_104777 "Purine salvage, Bos taurus"
xref: Reactome:REACT_108943 "Purine salvage, Saccharomyces cerevisiae"
xref: Reactome:REACT_109288 "Purine salvage, Drosophila melanogaster"
xref: Reactome:REACT_1923 "Purine salvage, Homo sapiens"
xref: Reactome:REACT_28109 "Purine salvage, Dictyostelium discoideum"
xref: Reactome:REACT_28847 "Purine salvage, Escherichia coli"
xref: Reactome:REACT_31632 "Purine salvage, Arabidopsis thaliana"
xref: Reactome:REACT_32479 "Purine salvage, Staphylococcus aureus N315"
xref: Reactome:REACT_78176 "Purine salvage, Oryza sativa"
xref: Reactome:REACT_79232 "Purine salvage, Xenopus tropicalis"
xref: Reactome:REACT_82121 "Purine salvage, Gallus gallus"
xref: Reactome:REACT_82482 "Purine salvage, Taeniopygia guttata"
xref: Reactome:REACT_84877 "Purine salvage, Mus musculus"
xref: Reactome:REACT_88584 "Purine salvage, Sus scrofa"
xref: Reactome:REACT_91689 "Purine salvage, Rattus norvegicus"
xref: Reactome:REACT_92683 "Purine salvage, Mycobacterium tuberculosis"
xref: Reactome:REACT_96464 "Purine salvage, Canis familiaris"
xref: Reactome:REACT_99628 "Purine salvage, Caenorhabditis elegans"
is_a: GO:0006139 ! nucleobase-containing compound metabolic process
is_a: GO:0043094 ! cellular metabolic compound salvage

[Term]
id: GO:0043163
name: cell envelope organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cell envelope, everything external to, but not including, the cytoplasmic membrane of bacteria, encompassing the periplasmic space, cell wall, and outer membrane if present." [GOC:jl]
subset: goslim_pir
synonym: "cell envelope organisation" EXACT [GOC:curators]
synonym: "cell envelope organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0045229 ! external encapsulating structure organization

[Term]
id: GO:0043167
name: ion binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with ions, charged atoms or groups of atoms." [GOC:jl]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
synonym: "atom binding" RELATED []
is_a: GO:0005488 ! binding

[Term]
id: GO:0043170
name: macromolecule metabolic process
namespace: biological_process
alt_id: GO:0043283
alt_id: GO:0044259
def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah]
subset: goslim_pir
synonym: "biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09]
synonym: "macromolecule metabolism" EXACT []
synonym: "multicellular organismal macromolecule metabolic process" NARROW []
synonym: "organismal macromolecule metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0043176
name: amine binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with any organic compound that is weakly basic in character and contains an amino or a substituted amino group." [GOC:jl]
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0043178
name: alcohol binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with an alcohol, any of a class of alkyl compounds containing a hydroxyl group." [GOC:jl, ISBN:0198506732]
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0043190
name: ATP-binding cassette (ABC) transporter complex
namespace: cellular_component
alt_id: GO:0043191
alt_id: GO:0043192
def: "A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter." [GOC:jl, GOC:mtg_sensu, PMID:11421269, PMID:15111107]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "ABC-type efflux permease complex" NARROW []
synonym: "ABC-type efflux porter complex" NARROW []
synonym: "ABC-type uptake permease complex" NARROW []
synonym: "ATP-binding cassette (ABC) transporter complex" RELATED []
synonym: "mating pheromone exporter" NARROW []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0016020 ! membrane
relationship: part_of GO:0044464 ! cell part

[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, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:go_curators]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
xref: NIF_Subcellular:sao1539965131
xref: Wikipedia:Organelle
is_a: GO:0005575 ! cellular_component

[Term]
id: GO:0043229
name: intracellular organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators]
subset: goslim_pir
is_a: GO:0043226 ! organelle
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0043230
name: extracellular organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi." [GOC:jl, PMID:9914479]
subset: goslim_pir
is_a: GO:0043226 ! organelle
intersection_of: GO:0043226 ! organelle
intersection_of: part_of GO:0005576 ! extracellular region
relationship: part_of GO:0005576 ! extracellular region

[Term]
id: GO:0043231
name: intracellular membrane-bounded organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators]
subset: goslim_pir
synonym: "intracellular membrane-enclosed organelle" EXACT []
is_a: GO:0043229 ! intracellular organelle

[Term]
id: GO:0043232
name: intracellular non-membrane-bounded organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators]
subset: goslim_mouse
subset: goslim_pir
synonym: "intracellular non-membrane-enclosed organelle" EXACT []
is_a: GO:0043229 ! intracellular organelle

[Term]
id: GO:0043235
name: receptor complex
namespace: cellular_component
def: "Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:go_curators]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex

[Term]
id: GO:0043256
name: laminin complex
namespace: cellular_component
def: "A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha, beta and gamma. Provides an integral part of the structural scaffolding of basement membranes." [GOC:jl, http://www.sdbonline.org/fly/newgene/laminna1.htm, PMID:10842354]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0031012 ! extracellular matrix

[Term]
id: GO:0043364
name: glycyl-radical enzyme activating activity
namespace: molecular_function
def: "Catalyzes the activation of an enzyme by generating an organic free radical on a glycine residue via a homolytic cleavage of S-adenosyl-L-methionine (SAM)." [GOC:jl, PMID:24486374]
comment: Changed term label and definition as requested https://github.com/geneontology/go-ontology/issues/14190
subset: goslim_pir
synonym: "catalysis of free radical formation" BROAD []
xref: EC:1.97.1
is_a: GO:0016491 ! oxidoreductase activity

[Term]
id: GO:0043412
name: macromolecule modification
namespace: biological_process
def: "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties." [GOC:go_curators]
subset: goslim_pir
is_a: GO:0043170 ! macromolecule metabolic process

[Term]
id: GO:0043446
name: cellular alkane metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving an alkane, any acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, as carried out by individual cells." [CHEBI:18310, GOC:jl, Wikipedia:Alkane]
subset: goslim_pir
synonym: "alkane metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0043449
name: cellular alkene metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving an alkene, any acyclic branched or unbranched hydrocarbon having one carbon-carbon double bond and the general formula CnH2n, as carried out by individual cells." [CHEBI:32878, GOC:jl, Wikipedia:Alkene]
subset: goslim_pir
synonym: "alkene metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0043452
name: cellular alkyne metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving an alkyne, any cyclic branched or unbranched hydrocarbon having a carbon-carbon triple bond and the general formula CnH2n-2, as carried out by individual cells." [CHEBI:22339, GOC:jl, Wikipedia:Alkyne]
subset: goslim_pir
synonym: "alkyne metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0043473
name: pigmentation
namespace: biological_process
def: "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells." [GOC:jl]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0043500
name: muscle adaptation
namespace: biological_process
def: "A process in which muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." [GOC:mtg_muscle, PMID:11181628, PMID:11449884, PMID:12605307]
subset: goslim_pir
synonym: "muscle plasticity" RELATED []
is_a: GO:0032501 ! multicellular organismal process
is_a: GO:0050896 ! response to stimulus

[Term]
id: GO:0043511
name: inhibin complex
namespace: cellular_component
def: "Heterodimeric hormone composed of an inhibin alpha subunit complexed with either an inhibin beta-A subunit, to form inhibin A, or an inhibin beta-B subunit, to form inhibin B." [GOC:jl]
comment: Note that the actions of the inhibin complex are the opposite of those of the activin complex, which is a dimer of an inhibin beta-A and/or inhibin beta-B subunit. See also the cellular component term 'activin complex ; GO:0048180'.
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0005576 ! extracellular region

[Term]
id: GO:0043527
name: tRNA methyltransferase complex
namespace: cellular_component
def: "A multimeric protein complex involved in the methylation of specific nucleotides in tRNA." [GOC:jl]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0043591
name: endospore external encapsulating structure
namespace: cellular_component
alt_id: GO:0055030
def: "The structures that lie outside the inner membrane and surround the entire endospore; consists of a peptidoglycan-containing inner layer (the endospore cortex) surrounded by a multilayered proteinaceous coat. An exosporium may be present as an extreme outer layer." [GOC:go_curators, PMID:15035041]
subset: goslim_pir
synonym: "endospore wall" EXACT [GOC:mah]
synonym: "peptidoglycan-based spore wall" EXACT [GOC:mtg_sensu]
synonym: "spore wall" BROAD [GOC:mtg_sensu]
is_a: GO:0005618 ! cell wall

[Term]
id: GO:0043603
name: cellular amide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells." [CHEBI:32988]
subset: goslim_pir
synonym: "amide metabolism" EXACT []
is_a: GO:0006807 ! nitrogen compound metabolic process

[Term]
id: GO:0044085
name: cellular component biogenesis
namespace: biological_process
alt_id: GO:0071843
def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah]
subset: goslim_pir
synonym: "cellular component biogenesis at cellular level" EXACT []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0044238
name: primary metabolic process
namespace: biological_process
def: "The chemical reactions and pathways 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, http://www.metacyc.org]
subset: goslim_pir
synonym: "primary metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0044255
name: cellular lipid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving lipids, as carried out by individual cells." [GOC:jl]
subset: goslim_pir
synonym: "cellular lipid metabolism" EXACT []
xref: Reactome:REACT_100469 "Fatty acid, triacylglycerol, and ketone body metabolism, Rattus norvegicus"
xref: Reactome:REACT_101288 "Peroxisomal lipid metabolism, Bos taurus"
xref: Reactome:REACT_101329 "Fatty acid, triacylglycerol, and ketone body metabolism, Mus musculus"
xref: Reactome:REACT_102412 "Fatty acid, triacylglycerol, and ketone body metabolism, Canis familiaris"
xref: Reactome:REACT_106581 "Peroxisomal lipid metabolism, Rattus norvegicus"
xref: Reactome:REACT_106990 "Fatty acid, triacylglycerol, and ketone body metabolism, Xenopus tropicalis"
xref: Reactome:REACT_107435 "Peroxisomal lipid metabolism, Danio rerio"
xref: Reactome:REACT_108484 "Peroxisomal lipid metabolism, Dictyostelium discoideum"
xref: Reactome:REACT_112736 "Peroxisomal lipid metabolism, Plasmodium falciparum"
xref: Reactome:REACT_16957 "Peroxisomal lipid metabolism, Homo sapiens"
xref: Reactome:REACT_22279 "Fatty acid, triacylglycerol, and ketone body metabolism, Homo sapiens"
xref: Reactome:REACT_28392 "Fatty acid, triacylglycerol, and ketone body metabolism, Arabidopsis thaliana"
xref: Reactome:REACT_28564 "Peroxisomal lipid metabolism, Canis familiaris"
xref: Reactome:REACT_28948 "Peroxisomal lipid metabolism, Mus musculus"
xref: Reactome:REACT_29328 "Fatty acid, triacylglycerol, and ketone body metabolism, Mycobacterium tuberculosis"
xref: Reactome:REACT_31891 "Fatty acid, triacylglycerol, and ketone body metabolism, Caenorhabditis elegans"
xref: Reactome:REACT_32011 "Fatty acid, triacylglycerol, and ketone body metabolism, Danio rerio"
xref: Reactome:REACT_32998 "Peroxisomal lipid metabolism, Schizosaccharomyces pombe"
xref: Reactome:REACT_34149 "Fatty acid, triacylglycerol, and ketone body metabolism, Taeniopygia guttata"
xref: Reactome:REACT_79191 "Peroxisomal lipid metabolism, Drosophila melanogaster"
xref: Reactome:REACT_79497 "Peroxisomal lipid metabolism, Taeniopygia guttata"
xref: Reactome:REACT_81034 "Peroxisomal lipid metabolism, Gallus gallus"
xref: Reactome:REACT_81319 "Peroxisomal lipid metabolism, Arabidopsis thaliana"
xref: Reactome:REACT_82818 "Peroxisomal lipid metabolism, Caenorhabditis elegans"
xref: Reactome:REACT_83359 "Fatty acid, triacylglycerol, and ketone body metabolism, Sus scrofa"
xref: Reactome:REACT_84205 "Fatty acid, triacylglycerol, and ketone body metabolism, Gallus gallus"
xref: Reactome:REACT_84404 "Peroxisomal lipid metabolism, Mycobacterium tuberculosis"
xref: Reactome:REACT_86890 "Fatty acid, triacylglycerol, and ketone body metabolism, Staphylococcus aureus N315"
xref: Reactome:REACT_87163 "Peroxisomal lipid metabolism, Staphylococcus aureus N315"
xref: Reactome:REACT_87905 "Fatty acid, triacylglycerol, and ketone body metabolism, Drosophila melanogaster"
xref: Reactome:REACT_89268 "Fatty acid, triacylglycerol, and ketone body metabolism, Dictyostelium discoideum"
xref: Reactome:REACT_90141 "Fatty acid, triacylglycerol, and ketone body metabolism, Plasmodium falciparum"
xref: Reactome:REACT_92117 "Peroxisomal lipid metabolism, Escherichia coli"
xref: Reactome:REACT_93461 "Fatty acid, triacylglycerol, and ketone body metabolism, Bos taurus"
xref: Reactome:REACT_94360 "Peroxisomal lipid metabolism, Saccharomyces cerevisiae"
xref: Reactome:REACT_96855 "Fatty acid, triacylglycerol, and ketone body metabolism, Escherichia coli"
xref: Reactome:REACT_97999 "Fatty acid, triacylglycerol, and ketone body metabolism, Schizosaccharomyces pombe"
xref: Reactome:REACT_98520 "Peroxisomal lipid metabolism, Oryza sativa"
xref: Reactome:REACT_98981 "Fatty acid, triacylglycerol, and ketone body metabolism, Saccharomyces cerevisiae"
xref: Reactome:REACT_99720 "Fatty acid, triacylglycerol, and ketone body metabolism, Oryza sativa"
xref: Reactome:REACT_99861 "Peroxisomal lipid metabolism, Xenopus tropicalis"
xref: Reactome:REACT_99881 "Peroxisomal lipid metabolism, Sus scrofa"
is_a: GO:0006629 ! lipid metabolic process

[Term]
id: GO:0044419
name: interspecies interaction between organisms
namespace: biological_process
def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc]
subset: goslim_candida
subset: goslim_pir
synonym: "interaction with another species" EXACT []
synonym: "interspecies interaction" EXACT []
synonym: "interspecies interaction with other organisms" EXACT []
is_a: GO:0051704 ! multi-organism process

[Term]
id: GO:0044464
name: cell part
namespace: cellular_component
def: "Any constituent part of a cell, the basic structural and functional unit of all organisms." [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_pir
synonym: "cellular subcomponent" EXACT [NIF_Subcellular:sao628508602]
synonym: "protoplast" RELATED [GOC:mah]
xref: NIF_Subcellular:sao628508602
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005575 ! cellular_component

[Term]
id: GO:0045177
name: apical part of cell
namespace: cellular_component
def: "The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue." [GOC:mah, ISBN:0815316194]
subset: goslim_pir
is_a: GO:0044464 ! cell part

[Term]
id: GO:0045178
name: basal part of cell
namespace: cellular_component
def: "The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue." [GOC:mah, ISBN:0185316194]
subset: goslim_pir
is_a: GO:0044464 ! cell part

[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_aspergillus
subset: goslim_candida
subset: goslim_pir
subset: goslim_plant
synonym: "translation factor activity" EXACT []
is_a: GO:0003674 ! molecular_function
relationship: part_of GO:0050789 ! regulation of biological process

[Term]
id: GO:0045202
name: synapse
namespace: cellular_component
def: "The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane." [ISBN:0198506732]
subset: goslim_agr
subset: goslim_mouse
subset: goslim_pir
subset: goslim_synapse
synonym: "electrotonic synapse" RELATED [NIF_Subcellular:sao1311109124]
synonym: "mixed synapse" NARROW [NIF_Subcellular:sao1506103497]
synonym: "synaptic junction" EXACT []
xref: NIF_Subcellular:sao914572699
xref: Wikipedia:Chemical_synapse
is_a: GO:0005575 ! cellular_component

[Term]
id: GO:0045229
name: external encapsulating structure organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell." [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
subset: goslim_pir
synonym: "external encapsulating structure organisation" EXACT [GOC:curators]
synonym: "external encapsulating structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah]
is_a: GO:0016043 ! cellular component organization

[Term]
id: GO:0045230
name: capsule organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the capsule, a protective structure surrounding some species of bacteria and fungi." [GOC:ai]
subset: goslim_pir
synonym: "capsule organisation" EXACT [GOC:curators]
synonym: "capsule organization and biogenesis" RELATED []
is_a: GO:0045229 ! external encapsulating structure organization

[Term]
id: GO:0045231
name: slime layer organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a slime layer. A slime layer is an easily removed, diffuse, unorganized layer of extracellular material that surrounds a cell." [GOC:ai]
subset: goslim_pir
synonym: "slime layer organisation" EXACT [GOC:curators]
synonym: "slime layer organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0045229 ! external encapsulating structure organization

[Term]
id: GO:0045239
name: tricarboxylic acid cycle enzyme complex
namespace: cellular_component
def: "Any of the heteromeric enzymes that act in the TCA cycle." [GOC:mah]
subset: goslim_pir
synonym: "TCA cycle enzyme complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0045251
name: electron transfer flavoprotein complex
namespace: cellular_component
def: "A protein complex facilitating the electron transfer from an acyl-CoA molecule to ubiquinone via its flavin adenine dinucleotide (FAD) cofactor. Usually contains an alpha and a beta subunit and the structural cofactor adenosine monophosphate (AMP). Part of a system that oxidizes an acyl-CoA molecule and reduces ubiquinone and other acceptors in the electron transport system." [GOC:bhm, ISBN:0198506732]
subset: goslim_pir
synonym: "ETF complex" EXACT [GOC:bhm]
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0045252
name: oxoglutarate dehydrogenase complex
namespace: cellular_component
def: "A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) ; EC:1.2.4.2 (E1), dihydrolipoamide S-succinyltransferase ; EC:2.3.1.61 (E2) and dihydrolipoamide dehydrogenase ; EC:1.8.1.4 (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2)." [MetaCyc:CPLX66-42, PMID:10848975]
comment: See also the molecular functions term 'oxoglutarate dehydrogenase (succinyl-transferring) activity ; GO:0004591', 'dihydrolipoyllysine-residue succinyltransferase activity ; GO:0004149' and 'dihydrolipoyl dehydrogenase activity ; GO:0004148'.
subset: goslim_pir
synonym: "dihydrolipoamide S-succinyltransferase complex" EXACT []
is_a: GO:0045239 ! tricarboxylic acid cycle enzyme complex

[Term]
id: GO:0045253
name: pyruvate dehydrogenase (lipoamide) phosphatase complex
namespace: cellular_component
def: "A complex of a regulatory and catalytic subunit that catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex." [PMID:9395502]
comment: See also the cellular component term 'cytosolic pyruvate dehydrogenase complex ; GO:0045250'.
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0045254
name: pyruvate dehydrogenase complex
namespace: cellular_component
alt_id: GO:0009364
def: "Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA; comprises subunits possessing three catalytic activities: pyruvate dehydrogenase (E1), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3)." [ISBN:0716720094]
comment: Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The functions of this complex are represented by the molecular function terms 'pyruvate dehydrogenase (lipoamide) activity ; GO:0004739', 'dihydrolipoamide S-acetyltransferase activity ; GO:0004742', and 'dihydrolipoamide dehydrogenase activity ; GO:0004148'.
subset: goslim_pir
synonym: "dihydrolipoyl dehydrogenase complex" BROAD []
synonym: "pyruvate dehydrogenase complex (lipoamide)" EXACT []
xref: Wikipedia:Pyruvate_dehydrogenase_complex
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0045273
name: respiratory chain complex II
namespace: cellular_component
def: "A part of the respiratory chain, containing the four polypeptide subunits of succinate dehydrogenase, flavin-adenine dinucleotide and iron-sulfur. Catalyzes the oxidation of succinate by ubiquinone. Connects the TCA cycle with the respiratory chain." [ISBN:0198547684]
subset: goslim_pir
synonym: "electron transport complex II" RELATED []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0016020 ! membrane
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0045275
name: respiratory chain complex III
namespace: cellular_component
alt_id: GO:0032842
alt_id: GO:0045285
def: "A protein complex that transfers electrons from ubiquinol to cytochrome c and translocates two protons across a membrane. The complex contains a core structure of three catalytic subunits: cytochrome b, the Rieske iron sulfur protein (ISP), and cytochrome c1, which are arranged in an integral membrane-bound dimeric complex; additional subunits are present, and vary among different species." [PMID:16228398, PMID:16352458, PMID:17200733]
subset: goslim_pir
synonym: "coenzyme Q-cytochrome c oxidoreductase complex" RELATED []
synonym: "coenzyme Q-cytochrome c reductase complex" RELATED []
synonym: "complex III" EXACT []
synonym: "CoQH2-cytochrome c reductase complex" RELATED []
synonym: "cytochrome bc(1) complex" EXACT []
synonym: "cytochrome bc1 complex" EXACT []
synonym: "electron transport complex III" RELATED []
synonym: "ubiquinol-cytochrome c oxidoreductase complex" EXACT []
synonym: "ubiquinol-cytochrome-c reductase complex" EXACT []
xref: Wikipedia:Coenzyme_Q_-_cytochrome_c_reductase
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0016020 ! membrane
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0045277
name: respiratory chain complex IV
namespace: cellular_component
alt_id: GO:0045287
def: "A part of the respiratory chain, containing the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2)." [ISBN:0198547684]
subset: goslim_pir
synonym: "cytochrome c oxidase complex" EXACT []
synonym: "electron transport complex IV" RELATED []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0016020 ! membrane
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0045293
name: mRNA editing complex
namespace: cellular_component
def: "A protein complex that posttranscriptionally catalyzes insertion, deletion or substitution of nucleotides at multiple sites within nascent mRNA transcripts to produce mature mRNAs in eukaryotes." [http://www.ejbiotechnology.info/content/vol1/issue1/full/4/, PMID:11564867, PMID:12139607, PMID:24316715]
subset: goslim_pir
synonym: "editosome" EXACT []
is_a: GO:0032991 ! protein-containing complex

[Term]
id: GO:0045333
name: cellular respiration
namespace: biological_process
def: "The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration)." [GOC:das, ISBN:0140513590, ISBN:0198506732]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
subset: goslim_yeast
synonym: "oxidative metabolic process" EXACT []
synonym: "oxidative metabolism" EXACT []
synonym: "respiration" BROAD []
xref: Wikipedia:Cellular_respiration
is_a: GO:0006091 ! generation of precursor metabolites and energy
is_a: GO:0055114 ! oxidation-reduction process

[Term]
id: GO:0045478
name: fusome organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fusome, a large intracellular spectrin-rich structure found in insect germline cells and mammalian hematopoietic cells." [GOC:dph, GOC:go_curators, GOC:jl, GOC:mah]
subset: goslim_pir
synonym: "fusome organisation" EXACT [GOC:curators]
synonym: "fusome organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0006996 ! organelle organization
relationship: part_of GO:0000003 ! reproduction
relationship: part_of GO:0032501 ! multicellular organismal process

[Term]
id: GO:0045499
name: chemorepellent activity
namespace: molecular_function
def: "Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a lower concentration of that signal." [GOC:ai]
subset: goslim_pir
synonym: "chemorepellant activity" EXACT []
is_a: GO:0005515 ! protein binding
relationship: part_of GO:0040011 ! locomotion
relationship: part_of GO:0050789 ! regulation of biological process
relationship: part_of GO:0050896 ! response to stimulus
relationship: part_of GO:0065009 ! regulation of molecular function
relationship: regulates GO:0038023 ! signaling receptor activity

[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_pir
synonym: "storage protein" RELATED []
synonym: "storage protein of fat body" RELATED []
synonym: "yolk protein" RELATED []
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0046483
name: heterocycle metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [CHEBI:5686, ISBN:0198506732]
subset: goslim_pir
synonym: "heterocycle metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0046490
name: isopentenyl diphosphate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving isopentenyl diphosphate, an isomer of dimethylallyl diphosphate and the key precursor of all isoprenoids." [ISBN:0198506732]
subset: goslim_pir
synonym: "IPP metabolic process" EXACT []
synonym: "IPP metabolism" EXACT []
synonym: "isopentenyl diphosphate metabolism" EXACT []
synonym: "isopentenyl pyrophosphate metabolic process" EXACT []
synonym: "isopentenyl pyrophosphate metabolism" EXACT []
is_a: GO:0006793 ! phosphorus metabolic process
is_a: GO:0044255 ! cellular lipid metabolic process

[Term]
id: GO:0046536
name: dosage compensation complex
namespace: cellular_component
def: "A protein or protein-RNA complex that localizes to one or more of the sex chromosome(s), where it acts to normalize transcription between different sexes." [GOC:kmv, GOC:mah]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005634 ! nucleus
relationship: part_of GO:0005694 ! chromosome

[Term]
id: GO:0046794
name: transport of virus
namespace: biological_process
def: "The directed movement of a virus, or part of a virus, into, out of, or within a host cell." [GOC:ai]
subset: goslim_pir
synonym: "viral transport" EXACT [GOC:bf, GOC:jl]
synonym: "virion transport" NARROW [GOC:bf, GOC:jl]
is_a: GO:0006810 ! transport
is_a: GO:0016032 ! viral process

[Term]
id: GO:0046812
name: host cell surface binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with the surface of a host cell." [GOC:ai]
subset: goslim_pir
is_a: GO:0005488 ! binding
relationship: part_of GO:0051704 ! multi-organism process

[Term]
id: GO:0046864
name: isoprenoid transport
namespace: biological_process
def: "The directed movement of isoprenoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Isoprenoids comprise a group of compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [GOC:ai]
subset: goslim_pir
is_a: GO:0006869 ! lipid transport

[Term]
id: GO:0046903
name: secretion
namespace: biological_process
def: "The controlled release of a substance by a cell or a tissue." [GOC:ai]
subset: goslim_pir
is_a: GO:0006810 ! transport

[Term]
id: GO:0046906
name: tetrapyrrole binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a tetrapyrrole, a compound containing four pyrrole nuclei variously substituted and linked to each other through carbons at the alpha position." [CHEBI:26932, GOC:curators, ISBN:0198506732]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "porphyrin binding" NARROW []
is_a: GO:0005488 ! binding

[Term]
id: GO:0046950
name: cellular ketone body metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism." [ISBN:0198506732]
subset: goslim_pir
synonym: "cellular ketone body metabolism" EXACT []
xref: Reactome:REACT_100444 "Ketone body metabolism, Caenorhabditis elegans"
xref: Reactome:REACT_101523 "Ketone body metabolism, Danio rerio"
xref: Reactome:REACT_107371 "Ketone body metabolism, Sus scrofa"
xref: Reactome:REACT_109409 "Ketone body metabolism, Mus musculus"
xref: Reactome:REACT_109752 "Ketone body metabolism, Mycobacterium tuberculosis"
xref: Reactome:REACT_110395 "Ketone body metabolism, Oryza sativa"
xref: Reactome:REACT_110725 "Ketone body metabolism, Xenopus tropicalis"
xref: Reactome:REACT_110872 "Ketone body metabolism, Bos taurus"
xref: Reactome:REACT_1861 "Ketone body metabolism, Homo sapiens"
xref: Reactome:REACT_29105 "Ketone body metabolism, Gallus gallus"
xref: Reactome:REACT_29141 "Ketone body metabolism, Taeniopygia guttata"
xref: Reactome:REACT_29697 "Ketone body metabolism, Canis familiaris"
xref: Reactome:REACT_31341 "Ketone body metabolism, Plasmodium falciparum"
xref: Reactome:REACT_34650 "Ketone body metabolism, Schizosaccharomyces pombe"
xref: Reactome:REACT_77702 "Ketone body metabolism, Saccharomyces cerevisiae"
xref: Reactome:REACT_78769 "Ketone body metabolism, Arabidopsis thaliana"
xref: Reactome:REACT_80825 "Ketone body metabolism, Drosophila melanogaster"
xref: Reactome:REACT_85192 "Ketone body metabolism, Dictyostelium discoideum"
xref: Reactome:REACT_89476 "Ketone body metabolism, Escherichia coli"
xref: Reactome:REACT_90520 "Ketone body metabolism, Rattus norvegicus"
xref: Reactome:REACT_95478 "Ketone body metabolism, Staphylococcus aureus N315"
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0048037
name: cofactor binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate." [ISBN:0198506732]
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0048180
name: activin complex
namespace: cellular_component
def: "A nonsteroidal regulator, composed of two covalently linked inhibin beta subunits, inhibin beta-A and inhibin beta-B (sometimes known as activin beta or activin/inhibin beta). There are three forms of activin complex, activin A, which is composed of 2 inhibin beta-A subunits, activin B, which is composed of 2 inhibin beta-B subunits, and activin AB, which is composed of an inhibin beta-A and an inhibin beta-B subunit." [GOC:go_curators, http://www.mercksource.com, http://www.stedmans.com/]
comment: Note that the actions of the activin complex are the opposite of those of the inhibin complex, which is a dimer of an inhibin beta-A or inhibin beta-B subunit and a inhibin alpha subunit. See 'inhibin complex ; GO:0043511'.
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0005576 ! extracellular region

[Term]
id: GO:0048284
name: organelle fusion
namespace: biological_process
def: "The creation of a single organelle from two or more organelles." [GOC:jid]
subset: goslim_pir
subset: goslim_yeast
is_a: GO:0006996 ! organelle organization

[Term]
id: GO:0048285
name: organelle fission
namespace: biological_process
def: "The creation of two or more organelles by division of one organelle." [GOC:jid]
subset: goslim_pir
subset: goslim_yeast
is_a: GO:0006996 ! organelle organization

[Term]
id: GO:0048308
name: organelle inheritance
namespace: biological_process
def: "The partitioning of organelles between daughter cells at cell division." [GOC:jid]
subset: goslim_pir
subset: goslim_yeast
is_a: GO:0006996 ! organelle organization

[Term]
id: GO:0048469
name: cell maturation
namespace: biological_process
def: "A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state." [GOC:go_curators]
subset: goslim_pir
synonym: "functional differentiation" RELATED [GOC:dph]
is_a: GO:0032502 ! developmental process
relationship: part_of GO:0032502 ! developmental process

[Term]
id: GO:0048476
name: Holliday junction resolvase complex
namespace: cellular_component
def: "A protein complex that mediates the conversion of a Holliday junction into two separate duplex DNA molecules; the complex includes a single- or multisubunit helicase that catalyzes the extension of heteroduplex DNA by branch migration and a nuclease that resolves the junction by nucleolytic cleavage." [PMID:11207366, PMID:12374758]
subset: goslim_pir
synonym: "Mus81-Eme1 complex" NARROW []
synonym: "resolvasome" EXACT [PMID:11207366]
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0044464 ! cell part

[Term]
id: GO:0048492
name: ribulose bisphosphate carboxylase complex
namespace: cellular_component
def: "A complex containing either both large and small subunits or just small subunits which carries out the activity of producing 3-phosphoglycerate from carbon dioxide and ribulose-1,5-bisphosphate." [GOC:mlg]
subset: goslim_pir
synonym: "RubisCO complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0048500
name: signal recognition particle
namespace: cellular_component
def: "A complex of protein and RNA which facilitates translocation of proteins across membranes." [GOC:mlg]
subset: goslim_metagenomics
subset: goslim_pir
xref: Wikipedia:Signal_recognition_particle
is_a: GO:0044464 ! cell part
is_a: GO:1990904 ! ribonucleoprotein complex
relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0048511
name: rhythmic process
namespace: biological_process
def: "Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism." [GOC:jid]
subset: goslim_pir
synonym: "rhythm" RELATED []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0048753
name: pigment granule organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pigment granule." [GOC:rc]
subset: goslim_pir
synonym: "pigment granule organisation" EXACT [GOC:curators]
synonym: "pigment granule organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0016050 ! vesicle organization
relationship: part_of GO:0043473 ! pigmentation

[Term]
id: GO:0048771
name: tissue remodeling
namespace: biological_process
def: "The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling." [GOC:ebc]
subset: goslim_pir
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0050761
name: depsipeptide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving depsipeptides, a linear or cyclic compound composed of both amino acids and hydroxy acids in peptide and ester bonds respectively." [GOC:go_curators]
subset: goslim_pir
synonym: "depsipeptide metabolism" EXACT []
is_a: GO:0006518 ! peptide metabolic process

[Term]
id: GO:0050789
name: regulation of biological process
namespace: biological_process
alt_id: GO:0050791
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: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
synonym: "regulation of physiological process" EXACT []
is_a: GO:0065007 ! biological regulation
intersection_of: GO:0008150 ! biological_process
intersection_of: regulates GO:0008150 ! biological_process
relationship: regulates GO:0008150 ! biological_process

[Term]
id: GO:0050817
name: coagulation
namespace: biological_process
def: "The process in which a fluid solution, or part of it, changes into a solid or semisolid mass." [ISBN:0198506732]
subset: goslim_pir
synonym: "clotting" EXACT []
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0050824
name: water binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with water (H2O)." [GOC:ai]
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0050840
name: extracellular matrix binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a component of the extracellular matrix." [GOC:ai]
subset: goslim_chembl
subset: goslim_pir
synonym: "adhesive extracellular matrix constituent" RELATED []
synonym: "extracellular matrix constituent binding" EXACT []
is_a: GO:0005488 ! binding

[Term]
id: GO:0050877
name: nervous system process
namespace: biological_process
def: "A organ system process carried out by any of the organs or tissues of neurological system." [GOC:ai, GOC:mtg_cardio]
comment: Discussion of class label and synonyms: https://github.com/geneontology/go-ontology/issues/13824
subset: goslim_agr
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
synonym: "neurological system process" EXACT []
synonym: "neurophysiological process" EXACT []
synonym: "pan-neural process" RELATED []
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0050878
name: regulation of body fluid levels
namespace: biological_process
def: "Any process that modulates the levels of body fluids." [GOC:ai, GOC:dph, GOC:tb]
subset: goslim_pir
is_a: GO:0065008 ! regulation of biological quality

[Term]
id: GO:0050879
name: multicellular organismal movement
namespace: biological_process
def: "Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism." [GOC:dph, GOC:mtg_muscle, GOC:tb]
subset: goslim_pir
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0050886
name: endocrine process
namespace: biological_process
def: "The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system." [ISBN:0721662544]
subset: goslim_pir
synonym: "endocrine physiological process" EXACT []
synonym: "endocrine physiology" EXACT []
is_a: GO:0032501 ! multicellular organismal process

[Term]
id: GO:0050896
name: response to stimulus
namespace: biological_process
alt_id: GO:0051869
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. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf]
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_manually_annotate
subset: goslim_agr
subset: goslim_mouse
subset: goslim_pir
synonym: "physiological response to stimulus" EXACT []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0051179
name: localization
namespace: biological_process
alt_id: GO:1902578
def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos]
subset: goslim_pir
synonym: "establishment and maintenance of cellular component location" NARROW []
synonym: "establishment and maintenance of localization" EXACT []
synonym: "establishment and maintenance of position" EXACT []
synonym: "establishment and maintenance of substance location" NARROW []
synonym: "establishment and maintenance of substrate location" NARROW []
synonym: "localisation" EXACT [GOC:mah]
synonym: "single organism localization" RELATED [GOC:TermGenie]
synonym: "single-organism localization" RELATED []
is_a: GO:0008150 ! biological_process
created_by: jl
creation_date: 2013-12-18T13:51:04Z

[Term]
id: GO:0051180
name: vitamin transport
namespace: biological_process
def: "The directed movement of vitamins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body." [GOC:ai]
subset: goslim_pir
synonym: "vitamin or cofactor transport" BROAD []
is_a: GO:0006810 ! transport

[Term]
id: GO:0051181
name: cofactor transport
namespace: biological_process
def: "The directed movement of a cofactor into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A cofactor is a substance that is required for the activity of an enzyme or other protein." [GOC:ai]
subset: goslim_pir
synonym: "vitamin or cofactor transport" BROAD []
is_a: GO:0006810 ! transport

[Term]
id: GO:0051186
name: cofactor metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate." [GOC:ai]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
synonym: "cofactor metabolism" EXACT []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0051189
name: prosthetic group metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving a prosthetic group, the non-amino acid portion of certain protein molecules. Prosthetic groups may be inorganic or organic and are usually required for the biological activity of the protein." [GOC:ai]
subset: goslim_pir
synonym: "coenzyme and prosthetic group metabolic process" BROAD []
synonym: "coenzyme and prosthetic group metabolism" BROAD []
synonym: "prosthetic group metabolism" EXACT []
is_a: GO:0051186 ! cofactor metabolic process
relationship: part_of GO:0019538 ! protein metabolic process

[Term]
id: GO:0051213
name: dioxygenase activity
namespace: molecular_function
def: "Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products." [DOI:10.1016/S0040-4020(03)00944-X, GOC:bf, http://www.onelook.com/]
subset: goslim_pir
is_a: GO:0016491 ! oxidoreductase activity

[Term]
id: GO:0051234
name: establishment of localization
namespace: biological_process
def: "Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [GOC:ai, GOC:dos]
subset: goslim_agr
subset: goslim_mouse
subset: goslim_pir
synonym: "establishment of localisation" EXACT [GOC:mah]
is_a: GO:0051179 ! localization

[Term]
id: GO:0051258
name: protein polymerization
namespace: biological_process
def: "The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein." [GOC:ai]
subset: goslim_pir
synonym: "protein polymer biosynthesis" EXACT []
synonym: "protein polymer biosynthetic process" EXACT []
synonym: "protein polymer formation" EXACT []
is_a: GO:0065003 ! protein-containing complex assembly

[Term]
id: GO:0051261
name: protein depolymerization
namespace: biological_process
def: "The process in which protein polymers, compounds composed of a large number of component monomers, are broken down. Depolymerization occurs by the successive removal of monomers from an existing poly- or oligomeric protein." [GOC:ai]
subset: goslim_pir
synonym: "protein polymer breakdown" EXACT []
synonym: "protein polymer catabolic process" EXACT []
synonym: "protein polymer catabolism" EXACT []
synonym: "protein polymer degradation" EXACT []
is_a: GO:0022411 ! cellular component disassembly

[Term]
id: GO:0051276
name: chromosome organization
namespace: biological_process
alt_id: GO:0007001
alt_id: GO:0051277
def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
synonym: "chromosome organisation" EXACT []
synonym: "chromosome organization and biogenesis" RELATED [GOC:mah]
synonym: "maintenance of genome integrity" RELATED []
synonym: "nuclear genome maintenance" RELATED []
is_a: GO:0006996 ! organelle organization

[Term]
id: GO:0051301
name: cell division
namespace: biological_process
def: "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells." [GOC:di, GOC:go_curators, GOC:pr]
comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
xref: Wikipedia:Cell_division
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0051540
name: metal cluster binding
namespace: molecular_function
def: "Interacting selectively and non-covalently with a cluster of atoms including both metal ions and nonmetal atoms, usually sulfur and oxygen. Examples include iron-sulfur clusters and nickel-iron-sulfur clusters." [GOC:jsg]
subset: goslim_pir
is_a: GO:0005488 ! binding

[Term]
id: GO:0051604
name: protein maturation
namespace: biological_process
def: "Any process leading to the attainment of the full functional capacity of a protein." [GOC:ai]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
is_a: GO:0019538 ! protein metabolic process
relationship: part_of GO:0043170 ! macromolecule metabolic process

[Term]
id: GO:0051606
name: detection of stimulus
namespace: biological_process
def: "The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal." [GOC:add, GOC:ai, GOC:dph, GOC:mah]
subset: goslim_pir
synonym: "perception of stimulus" RELATED []
synonym: "stimulus detection" EXACT []
synonym: "stimulus sensing" RELATED []
is_a: GO:0050896 ! response to stimulus

[Term]
id: GO:0051640
name: organelle localization
namespace: biological_process
def: "Any process in which an organelle is transported to, and/or maintained in, a specific location." [GOC:ai]
subset: goslim_pir
synonym: "establishment and maintenance of organelle localization" EXACT []
synonym: "organelle localisation" EXACT [GOC:mah]
is_a: GO:0051641 ! cellular localization

[Term]
id: GO:0051641
name: cellular localization
namespace: biological_process
alt_id: GO:1902580
def: "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane." [GOC:tb, GOC:vw]
subset: goslim_pir
synonym: "cellular localisation" EXACT [GOC:mah]
synonym: "establishment and maintenance of cellular localization" EXACT []
synonym: "establishment and maintenance of localization in cell or cell membrane" EXACT []
synonym: "intracellular localization" NARROW []
synonym: "localization within cell" NARROW []
synonym: "single organism cellular localization" EXACT [GOC:TermGenie]
synonym: "single-organism cellular localization" RELATED []
is_a: GO:0051179 ! localization
created_by: jl
creation_date: 2013-12-18T14:04:32Z

[Term]
id: GO:0051703
name: intraspecies interaction between organisms
namespace: biological_process
def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai]
subset: goslim_pir
synonym: "intraspecies interaction with other organisms" EXACT []
is_a: GO:0051704 ! multi-organism process

[Term]
id: GO:0051704
name: multi-organism process
namespace: biological_process
alt_id: GO:0051706
def: "A biological process which involves another organism of the same or different species." [GOC:jl]
subset: goslim_pir
synonym: "interaction between organisms" EXACT []
synonym: "physiological interaction between organisms" EXACT []
synonym: "physiological interaction with other organism" EXACT []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0051705
name: multi-organism behavior
namespace: biological_process
alt_id: GO:0023032
alt_id: GO:0044709
def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai]
subset: goslim_pir
synonym: "behavioral interaction between organisms" EXACT []
synonym: "behavioral interaction with other organism" EXACT []
synonym: "behavioral signaling" NARROW []
synonym: "behavioral signalling" NARROW [GOC:mah]
synonym: "behavioural interaction between organisms" EXACT []
synonym: "behavioural interaction with other organism" EXACT []
is_a: GO:0051704 ! multi-organism process

[Term]
id: GO:0052314
name: phytoalexin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving phytoalexins, any of a range of substances produced by plants as part of their defense response." [Wikipedia:Phytoalexin]
subset: goslim_pir
synonym: "phytoalexin metabolism" EXACT []
is_a: GO:0009404 ! toxin metabolic process

[Term]
id: GO:0055044
name: symplast
namespace: cellular_component
def: "The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata." [GOC:mtg_sensu]
subset: goslim_pir
xref: Wikipedia:Symplast
is_a: GO:0005575 ! cellular_component

[Term]
id: GO:0055114
name: oxidation-reduction process
namespace: biological_process
def: "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph]
subset: goslim_pir
synonym: "oxidation reduction" EXACT [GOC:curators]
synonym: "oxidoreductase process" EXACT systematic_synonym []
xref: Wikipedia:Redox
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0060089
name: molecular transducer activity
namespace: molecular_function
def: "A compound molecular function in which an effector function is controlled by one or more regulatory components." [GOC:dos, GOC:pdt]
subset: gocheck_do_not_manually_annotate
subset: goslim_pir
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0060090
name: molecular adaptor activity
namespace: molecular_function
def: "The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way." [GOC:mtg_MIT_16mar07, GOC:vw]
subset: goslim_pir
synonym: "binding, bridging" EXACT []
is_a: GO:0005488 ! binding

[Term]
id: GO:0061024
name: membrane organization
namespace: biological_process
alt_id: GO:0016044
alt_id: GO:0044802
def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
synonym: "cellular membrane organisation" EXACT [GOC:curators]
synonym: "cellular membrane organization" EXACT []
synonym: "membrane organisation" EXACT [GOC:mah]
synonym: "membrane organization and biogenesis" RELATED [GOC:mah]
synonym: "single-organism membrane organization" RELATED []
xref: Reactome:REACT_101524 "Membrane Trafficking, Dictyostelium discoideum"
xref: Reactome:REACT_103082 "Membrane Trafficking, Schizosaccharomyces pombe"
xref: Reactome:REACT_11123 "Membrane Trafficking, Homo sapiens"
xref: Reactome:REACT_29278 "Membrane Trafficking, Sus scrofa"
xref: Reactome:REACT_32337 "Membrane Trafficking, Taeniopygia guttata"
xref: Reactome:REACT_33741 "Membrane Trafficking, Bos taurus"
xref: Reactome:REACT_34084 "Membrane Trafficking, Caenorhabditis elegans"
xref: Reactome:REACT_78213 "Membrane Trafficking, Plasmodium falciparum"
xref: Reactome:REACT_78288 "Membrane Trafficking, Xenopus tropicalis"
xref: Reactome:REACT_83546 "Membrane Trafficking, Oryza sativa"
xref: Reactome:REACT_86557 "Membrane Trafficking, Arabidopsis thaliana"
xref: Reactome:REACT_87431 "Membrane Trafficking, Drosophila melanogaster"
xref: Reactome:REACT_88307 "Membrane Trafficking, Mus musculus"
xref: Reactome:REACT_91154 "Membrane Trafficking, Saccharomyces cerevisiae"
xref: Reactome:REACT_93714 "Membrane Trafficking, Danio rerio"
xref: Reactome:REACT_95586 "Membrane Trafficking, Gallus gallus"
xref: Reactome:REACT_96516 "Membrane Trafficking, Canis familiaris"
xref: Reactome:REACT_97881 "Membrane Trafficking, Rattus norvegicus"
is_a: GO:0016043 ! cellular component organization
created_by: janelomax
creation_date: 2010-02-08T02:43:11Z

[Term]
id: GO:0065003
name: protein-containing complex assembly
namespace: biological_process
alt_id: GO:0006461
def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
synonym: "chaperone activity" RELATED []
synonym: "macromolecular complex assembly" RELATED []
synonym: "macromolecule complex assembly" RELATED []
synonym: "protein complex assembly" RELATED []
synonym: "protein complex formation" RELATED []
is_a: GO:0022607 ! cellular component assembly

[Term]
id: GO:0065007
name: biological regulation
namespace: biological_process
def: "Any process that modulates a measurable attribute of any biological process, quality or function." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw]
subset: gocheck_do_not_annotate
subset: goslim_pir
synonym: "regulation" BROAD []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0065008
name: regulation of biological quality
namespace: biological_process
def: "Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw]
subset: goslim_pir
synonym: "regulation of biological attribute" EXACT []
synonym: "regulation of biological characteristic" EXACT []
is_a: GO:0065007 ! biological regulation

[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_agr
subset: goslim_pir
synonym: "regulation of a molecular function" EXACT []
is_a: GO:0065007 ! biological regulation
intersection_of: GO:0008150 ! biological_process
intersection_of: regulates GO:0003674 ! molecular_function
relationship: regulates GO:0003674 ! molecular_function

[Term]
id: GO:0071256
name: translocon complex
namespace: cellular_component
alt_id: GO:0031206
def: "A protein complex that constitutes a specific site of protein translocation across the endoplasmic reticulum, which involves the signal recognition particle receptor. The complex contains a core heterotrimer of alpha, beta and gamma subunits, and may contain additional proteins." [GOC:mah, PMID:10611978, PMID:18166647, PMID:8612571]
subset: goslim_pir
synonym: "Sec complex-associated translocon complex" NARROW [GOC:mah]
is_a: GO:0032991 ! protein-containing complex
is_a: GO:0044464 ! cell part
relationship: part_of GO:0005783 ! endoplasmic reticulum
relationship: part_of GO:0016020 ! membrane
created_by: midori
creation_date: 2009-12-08T02:08:03Z

[Term]
id: GO:0071555
name: cell wall organization
namespace: biological_process
alt_id: GO:0007047
alt_id: GO:0044234
def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, 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." [GOC:mah]
subset: goslim_candida
subset: goslim_pir
synonym: "cell wall organisation" EXACT [GOC:curators]
synonym: "cell wall organisation in other organism" EXACT [GOC:mah]
synonym: "cell wall organization and biogenesis" RELATED [GOC:mah]
synonym: "cell wall organization at cellular level" EXACT [GOC:mah]
synonym: "cell wall organization in other organism" EXACT []
synonym: "cellular cell wall organisation" EXACT [GOC:curators]
synonym: "cellular cell wall organization" EXACT []
is_a: GO:0045229 ! external encapsulating structure organization
created_by: midori
creation_date: 2010-01-13T03:33:07Z

[Term]
id: GO:1902600
name: proton transmembrane transport
namespace: biological_process
alt_id: GO:0006818
alt_id: GO:0015992
def: "The directed movement of a proton across a membrane." [GO_REF:0000069, GOC:pr, GOC:TermGenie]
subset: goslim_pir
synonym: "hydrogen ion transmembrane transport" EXACT []
synonym: "hydrogen ion transport" RELATED []
synonym: "hydrogen transmembrane transport" EXACT []
synonym: "hydrogen transport" BROAD []
synonym: "passive proton transport, down the electrochemical gradient" NARROW []
synonym: "proton transmembrane transport" EXACT []
synonym: "proton transport" BROAD []
xref: Reactome:REACT_100717 "The proton buffering model, Gallus gallus"
xref: Reactome:REACT_102006 "Mitochondrial Uncoupling Proteins, Xenopus tropicalis"
xref: Reactome:REACT_103123 "Mitochondrial Uncoupling Proteins, Mus musculus"
xref: Reactome:REACT_104490 "Mitochondrial Uncoupling Proteins, Arabidopsis thaliana"
xref: Reactome:REACT_105995 "Mitochondrial Uncoupling Proteins, Gallus gallus"
xref: Reactome:REACT_106176 "Mitochondrial Uncoupling Proteins, Canis familiaris"
xref: Reactome:REACT_106794 "The proton buffering model, Arabidopsis thaliana"
xref: Reactome:REACT_110839 "Mitochondrial Uncoupling Proteins, Bos taurus"
xref: Reactome:REACT_29555 "The proton buffering model, Canis familiaris"
xref: Reactome:REACT_30770 "Mitochondrial Uncoupling Proteins, Taeniopygia guttata"
xref: Reactome:REACT_31883 "The proton buffering model, Xenopus tropicalis"
xref: Reactome:REACT_6196 "The proton buffering model, Homo sapiens"
xref: Reactome:REACT_6341 "Mitochondrial Uncoupling Proteins, Homo sapiens"
xref: Reactome:REACT_77530 "Mitochondrial Uncoupling Proteins, Oryza sativa"
xref: Reactome:REACT_80235 "The proton buffering model, Oryza sativa"
xref: Reactome:REACT_82088 "The proton buffering model, Sus scrofa"
xref: Reactome:REACT_83467 "Mitochondrial Uncoupling Proteins, Sus scrofa"
xref: Reactome:REACT_88310 "The proton buffering model, Rattus norvegicus"
xref: Reactome:REACT_89771 "The proton buffering model, Taeniopygia guttata"
xref: Reactome:REACT_90272 "The proton buffering model, Danio rerio"
xref: Reactome:REACT_92912 "Mitochondrial Uncoupling Proteins, Danio rerio"
xref: Reactome:REACT_92975 "The proton buffering model, Bos taurus"
xref: Reactome:REACT_94505 "Mitochondrial Uncoupling Proteins, Rattus norvegicus"
xref: Reactome:REACT_95151 "The proton buffering model, Mus musculus"
is_a: GO:0006811 ! ion transport
created_by: pr
creation_date: 2013-12-20T11:08:37Z

[Term]
id: GO:1990904
name: ribonucleoprotein complex
namespace: cellular_component
alt_id: GO:0030529
alt_id: GO:1990903
def: "A macromolecular complex containing both protein and RNA molecules." [GOC:vesicles]
subset: goslim_pir
synonym: "extracellular ribonucleoprotein complex" NARROW []
synonym: "intracellular ribonucleoprotein complex" NARROW []
synonym: "protein-RNA complex" EXACT []
synonym: "ribonucleoprotein complex" EXACT []
synonym: "RNA-protein complex" EXACT []
synonym: "RNP" EXACT []
xref: Wikipedia:Ribonucleoprotein
is_a: GO:0032991 ! protein-containing complex
created_by: pr
creation_date: 2015-11-19T12:26:37Z

[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_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
transitive_over: part_of ! part of

[Typedef]
id: never_in_taxon
name: never_in_taxon
namespace: external
xref: RO:0002161
expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y" []
is_metadata_tag: true
is_class_level: true

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

[Typedef]
id: regulates
name: regulates
namespace: external
xref: RO:0002211
is_transitive: true
transitive_over: part_of ! part of

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