An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term BFO:0000050 external part_of part of BFO:0000051 chebi_ontology external false has_part has part BFO:0000066 external occurs_in occurs in aggregate of aggregate_of http://purl.obolibrary.org/obo/omrse.owl is aggregate of c-ppart-of_at properContinuantPartOfAt b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'. http://purl.obolibrary.org/obo/bfo.owl (iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] proper part of continuant at all times c-part-of_at continuantPartOfAt Mary’s arm continuant_part_of Mary in the time of her life prior to her operation the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. [copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: continuant BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' http://purl.obolibrary.org/obo/bfo.owl b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] part of continuant at all times c-has-part-object_at [copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation [copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' [copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. http://purl.obolibrary.org/obo/bfo.owl [copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) has continuant part at all times that part exists has specified input has specified output Note: this will end up being a subproperty of has-characteristic when we add it, TBD depends on discussion of whether has-characteristic is functional has quality has part has participant occurs in part of enabled by concretizes intended to realize executes realizes has characteristic https://github.com/oborel/obo-relations/pull/284 http://purl.obolibrary.org/obo/IAO_0000136 is about A duck swimming in a pond is partially surrounded by air and partially surrounded by water. x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x Definition modified from 'surrounded by'. partially_surrounded_by A relation between a process and a disposition such that the existence of the disposition is caused by the execution of the process. Consider ceding to RO cjm 2018-11-03T20:58:13Z generates is in aggregate GOREL:0002003 external results_in_distribution_of results_in_distribution_of GOREL:0002004 external results_in_fission_of results_in_fission_of GOREL:0002005 external results_in_fusion_of results_in_fusion_of The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input see is_input_of example_of_usage A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification RO:0000053 external bearer_of bearer of RO:0000057 external has_participant has participant RO:0000087 chebi_ontology false false has_role has role RO:0002211 external regulates regulates regulates (processual) RO:0002212 external negatively_regulates negatively regulates RO:0002213 external positively_regulates positively regulates RO:0002215 external capable_of capable of RO:0002216 external capable_of_part_of capable of part of surrounded by RO:0002224 external starts_with starts with RO:0002230 external ends_with ends with RO:0002233 external has_input has input RO:0002234 external has_output has output RO:0002295 external results_in_developmental_progression_of results in developmental progression of RO:0002296 external results_in_development_of results in development of RO:0002297 external results_in_formation_of results in formation of RO:0002298 external results_in_morphogenesis_of results in morphogenesis of RO:0002313 external transports_or_maintains_localization_of transports or maintains localization of RO:0002315 external results_in_acquisition_of_features_of results in acquisition of features of RO:0002338 external has_target_start_location has target start location RO:0002339 external has_target_end_location has target end location RO:0002341 external results_in_transport_along results in transport along RO:0002342 external results_in_transport_across results in transport across RO:0002344 external results_in_transport_to_from_or_in results in transport to from or in RO:0002578 external directly_regulates directly regulates RO:0002588 external results_in_assembly_of results_in_assembly_of RO:0002590 external results_in_disassembly_of results_in_disassembly_of RO:0002592 external results_in_organization_of results_in_organization_of RO:0002608 external process_has_causal_agent process has causal agent RO:0004007 external has_primary_input_or_output has primary input or output RO:0004008 external has_primary_output has primary output RO:0004009 external has_primary_input has primary input chebi_ontology false false has functional parent chebi_ontology false false has parent hydride chebi_ontology true false is conjugate acid of chebi_ontology true false is conjugate base of chebi_ontology false false is substituent group from chebi_ontology true is tautomer of http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) lacks_plasma_membrane_part has number of atomic nuclei entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa. Wikipedia:Volatile_organic_compound chebi_ontology VOC VOCs volatile organic compounds volatile organic compound VOC ChEBI VOCs ChEBI volatile organic compounds ChEBI An alkanesulfonate in which the carbon at position 1 is attached to R, which can represent hydrogens, a carbon chain, or other groups. -1 CH2O3SR 94.091 93.97246 C(S([O-])(=O)=O)* CHEBI:22318 MetaCyc:Alkanesulfonates chebi_ontology alkanesulfonate oxoanions alkanesulfonates an alkanesulfonate alkanesulfonate oxoanion alkanesulfonate oxoanions ChEBI alkanesulfonates ChEBI an alkanesulfonate UniProt An organic cation obtained by protonation of the amino group of any tertiary amino compound. +1 HNR3 15.015 15.01090 [NH+](*)(*)* chebi_ontology a tertiary amine tertiary amine(1+) tertiary ammonium ions tertiary ammonium ion a tertiary amine UniProt tertiary amine(1+) ChEBI tertiary ammonium ions ChEBI A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water. Wikipedia:Mineral_acid chebi_ontology inorganic acids mineral acid mineral acids inorganic acid inorganic acids ChEBI mineral acid ChEBI mineral acids ChEBI Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). Wikipedia:https://en.wikipedia.org/wiki/Gas chebi_ontology gas molecular entities gaseous molecular entities gaseous molecular entity gas molecular entity gas molecular entities ChEBI gaseous molecular entities ChEBI gaseous molecular entity ChEBI -1 CH2NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1 KXDHJXZQYSOELW-UHFFFAOYSA-M 60.03212 60.00910 NC([O-])=O Beilstein:3903503 CAS:302-11-4 Gmelin:239604 carbamate chebi_ontology Carbamat Karbamat carbamate ion carbamic acid, ion(1-) carbamate Beilstein:3903503 Beilstein CAS:302-11-4 ChemIDplus Gmelin:239604 Gmelin carbamate IUPAC carbamate UniProt Carbamat ChEBI Karbamat ChEBI carbamate ion ChemIDplus carbamic acid, ion(1-) ChemIDplus A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. CHEBI:13699 CHEBI:2377 KEGG:C00028 KEGG:C16722 Acceptor chebi_ontology A Akzeptor Hydrogen-acceptor Oxidized donor accepteur acceptor Acceptor KEGG_COMPOUND A KEGG_COMPOUND Akzeptor ChEBI Hydrogen-acceptor KEGG_COMPOUND Oxidized donor KEGG_COMPOUND accepteur ChEBI An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. 0 H3N InChI=1S/H3N/h1H3 QGZKDVFQNNGYKY-UHFFFAOYSA-N 17.03056 17.02655 [H]N([H])[H] CHEBI:13405 CHEBI:13406 CHEBI:13407 CHEBI:13771 CHEBI:22533 CHEBI:44269 CHEBI:44284 CHEBI:44404 CHEBI:7434 Beilstein:3587154 CAS:7664-41-7 Drug_Central:4625 Gmelin:79 HMDB:HMDB0000051 KEGG:C00014 KEGG:D02916 KNApSAcK:C00007267 MetaCyc:AMMONIA MolBase:930 PDBeChem:NH3 PMID:110589 PMID:11139349 PMID:11540049 PMID:11746427 PMID:11783653 PMID:13753780 PMID:14663195 PMID:15092448 PMID:15094021 PMID:15554424 PMID:15969015 PMID:16008360 PMID:16050680 PMID:16348008 PMID:16349403 PMID:16614889 PMID:16664306 PMID:16842901 PMID:17025297 PMID:17439666 PMID:17569513 PMID:17737668 PMID:18670398 PMID:22002069 PMID:22081570 PMID:22088435 PMID:22100291 PMID:22130175 PMID:22150211 PMID:22240068 PMID:22290316 PMID:22342082 PMID:22385337 PMID:22443779 PMID:22560242 Reaxys:3587154 Wikipedia:Ammonia AMMONIA Ammonia ammonia azane chebi_ontology Ammoniak NH3 R-717 [NH3] ammoniac amoniaco spirit of hartshorn ammonia PMID:16842901 Europe PMC PMID:17025297 Europe PMC PMID:17439666 Europe PMC PMID:17569513 Europe PMC PMID:17737668 Europe PMC PMID:18670398 Europe PMC PMID:22002069 Europe PMC PMID:22081570 Europe PMC PMID:22088435 Europe PMC PMID:22100291 Europe PMC PMID:22130175 Europe PMC PMID:22150211 Europe PMC PMID:22240068 Europe PMC PMID:22290316 Europe PMC PMID:22342082 Europe PMC PMID:22385337 Europe PMC PMID:22443779 Europe PMC PMID:22560242 Europe PMC Reaxys:3587154 Reaxys AMMONIA PDBeChem Ammonia KEGG_COMPOUND ammonia IUPAC azane IUPAC Ammoniak ChemIDplus NH3 IUPAC NH3 KEGG_COMPOUND NH3 UniProt R-717 ChEBI [NH3] MolBase ammoniac ChEBI amoniaco ChEBI spirit of hartshorn ChemIDplus Beilstein:3587154 Beilstein CAS:7664-41-7 ChemIDplus CAS:7664-41-7 KEGG COMPOUND CAS:7664-41-7 NIST Chemistry WebBook Drug_Central:4625 DrugCentral Gmelin:79 Gmelin PMID:110589 Europe PMC PMID:11139349 Europe PMC PMID:11540049 Europe PMC PMID:11746427 Europe PMC PMID:11783653 Europe PMC PMID:13753780 Europe PMC PMID:14663195 Europe PMC PMID:15092448 Europe PMC PMID:15094021 Europe PMC PMID:15554424 Europe PMC PMID:15969015 Europe PMC PMID:16008360 Europe PMC PMID:16050680 Europe PMC PMID:16348008 Europe PMC PMID:16349403 Europe PMC PMID:16614889 Europe PMC PMID:16664306 Europe PMC A six-carbon aromatic annulene in which each carbon atom donates one of its two 2p electrons into a delocalised pi system. A toxic, flammable liquid byproduct of coal distillation, it is used as an industrial solvent. Benzene is a carcinogen that also damages bone marrow and the central nervous system. 0 C6H6 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N 78.11184 78.04695 c1ccccc1 CHEBI:13876 CHEBI:22703 CHEBI:3025 CHEBI:41187 Beilstein:969212 CAS:71-43-2 Gmelin:1671 HMDB:HMDB0001505 KEGG:C01407 PDBeChem:BNZ PMID:11684179 PMID:11993966 PMID:12857942 PMID:14677922 PMID:15468289 PMID:15935818 PMID:16161967 PMID:17373369 PMID:18072742 PMID:18407866 PMID:18409691 PMID:18836923 PMID:19228219 PMID:21325737 PMID:23088855 PMID:23222815 PMID:23534829 PMID:6353911 PMID:8124204 Reaxys:969212 UM-BBD_compID:c0142 Wikipedia:Benzene BENZENE Benzene benzene chebi_ontology Benzen Benzine Benzol Bicarburet of hydrogen Coal naphtha Mineral naphtha Phene Pyrobenzol Pyrobenzole [6]annulene benzole cyclohexatriene phenyl hydride benzene Beilstein:969212 Beilstein CAS:71-43-2 ChemIDplus CAS:71-43-2 KEGG COMPOUND CAS:71-43-2 NIST Chemistry WebBook Gmelin:1671 Gmelin PMID:11684179 Europe PMC PMID:11993966 Europe PMC PMID:12857942 Europe PMC PMID:14677922 Europe PMC PMID:15468289 Europe PMC PMID:15935818 Europe PMC PMID:16161967 Europe PMC PMID:17373369 Europe PMC PMID:18072742 Europe PMC PMID:18407866 Europe PMC PMID:18409691 Europe PMC PMID:18836923 Europe PMC PMID:19228219 Europe PMC PMID:21325737 Europe PMC PMID:23088855 Europe PMC PMID:23222815 Europe PMC PMID:23534829 Europe PMC PMID:6353911 Europe PMC PMID:8124204 Europe PMC Reaxys:969212 Reaxys UM-BBD_compID:c0142 UM-BBD BENZENE PDBeChem Benzene KEGG_COMPOUND benzene ChEBI benzene IUPAC benzene UniProt Benzen IUPAC Benzine UM-BBD Benzol ChemIDplus Bicarburet of hydrogen ChemIDplus Coal naphtha ChemIDplus Mineral naphtha ChemIDplus Phene ChemIDplus Pyrobenzol ChemIDplus Pyrobenzole ChemIDplus [6]annulene NIST_Chemistry_WebBook benzole NIST_Chemistry_WebBook cyclohexatriene UM-BBD phenyl hydride UM-BBD -1 HO3S InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3)/p-1 LSNNMFCWUKXFEE-UHFFFAOYSA-M 81.07214 80.96519 OS([O-])=O CHEBI:13367 CHEBI:5598 CAS:15181-46-1 Gmelin:1455 KEGG:C11481 PDBeChem:SO3 hydrogen(trioxidosulfate)(1-) hydrogensulfite(1-) hydrogentrioxosulfate(1-) hydrogentrioxosulfate(IV) hydroxidodioxidosulfate(1-) monohydrogentrioxosulfate chebi_ontology Bisulfite HSO3(-) HSO3- Hydrogen sulfite [SO2(OH)](-) bisulfite bisulphite hydrogen sulfite(1-) hydrosulfite anion hydrogensulfite CAS:15181-46-1 ChemIDplus CAS:15181-46-1 KEGG COMPOUND Gmelin:1455 Gmelin hydrogen(trioxidosulfate)(1-) IUPAC hydrogensulfite(1-) IUPAC hydrogentrioxosulfate(1-) IUPAC hydrogentrioxosulfate(IV) IUPAC hydroxidodioxidosulfate(1-) IUPAC monohydrogentrioxosulfate IUPAC Bisulfite KEGG_COMPOUND HSO3(-) IUPAC HSO3- KEGG_COMPOUND Hydrogen sulfite KEGG_COMPOUND [SO2(OH)](-) IUPAC bisulfite ChemIDplus bisulphite ChemIDplus hydrogen sulfite(1-) ChemIDplus hydrosulfite anion ChemIDplus A sulfur oxoanion that is the conjugate base of hydrogen sulfite (H2SO3). -2 O3S InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3)/p-2 LSNNMFCWUKXFEE-UHFFFAOYSA-L 80.06420 79.95791 [O-]S([O-])=O CHEBI:15139 CHEBI:45548 CAS:14265-45-3 Gmelin:1449 PDBeChem:SO3 sulfite trioxidosulfate(2-) trioxosulfate(2-) trioxosulfate(IV) chebi_ontology SO3 SO3(2-) SULFITE ION [SO3](2-) sulphite sulfite CAS:14265-45-3 ChemIDplus Gmelin:1449 Gmelin sulfite IUPAC sulfite UniProt trioxidosulfate(2-) IUPAC trioxosulfate(2-) IUPAC trioxosulfate(IV) IUPAC SO3 ChEBI SO3(2-) IUPAC SULFITE ION PDBeChem [SO3](2-) IUPAC sulphite ChEBI SO:0000253 A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. CHEBI:14202 CHEBI:4697 KEGG:C01351 Donor chebi_ontology Donator donneur donor Donor KEGG_COMPOUND Donator ChEBI donneur ChEBI SO:0000252 An acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, and therefore consisting entirely of hydrogen atoms and saturated carbon atoms. 0 CH3R 15.035 15.02348 C[*] CHEBI:13435 CHEBI:22317 CHEBI:2576 KEGG:C01371 Alkane alkane alkanes chebi_ontology Alkan RH alcane alcanes alcano alcanos an alkane alkane Alkane KEGG_COMPOUND alkane IUPAC alkanes IUPAC Alkan ChEBI RH KEGG_COMPOUND alcane IUPAC alcanes IUPAC alcano IUPAC alcanos IUPAC an alkane UniProt An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids. acyl group alkanoyl chebi_ontology acyl groups alkanoyl group groupe acyle acyl group acyl group IUPAC alkanoyl IUPAC acyl groups ChEBI alkanoyl group ChEBI groupe acyle IUPAC A univalent group -CnH2n+1 derived from an alkane by removal of a hydrogen atom from any carbon atom. alkyl group alkyl groups chebi_ontology groupe alkyle grupo alquilo grupos alquilo alkyl group alkyl group IUPAC alkyl groups IUPAC groupe alkyle IUPAC grupo alquilo IUPAC grupos alquilo IUPAC A monoatomic or polyatomic species having one or more elementary charges of the electron. Anion anion chebi_ontology Anionen aniones anions anion Anion ChEBI anion ChEBI anion IUPAC Anionen ChEBI aniones ChEBI anions IUPAC A monocarboxylic acid amide in which the amide linkage is bonded directly to an arene ring system. chebi_ontology arenecarboxamides arenecarboxamide arenecarboxamides ChEBI A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base). KEGG:C00701 Base base chebi_ontology Base1 Base2 Basen Nucleobase bases base Base ChEBI base ChEBI base IUPAC Base1 KEGG_COMPOUND Base2 KEGG_COMPOUND Basen ChEBI Nucleobase KEGG_COMPOUND bases ChEBI chebi_ontology benzamides Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives. chebi_ontology benzenes The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid. 0 CH2NO 44.03272 44.01364 *C(N)=O PMID:24168430 carbamoyl chebi_ontology -C(O)NH2 -CONH2 aminocarbonyl carbamyl carbamyl group carboxamide carbamoyl group PMID:24168430 Europe PMC carbamoyl IUPAC -C(O)NH2 ChEBI -CONH2 IUPAC aminocarbonyl IUPAC carbamyl ChEBI carbamyl group ChEBI carboxamide IUPAC 0 CO 28.01010 27.99491 O=C(*)* carbonyl carbonyl group chebi_ontology >C=O carbonyl group carbonyl IUPAC carbonyl group ChEBI carbonyl group UniProt >C=O IUPAC An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group). Wikipedia:Cofactor_(biochemistry) cofactor cofactors chebi_ontology cofactor cofactor IUPAC cofactors IUPAC copper molecular entity chebi_ontology copper compounds copper molecular entities copper molecular entity copper molecular entity ChEBI copper compounds ChEBI copper molecular entities ChEBI Cu 63.546 62.92960 copper cation chebi_ontology Cu cation copper cations copper cation copper cation IUPAC Cu cation UniProt copper cations ChEBI Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. chebi_ontology drugs medicine drug drugs ChEBI medicine ChEBI chebi_ontology monoatomic cations monoatomic cation monoatomic cations ChEBI A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction. enzyme inhibitor chebi_ontology enzyme inhibitors inhibidor enzimatico inhibidores enzimaticos inhibiteur enzymatique inhibiteurs enzymatiques enzyme inhibitor enzyme inhibitor IUPAC enzyme inhibitors ChEBI inhibidor enzimatico ChEBI inhibidores enzimaticos ChEBI inhibiteur enzymatique ChEBI inhibiteurs enzymatiques ChEBI A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology chemical entity chemical entity UniProt A role played by the molecular entity or part thereof within a biological context. chebi_ontology biological function biological role biological function ChEBI A defined linked collection of atoms or a single atom within a molecular entity. group chebi_ontology Gruppe Rest groupe grupo grupos group group IUPAC Gruppe ChEBI Rest ChEBI groupe IUPAC grupo IUPAC grupos IUPAC A cyclic compound having as ring members atoms of carbon and at least of one other element. chebi_ontology organic heterocycle organic heterocyclic compounds organic heterocyclic compound organic heterocycle ChEBI organic heterocyclic compounds ChEBI A compound consisting of carbon and hydrogen only. hydrocarbon hydrocarbons chebi_ontology Kohlenwasserstoff Kohlenwasserstoffe hidrocarburo hidrocarburos hydrocarbure hydrocarbon hydrocarbon IUPAC hydrocarbons IUPAC Kohlenwasserstoff ChEBI Kohlenwasserstoffe ChEBI hidrocarburo IUPAC hidrocarburos IUPAC hydrocarbure IUPAC Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). chebi_ontology hydroxides A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). oxoacid oxoacids chebi_ontology oxacids oxiacids oxo acid oxy-acids oxyacids oxoacid oxoacid IUPAC oxoacids IUPAC oxacids ChEBI oxiacids ChEBI oxo acid ChEBI oxy-acids ChEBI oxyacids ChEBI chebi_ontology inorganic anions inorganic anion inorganic anions ChEBI A molecular entity that contains no carbon. chebi_ontology anorganische Verbindungen inorganic compounds inorganic entity inorganic molecular entities inorganics inorganic molecular entity anorganische Verbindungen ChEBI inorganic compounds ChEBI inorganic entity ChEBI inorganic molecular entities ChEBI inorganics ChEBI chebi_ontology inorganic oxides inorganic oxide inorganic oxides ChEBI A salt is an assembly of cations and anions. salt chebi_ontology Salz Salze ionic compound ionic compounds sal sales salts sel sels salt salt IUPAC Salz ChEBI Salze ChEBI ionic compound ChEBI ionic compounds ChEBI sal ChEBI sales ChEBI salts ChEBI sel ChEBI sels ChEBI chebi_ontology organic salts organisches Salz organic salt organic salts ChEBI organisches Salz ChEBI A molecular entity having a net electric charge. Ion ion chebi_ontology Ionen iones ions ion Ion ChEBI ion ChEBI ion IUPAC Ionen ChEBI iones ChEBI ions ChEBI Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. CHEBI:26619 CHEBI:35220 metabolite chebi_ontology metabolites primary metabolites secondary metabolites metabolite metabolite IUPAC metabolites ChEBI primary metabolites ChEBI secondary metabolites ChEBI chebi_ontology a metal cation metal cations metal cation a metal cation UniProt metal cations ChEBI A 1,1-diunsubstituted alkanesulfonate that is the conjugate base of methanesulfonic acid. -1 CH3O3S InChI=1S/CH4O3S/c1-5(2,3)4/h1H3,(H,2,3,4)/p-1 AFVFQIVMOAPDHO-UHFFFAOYSA-M 95.09872 94.98084 CS([O-])(=O)=O MetaCyc:CPD-3746 UM-BBD_compID:c0347 methanesulfonate chebi_ontology methylsulfonate methanesulfonate UM-BBD_compID:c0347 UM-BBD methanesulfonate IUPAC methanesulfonate UniProt methylsulfonate UM-BBD Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule chebi_ontology Molekuel molecula molecules neutral molecular compounds molecule molecule IUPAC Molekuel ChEBI molecula IUPAC molecules IUPAC neutral molecular compounds IUPAC +1 0.00000 [*+] chebi_ontology monoatomic monocations monovalent inorganic cations monoatomic monocation monoatomic monocations ChEBI monovalent inorganic cations ChEBI chebi_ontology monoatomic polycations multivalent inorganic cations monoatomic polycation monoatomic polycations ChEBI multivalent inorganic cations ChEBI 0 N 14.007 14.00307 WebElements:N nitrogen chebi_ontology 7N N Stickstoff azote nitrogen nitrogeno nitrogen atom nitrogen IUPAC 7N IUPAC N IUPAC Stickstoff ChEBI azote IUPAC nitrogen ChEBI nitrogeno ChEBI nonmetal chebi_ontology Nichtmetall Nichtmetalle no metal no metales non-metal non-metaux nonmetal nonmetals nonmetal atom nonmetal IUPAC Nichtmetall ChEBI Nichtmetalle ChEBI no metal ChEBI no metales ChEBI non-metal ChEBI non-metaux ChEBI nonmetal ChEBI nonmetals ChEBI chebi_ontology organic heteromonocyclic compounds organic heteromonocyclic compound organic heteromonocyclic compounds ChEBI Any organic ion with a net negative charge. chebi_ontology organic anions organic anion organic anions ChEBI Any organic ion with a net positive charge. chebi_ontology organic cations organic cation organic cations ChEBI chebi_ontology organic ions organic ion organic ions ChEBI An oxide is a chemical compound of oxygen with other chemical elements. oxide chebi_ontology oxides oxide oxide ChEBI oxides ChEBI 0 O InChI=1S/O QVGXLLKOCUKJST-UHFFFAOYSA-N 15.99940 15.99491 [O] KEGG:C00007 WebElements:O oxygen chebi_ontology 8O O Sauerstoff oxigeno oxygen oxygene oxygen atom oxygen IUPAC 8O IUPAC O IUPAC Sauerstoff ChEBI oxigeno ChEBI oxygen ChEBI oxygene ChEBI oxygen molecular entity chebi_ontology oxygen molecular entities oxygen molecular entity oxygen molecular entity ChEBI oxygen molecular entities ChEBI chebi_ontology piperazines Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives. chebi_ontology pyridines 0 S InChI=1S/S NINIDFKCEFEMDL-UHFFFAOYSA-N 32.06600 31.97207 [S] CAS:7704-34-9 KEGG:C00087 KEGG:D06527 PPDB:605 WebElements:S sulfur chebi_ontology 16S Elemental sulfur S Schwefel azufre soufre sulfur sulphur theion sulfur atom CAS:7704-34-9 ChemIDplus CAS:7704-34-9 NIST Chemistry WebBook sulfur IUPAC 16S IUPAC Elemental sulfur KEGG_COMPOUND S IUPAC S KEGG_COMPOUND Schwefel ChEBI azufre ChEBI soufre ChEBI sulfur ChEBI sulfur UniProt sulphur ChEBI theion IUPAC sulfur molecular entity chebi_ontology sulfur molecular entities sulfur molecular entity sulfur molecular entity ChEBI sulfur molecular entities ChEBI Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Wikipedia:Micronutrient chebi_ontology micronutrients trace elements micronutrient micronutrients ChEBI trace elements ChEBI An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell. transition element chebi_ontology Uebergangselement Uebergangsmetalle metal de transicion metal de transition metales de transicion metaux de transition transition element transition elements transition metal transition metals transition element atom transition element IUPAC Uebergangselement ChEBI Uebergangsmetalle ChEBI metal de transicion ChEBI metal de transition ChEBI metales de transicion ChEBI metaux de transition ChEBI transition element ChEBI transition elements ChEBI transition metal ChEBI transition metals ChEBI +3 0.00000 [*+3] chebi_ontology monoatomic trications trivalent inorganic cations monoatomic trication monoatomic trications ChEBI trivalent inorganic cations ChEBI A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid. chebi_ontology univalent acyl group univalent carboacyl groups univalent carboxylic acyl groups univalent carboacyl group univalent acyl group ChEBI univalent carboacyl groups ChEBI univalent carboxylic acyl groups ChEBI An alkanesulfonic acid in which the alkyl group directly linked to the sulfo functionality is methyl. 0 CH4O3S InChI=1S/CH4O3S/c1-5(2,3)4/h1H3,(H,2,3,4) AFVFQIVMOAPDHO-UHFFFAOYSA-N 96.10666 95.98812 CS(O)(=O)=O CHEBI:6813 Beilstein:1446024 CAS:75-75-2 Gmelin:1681 KEGG:C11145 MetaCyc:CPD-3746 PMID:24304088 PMID:24593036 Reaxys:1446024 Wikipedia:Methanesulfonic_acid Methanesulfonic acid methanesulfonic acid chebi_ontology Methansulfonsaeure methylsulfonic acid methanesulfonic acid Beilstein:1446024 Beilstein CAS:75-75-2 ChemIDplus CAS:75-75-2 KEGG COMPOUND CAS:75-75-2 NIST Chemistry WebBook Gmelin:1681 Gmelin PMID:24304088 Europe PMC PMID:24593036 Europe PMC Reaxys:1446024 Reaxys Methanesulfonic acid KEGG_COMPOUND methanesulfonic acid IUPAC Methansulfonsaeure ChEBI methylsulfonic acid NIST_Chemistry_WebBook 0 C InChI=1S/C OKTJSMMVPCPJKN-UHFFFAOYSA-N 12.01070 12.00000 [C] CHEBI:23009 CHEBI:3399 CAS:7440-44-0 KEGG:C06265 WebElements:C carbon chebi_ontology 6C C Carbon Kohlenstoff carbon carbone carbonium carbono carbon atom CAS:7440-44-0 ChemIDplus CAS:7440-44-0 KEGG COMPOUND carbon IUPAC 6C IUPAC C IUPAC C KEGG_COMPOUND Carbon KEGG_COMPOUND Kohlenstoff ChEBI carbon ChEBI carbone ChEBI carbonium ChEBI carbono ChEBI An aromatic amide that consists of benzene bearing a single carboxamido substituent. The parent of the class of benzamides. 0 C7H7NO InChI=1S/C7H7NO/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H2,8,9) KXDAEFPNCMNJSK-UHFFFAOYSA-N 121.13662 121.05276 NC(=O)c1ccccc1 CHEBI:22701 CHEBI:3021 CHEBI:46351 Beilstein:385876 CAS:55-21-0 HMDB:HMDB0004461 KEGG:C09815 PMID:20133863 Reaxys:385876 UM-BBD_compID:c0368 Wikipedia:Benzamide Benzamide benzamide chebi_ontology Benzenecarboxamide Benzoic acid amide Benzoylamide PhC(=O)NH2 PhC(O)NH2 Phenylcarboxamide Phenylcarboxyamide benzamide Beilstein:385876 Beilstein CAS:55-21-0 ChemIDplus CAS:55-21-0 KEGG COMPOUND CAS:55-21-0 NIST Chemistry WebBook PMID:20133863 Europe PMC Reaxys:385876 Reaxys UM-BBD_compID:c0368 UM-BBD Benzamide KEGG_COMPOUND benzamide IUPAC Benzenecarboxamide ChemIDplus Benzoic acid amide ChemIDplus Benzoylamide ChemIDplus PhC(=O)NH2 ChEBI PhC(O)NH2 ChEBI Phenylcarboxamide ChemIDplus Phenylcarboxyamide ChemIDplus A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised. 0 CH3NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4) KXDHJXZQYSOELW-UHFFFAOYSA-N 61.04006 61.01638 NC(O)=O CHEBI:22504 CHEBI:23002 CHEBI:3386 CHEBI:44573 Beilstein:1734754 CAS:463-77-4 DrugBank:DB04261 Gmelin:130345 KEGG:C01563 PDBeChem:OUT Wikipedia:Carbamic_acid CARBAMIC ACID Carbamic acid carbamic acid chebi_ontology Aminoameisensaeure Aminoformic acid Carbamate Carbamidsaeure carbamic acid Beilstein:1734754 Beilstein CAS:463-77-4 ChemIDplus CAS:463-77-4 KEGG COMPOUND Gmelin:130345 Gmelin CARBAMIC ACID PDBeChem Carbamic acid KEGG_COMPOUND carbamic acid IUPAC Aminoameisensaeure ChEBI Aminoformic acid KEGG_COMPOUND Carbamate KEGG_COMPOUND Carbamidsaeure ChEBI 0 Cu InChI=1S/Cu RYGMFSIKBFXOCR-UHFFFAOYSA-N 63.54600 62.92960 [Cu] CHEBI:23376 CHEBI:3874 CAS:7440-50-8 Gmelin:16269 KEGG:C00070 WebElements:Cu copper chebi_ontology 29Cu Copper Cu Kupfer cobre copper cuivre cuprum copper atom CAS:7440-50-8 ChemIDplus CAS:7440-50-8 KEGG COMPOUND Gmelin:16269 Gmelin copper IUPAC 29Cu IUPAC Copper KEGG_COMPOUND Cu ChEBI Cu IUPAC Kupfer ChEBI cobre ChEBI copper ChEBI cuivre ChEBI cuprum IUPAC An onium cation obtained by protonation of ammonia. +1 H4N InChI=1S/H3N/h1H3/p+1 QGZKDVFQNNGYKY-UHFFFAOYSA-O 18.03850 18.03383 [H][N+]([H])([H])[H] CHEBI:22534 CHEBI:49783 CHEBI:7435 CAS:14798-03-9 Gmelin:84 KEGG:C01342 MetaCyc:AMMONIUM MolBase:929 PDBeChem:NH4 PMID:11319011 PMID:11341317 PMID:12096804 PMID:14512268 PMID:14879753 PMID:16345391 PMID:16903292 PMID:17392693 PMID:18515490 PMID:19199063 PMID:19596600 PMID:19682559 PMID:19716251 PMID:21993530 PMID:22265469 PMID:22524020 PMID:22562341 PMID:22631217 Reaxys:16093784 Wikipedia:Ammonium ammonium azanium chebi_ontology Ammonium(1+) NH4(+) NH4+ [NH4](+) ammonium ion ammonium CAS:14798-03-9 ChemIDplus CAS:14798-03-9 NIST Chemistry WebBook Gmelin:84 Gmelin PMID:11319011 Europe PMC PMID:11341317 Europe PMC PMID:12096804 Europe PMC PMID:14512268 Europe PMC PMID:14879753 Europe PMC PMID:16345391 Europe PMC PMID:16903292 Europe PMC PMID:17392693 Europe PMC PMID:18515490 Europe PMC PMID:19199063 Europe PMC PMID:19596600 Europe PMC PMID:19682559 Europe PMC PMID:19716251 Europe PMC PMID:21993530 Europe PMC PMID:22265469 Europe PMC PMID:22524020 Europe PMC PMID:22562341 Europe PMC PMID:22631217 Europe PMC Reaxys:16093784 Reaxys ammonium ChEBI ammonium IUPAC azanium IUPAC Ammonium(1+) ChemIDplus NH4(+) IUPAC NH4(+) UniProt NH4+ KEGG_COMPOUND [NH4](+) MolBase ammonium ion PDBeChem An ion of copper carrying a double positive charge. +2 Cu InChI=1S/Cu/q+2 JPVYNHNXODAKFH-UHFFFAOYSA-N 63.54600 62.92850 [Cu++] CHEBI:20882 CHEBI:23380 CHEBI:49550 CAS:15158-11-9 Gmelin:6855 PDBeChem:CU PMID:23900424 PMID:24168430 Reaxys:3587177 copper(2+) copper(2+) ion copper(II) cation chebi_ontology COPPER (II) ION Cu(2+) Cu(II) Cu2+ copper(II) cation copper, ion (Cu2+) cupric ion copper(2+) CAS:15158-11-9 ChemIDplus Gmelin:6855 Gmelin PMID:23900424 Europe PMC PMID:24168430 Europe PMC Reaxys:3587177 Reaxys copper(2+) IUPAC copper(2+) ion IUPAC copper(II) cation IUPAC COPPER (II) ION PDBeChem Cu(2+) UniProt Cu(II) ChEBI Cu2+ ChEBI copper(II) cation ChEBI copper, ion (Cu2+) ChemIDplus cupric ion ChEBI +3 Cu InChI=1S/Cu/q+3 XYNZKHQSHVOGHB-UHFFFAOYSA-N 63.544 62.92795 [Cu+3] CHEBI:20883 CHEBI:23381 PDBeChem:CU3 Cu(3+) copper(3+) copper(3+) ion copper(III) cation chebi_ontology Cu(III) Cu3+ copper(III) cation copper(3+) Cu(3+) IUPAC copper(3+) IUPAC copper(3+) ion IUPAC copper(III) cation IUPAC Cu(III) ChEBI Cu3+ ChEBI copper(III) cation ChEBI The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated. -1 CO2R 44.00950 43.98983 [O-]C([*])=O CHEBI:13626 CHEBI:13945 CHEBI:23026 CHEBI:58657 chebi_ontology a carboxylate carboxylic acid anions carboxylic anions carboxylic acid anion a carboxylate UniProt carboxylic acid anions ChEBI carboxylic anions ChEBI 0 H2O3S InChI=1S/H2O3S/c1-4(2)3/h4H,(H,1,2,3) BDHFUVZGWQCTTF-UHFFFAOYSA-N 82.08008 81.97247 [H]S(O)(=O)=O Gmelin:1404640 hydridohydroxidodioxidosulfur sulfonic acid chebi_ontology HSHO3 Sulfonsaeure [SHO2(OH)] acide sulfonique sulphonic acid sulfonic acid Gmelin:1404640 Gmelin hydridohydroxidodioxidosulfur IUPAC sulfonic acid IUPAC HSHO3 IUPAC Sulfonsaeure ChEBI [SHO2(OH)] IUPAC acide sulfonique ChEBI sulphonic acid ChEBI -1 H2N InChI=1S/H2N/h1H2/q-1 HYGWNUKOUCZBND-UHFFFAOYSA-N 16.02262 16.01927 [H][N-][H] amide azanide dihydridonitrate(1-) chebi_ontology NH2(-) azanide amide IUPAC azanide IUPAC dihydridonitrate(1-) IUPAC NH2(-) IUPAC A divalent inorganic anion resulting from the removal of two protons from ammonia. -2 HN InChI=1S/HN/h1H/q-2 DZQYTNGKSBCIOE-UHFFFAOYSA-N 15.01468 15.01200 [N--][H] azanediide hydridonitrate(2-) chebi_ontology NH(2-) imide hydridonitrate(2-) azanediide IUPAC hydridonitrate(2-) IUPAC NH(2-) IUPAC imide IUPAC A carboxamide derived from a monocarboxylic acid. 0 CNOR3 42.01680 41.99799 [*]N([*])C([*])=O CHEBI:13211 CHEBI:22207 CHEBI:25383 CHEBI:6977 chebi_ontology monocarboxylic acid amides monocarboxylic acid amide monocarboxylic acid amides ChEBI 0 HO3S 81.07214 80.96464 S(=O)(O)(*)=O PDBeChem:SFO SULFO GROUP hydroxydioxo-lambda(6)-sulfanyl hydroxysulfonyl sulfo chebi_ontology -S(O)2(OH) sulfo group SULFO GROUP PDBeChem hydroxydioxo-lambda(6)-sulfanyl IUPAC hydroxysulfonyl IUPAC sulfo IUPAC -S(O)2(OH) IUPAC 0 Cu InChI=1S/Cu RYGMFSIKBFXOCR-UHFFFAOYSA-N 63.54600 62.92960 [Cu] CAS:7440-50-8 copper copper(0) chebi_ontology Cu(0) Cun copper(0) CAS:7440-50-8 ChemIDplus CAS:7440-50-8 NIST Chemistry WebBook copper IUPAC copper(0) IUPAC Cu(0) ChEBI Cun IUPAC Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force. 0 0.0 0.0 * CHEBI:10581 CHEBI:14383 KEGG:C00205 photon chebi_ontology Lichtquant Light foton gamma hnu light quantum photon photon IUPAC Lichtquant ChEBI Light KEGG_COMPOUND foton ChEBI gamma IUPAC hnu IUPAC hnu UniProt light quantum ChEBI +2 0.00000 [*++] CHEBI:23856 CHEBI:4665 KEGG:C00572 chebi_ontology Divalent cation divalent inorganic cations monoatomic dications monoatomic dication Divalent cation KEGG_COMPOUND divalent inorganic cations ChEBI monoatomic dications ChEBI A methanesulfonate (mesylate) salt that is the monomesylate salt of imatinib. Used for treatment of chronic myelogenous leukemia and gastrointestinal stromal tumours. 0 C29H31N7O.CH4O3S C30H35N7O4S InChI=1S/C29H31N7O.CH4O3S/c1-21-5-10-25(18-27(21)34-29-31-13-11-26(33-29)24-4-3-12-30-19-24)32-28(37)23-8-6-22(7-9-23)20-36-16-14-35(2)15-17-36;1-5(2,3)4/h3-13,18-19H,14-17,20H2,1-2H3,(H,32,37)(H,31,33,34);1H3,(H,2,3,4) YLMAHDNUQAMNNX-UHFFFAOYSA-N 589.70968 589.24712 CS(O)(=O)=O.CN1CCN(CC1)Cc1ccc(cc1)C(=O)Nc1ccc(C)c(Nc2nccc(n2)-c2cccnc2)c1 Beilstein:10229624 CAS:220127-57-1 DrugBank:DB00619 HMDB:HMDB0014757 KEGG:D01441 PMID:12047970 PMID:12616857 PMID:12669406 PMID:12975485 PMID:14760091 PMID:15059881 PMID:15161340 PMID:15206509 PMID:15250677 PMID:15601563 PMID:15727903 PMID:16570351 PMID:16805961 PMID:16835496 PMID:17212133 PMID:18422477 PMID:19073506 PMID:19258052 PMID:19508953 PMID:19542718 PMID:19568828 PMID:21084823 PMID:21333826 PMID:23462796 Patent:RU2365587 Patent:WO2004106326 Patent:WO2011161689 Patent:WO9903854 Reaxys:10229624 4-[(4-methylpiperazin-1-yl)methyl]-N-{4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl}benzamide methanesulfonate chebi_ontology Gleevec Glivec imatinib mesilate imatinib mesylate imatinib methansulfonate imatinib monomesylate imatinib methanesulfonate Beilstein:10229624 Beilstein CAS:220127-57-1 ChemIDplus CAS:220127-57-1 KEGG DRUG PMID:12047970 Europe PMC PMID:12616857 Europe PMC PMID:12669406 Europe PMC PMID:12975485 Europe PMC PMID:14760091 Europe PMC PMID:15059881 Europe PMC PMID:15161340 Europe PMC PMID:15206509 Europe PMC PMID:15250677 Europe PMC PMID:15601563 Europe PMC PMID:15727903 Europe PMC PMID:16570351 Europe PMC PMID:16805961 Europe PMC PMID:16835496 Europe PMC PMID:17212133 Europe PMC PMID:18422477 Europe PMC PMID:19073506 Europe PMC PMID:19258052 Europe PMC PMID:19508953 Europe PMC PMID:19542718 Europe PMC PMID:19568828 Europe PMC PMID:21084823 Europe PMC PMID:21333826 Europe PMC PMID:23462796 Europe PMC Reaxys:10229624 Reaxys 4-[(4-methylpiperazin-1-yl)methyl]-N-{4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl}benzamide methanesulfonate IUPAC Gleevec DrugBank Glivec DrugBank imatinib mesilate DrugBank imatinib mesylate KEGG_DRUG imatinib methansulfonate DrugBank imatinib monomesylate ChEBI An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. CHEBI:22473 CHEBI:2633 KEGG:C00241 Amide amides chebi_ontology amide Amide KEGG_COMPOUND amides IUPAC Intended use of the molecular entity or part thereof by humans. chebi_ontology application A particle not known to have substructure. elementary particle chebi_ontology elementary particles fundamental particle elementary particle IUPAC elementary particles ChEBI A monoatomic entity is a molecular entity consisting of a single atom. chebi_ontology atomic entity monoatomic entities monoatomic entity atomic entity ChEBI monoatomic entities ChEBI chebi_ontology oxoacid derivatives oxoacid derivative oxoacid derivatives ChEBI chebi_ontology inorganic hydrides inorganic hydride inorganic hydrides ChEBI An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system. chebi_ontology organic fundamental parents organic parent hydrides organic fundamental parent organic fundamental parents ChEBI organic parent hydrides ChEBI Any substituent group which does not contain carbon. chebi_ontology inorganic groups inorganic group inorganic groups ChEBI Any substituent group or skeleton containing carbon. chebi_ontology organic groups organic group organic groups ChEBI A univalent group formed by removing a hydrogen atom from a hydrocarbon. hydrocarbyl group hydrocarbyl groups chebi_ontology groupe hydrocarbyle grupo hidrocarbilo grupos hidrocarbilo hydrocarbyl group hydrocarbyl group IUPAC hydrocarbyl groups IUPAC groupe hydrocarbyle IUPAC grupo hidrocarbilo IUPAC grupos hidrocarbilo IUPAC Any organic substituent group, regardless of functional type, having one free valence at a carbon atom. organyl group organyl groups chebi_ontology groupe organyle grupo organilo grupos organilo organyl group organyl group IUPAC organyl groups IUPAC groupe organyle IUPAC grupo organilo IUPAC grupos organilo IUPAC Heavy nuclear particle: proton or neutron. nucleon chebi_ontology Nukleon Nukleonen nucleons nucleon nucleon IUPAC nucleon IUPAC Nukleon ChEBI Nukleonen ChEBI nucleons ChEBI A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. primary amide primary amides chebi_ontology primary amide primary amide IUPAC primary amides IUPAC A molecular entity all atoms of which have the same atomic number. chebi_ontology homoatomic entity homoatomic molecular entities homoatomic molecular entity elemental molecular entity homoatomic entity ChEBI homoatomic molecular entities ChEBI homoatomic molecular entity ChEBI An organosulfur compound is a compound containing at least one carbon-sulfur bond. CHEBI:23010 CHEBI:25714 Wikipedia:Organosulfur_compounds organosulfur compound chebi_ontology organosulfur compounds organosulfur compound organosulfur compound ChEBI organosulfur compounds ChEBI An anion consisting of more than one atom. chebi_ontology polyatomic anions polyatomic anion polyatomic anions ChEBI A nutrient is a food component that an organism uses to survive and grow. chebi_ontology nutrients nutrient nutrients ChEBI A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. chebi_ontology heteroorganic entities organoelement compounds heteroorganic entity heteroorganic entities ChEBI organoelement compounds ChEBI Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogens chebi_ontology group 15 elements group V elements nitrogenoideos nitrogenoides pnictogene pnictogenes pnictogen pnictogens IUPAC group 15 elements ChEBI group V elements ChEBI nitrogenoideos ChEBI nitrogenoides ChEBI pnictogene ChEBI pnictogenes ChEBI A p-block molecular entity containing any pnictogen. pnictogen molecular entity chebi_ontology pnictogen molecular entities pnictogen molecular entity pnictogen molecular entity ChEBI pnictogen molecular entities ChEBI Any p-block element belonging to the group 16 family of the periodic table. PMID:17084588 chalcogen chalcogens chebi_ontology Chalkogen Chalkogene anfigeno anfigenos calcogeno calcogenos chalcogene chalcogenes group 16 elements group VI elements chalcogen PMID:17084588 Europe PMC chalcogen IUPAC chalcogens IUPAC Chalkogen ChEBI Chalkogene ChEBI anfigeno ChEBI anfigenos ChEBI calcogeno ChEBI calcogenos ChEBI chalcogene ChEBI chalcogenes ChEBI group 16 elements ChEBI group VI elements ChEBI Any p-block molecular entity containing a chalcogen. chalcogen molecular entity chebi_ontology chalcogen compounds chalcogen molecular entities chalcogen molecular entity chalcogen molecular entity ChEBI chalcogen compounds ChEBI chalcogen molecular entities ChEBI group 14 elements chebi_ontology carbon group element carbon group elements carbonoides cristallogene cristallogenes group IV elements carbon group element atom group 14 elements IUPAC carbon group element ChEBI carbon group elements ChEBI carbonoides ChEBI cristallogene ChEBI cristallogenes ChEBI group IV elements ChEBI An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group elements chebi_ontology Hauptgruppenelement Hauptgruppenelemente main group element main group element atom main group elements IUPAC Hauptgruppenelement ChEBI Hauptgruppenelemente ChEBI main group element ChEBI group 11 elements chebi_ontology coinage metals copper group element copper group elements copper group element atom group 11 elements IUPAC coinage metals ChEBI copper group element ChEBI copper group elements ChEBI chebi_ontology oxoacids of sulfur sulfur oxoacids sulfur oxoacid oxoacids of sulfur ChEBI sulfur oxoacids ChEBI sulfur oxoacid derivative chebi_ontology sulfur oxoacid derivatives sulfur oxoacid derivative sulfur oxoacid derivative ChEBI sulfur oxoacid derivatives ChEBI sulfur oxoanion chebi_ontology oxoanions of sulfur sulfur oxoanions sulfur oxoanion sulfur oxoanion ChEBI oxoanions of sulfur ChEBI sulfur oxoanions ChEBI chalcogen oxoacid chebi_ontology chalcogen oxoacids chalcogen oxoacid chalcogen oxoacid ChEBI chalcogen oxoacids ChEBI chalcogen oxoanion chebi_ontology chalcogen oxoanions chalcogen oxoanion chalcogen oxoanion ChEBI chalcogen oxoanions ChEBI A molecular entity containing one or more atoms of a transition element. chebi_ontology transition element molecular entities transition metal molecular entity transition element molecular entity transition element molecular entities ChEBI transition metal molecular entity ChEBI chebi_ontology transition element cations transition metal cation transition element cation transition element cations ChEBI transition metal cation ChEBI An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. CHEBI:25217 CHEBI:6788 KEGG:C00050 PMID:21784043 Wikipedia:Metal chebi_ontology elemental metal elemental metals metal element metal elements metals metal atom PMID:21784043 Europe PMC elemental metal ChEBI elemental metals ChEBI metal element ChEBI metal elements ChEBI metals ChEBI The sulfur oxoanion formed by deprotonation of sulfonic acid. -1 HO3S InChI=1S/H2O3S/c1-4(2)3/h4H,(H,1,2,3)/p-1 BDHFUVZGWQCTTF-UHFFFAOYSA-M 81.07214 80.96519 [H]S([O-])(=O)=O Gmelin:971569 hydridotrioxidosulfate(1-) chebi_ontology SHO3(-) [SHO3](-) sulfonates sulfonate Gmelin:971569 Gmelin hydridotrioxidosulfate(1-) IUPAC SHO3(-) IUPAC [SHO3](-) IUPAC sulfonates ChEBI An organic derivative of sulfonic acid in which the sulfo group is linked directly to carbon. 0 HO3SR 81.07100 80.96464 OS([*])(=O)=O chebi_ontology organosulfonic acids sulfonic acids organosulfonic acid organosulfonic acids ChEBI sulfonic acids ChEBI sulfonic acid derivative chebi_ontology derivatives of sulfonic acid sulfonic acid derivatives sulfonic acid derivative sulfonic acid derivative ChEBI derivatives of sulfonic acid ChEBI sulfonic acid derivatives ChEBI An organic anion obtained by deprotonation of the sufonate group(s) of any organosulfonic acid. -1 O3SR 80.064 79.95681 *S([O-])(=O)=O chebi_ontology organosulfonate organosulfonate oxoanions organosulfonates organosulfonate oxoanion organosulfonate ChEBI organosulfonate oxoanions ChEBI organosulfonates ChEBI chebi_ontology s-block element s-block elements s-block element atom s-block element ChEBI s-block elements ChEBI Any main group element atom belonging to the p-block of the periodic table. chebi_ontology p-block element p-block elements p-block element atom p-block element ChEBI p-block elements ChEBI chebi_ontology d-block element d-block elements d-block element atom d-block element ChEBI d-block elements ChEBI A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. 0 CHO2R 45.01740 44.99765 OC([*])=O CHEBI:13428 CHEBI:13627 CHEBI:23027 PMID:17147560 PMID:18433345 Wikipedia:Carboxylic_acid carboxylic acid carboxylic acids chebi_ontology Carbonsaeure Carbonsaeuren Karbonsaeure RC(=O)OH acide carboxylique acides carboxyliques acido carboxilico acidos carboxilicos carboxylic acid PMID:17147560 Europe PMC PMID:18433345 Europe PMC carboxylic acid IUPAC carboxylic acids IUPAC Carbonsaeure ChEBI Carbonsaeuren ChEBI Karbonsaeure ChEBI RC(=O)OH IUPAC acide carboxylique IUPAC acides carboxyliques IUPAC acido carboxilico IUPAC acidos carboxilicos IUPAC A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. chebi_ontology main group compounds main group molecular entities main group molecular entity main group compounds ChEBI main group molecular entities ChEBI carbon group molecular entity chebi_ontology carbon group molecular entities carbon group molecular entity carbon group molecular entity ChEBI carbon group molecular entities ChEBI Any molecule that consists of a series of atoms joined together to form a ring. Wikipedia:Cyclic_compound chebi_ontology cyclic compounds cyclic compound cyclic compounds ChEBI A cyclic compound having as ring members atoms of the same element only. homocyclic compound homocyclic compounds chebi_ontology isocyclic compounds homocyclic compound homocyclic compound IUPAC homocyclic compounds IUPAC isocyclic compounds IUPAC A homocyclic compound in which all of the ring members are carbon atoms. carbocyclic compound carbocyclic compounds chebi_ontology carbocycle carbocyclic compound carbocyclic compound IUPAC carbocyclic compounds IUPAC carbocycle ChEBI chebi_ontology hydrogen compounds hydrogen molecular entities hydrogen molecular entity hydrogen compounds ChEBI hydrogen molecular entities ChEBI Any acyclic or cyclic, saturated or unsaturated carbon compound, excluding aromatic compounds. aliphatic compounds chebi_ontology aliphatic compound aliphatic compounds IUPAC A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character. aromatic compounds aromatic molecular entity chebi_ontology aromatics aromatische Verbindungen aromatic compound aromatic compounds IUPAC aromatic molecular entity IUPAC aromatics ChEBI aromatische Verbindungen ChEBI Any monocyclic or polycyclic aromatic hydrocarbon. arene arenes chebi_ontology aromatic hydrocarbons arene arene IUPAC arenes IUPAC aromatic hydrocarbons IUPAC chebi_ontology organic aromatic compounds organic aromatic compound organic aromatic compounds ChEBI chebi_ontology monocyclic compounds monocyclic compound monocyclic compounds ChEBI A mancude monocyclic hydrocarbon without side chains of the general formula CnHn (n is an even number) or CnHn+1 (n is an odd number). In systematic nomenclature an annulene with seven or more carbon atoms may be named [n]annulene, where n is the number of carbon atoms. annulene annulenes chebi_ontology annulene annulene IUPAC annulenes IUPAC cyclic hydrocarbon chebi_ontology cyclic hydrocarbons cyclic hydrocarbon cyclic hydrocarbon ChEBI cyclic hydrocarbons ChEBI monocyclic hydrocarbon monocyclic hydrocarbons chebi_ontology monocyclic hydrocarbons monocyclic hydrocarbon monocyclic hydrocarbon ChEBI monocyclic hydrocarbons IUPAC monocyclic hydrocarbons ChEBI heteromonocyclic compound heteromonocyclic compounds chebi_ontology heteromonocyclic compound heteromonocyclic compound IUPAC heteromonocyclic compounds IUPAC An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity chebi_ontology s-block compounds s-block molecular entities s-block molecular entity s-block molecular entity ChEBI s-block compounds ChEBI s-block molecular entities ChEBI A main group molecular entity that contains one or more atoms of a p-block element. chebi_ontology p-block compounds p-block molecular entities p-block molecular entitiy p-block molecular entity p-block compounds ChEBI p-block molecular entities ChEBI p-block molecular entitiy ChEBI A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element. d-block molecular entity chebi_ontology d-block compounds d-block molecular entities d-block molecular entity d-block molecular entity ChEBI d-block compounds ChEBI d-block molecular entities ChEBI Hydrides are chemical compounds of hydrogen with other chemical elements. chebi_ontology hydrides When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue. amino-acid residue chebi_ontology amino acid residue amino-acid residues amino-acid residue amino-acid residue IUPAC amino acid residue ChEBI amino-acid residues JCBN A carboxylic acid containing one or more amino groups. CHEBI:13815 CHEBI:22477 Wikipedia:Amino_acid chebi_ontology Aminocarbonsaeure Aminokarbonsaeure Aminosaeure amino acids amino acid Aminocarbonsaeure ChEBI Aminokarbonsaeure ChEBI Aminosaeure ChEBI amino acids ChEBI copper group molecular entity chebi_ontology copper group molecular entities copper group molecular entity copper group molecular entity ChEBI copper group molecular entities ChEBI Any organic molecule that consists of atoms connected in the form of a ring. chebi_ontology organic cyclic compounds organic cyclic compound organic cyclic compounds ChEBI chebi_ontology benzenoid aromatic compounds benzenoid compound benzenoid aromatic compound benzenoid aromatic compounds ChEBI benzenoid compound ChEBI chebi_ontology aromatic annulenes aromatic annulene aromatic annulenes ChEBI A monocyclic aromatic hydrocarbon. chebi_ontology monocyclic arenes monocyclic arene monocyclic arenes ChEBI An amino compound in which the amino group is linked directly to an aromatic system. CHEBI:13827 CHEBI:22622 CHEBI:22646 CHEBI:2834 CHEBI:2863 chebi_ontology aromatic amines aryl amine aryl amines arylamine arylamines aromatic amine aromatic amines ChEBI aryl amine ChEBI aryl amines ChEBI arylamine ChEBI arylamines ChEBI A substance used in a chemical reaction to detect, measure, examine, or produce other substances. reagent chebi_ontology reactif reactivo reagents reagent reagent IUPAC reactif IUPAC reactivo IUPAC reagents ChEBI chebi_ontology macronutrient chebi_ontology nitrogen hydrides nitrogen hydride nitrogen hydrides ChEBI Saturated acyclic nitrogen hydrides having the general formula NnHn+2. chebi_ontology azanes azane azanes ChEBI A substance that diminishes the rate of a chemical reaction. inhibitor chebi_ontology inhibidor inhibiteur inhibitors inhibitor inhibitor IUPAC inhibidor ChEBI inhibiteur ChEBI inhibitors ChEBI Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compounds chebi_ontology organonitrogens organonitrogen compound organonitrogen compounds IUPAC organonitrogens ChEBI An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. CHEBI:33274 CHEBI:33436 oxoanion chebi_ontology oxoacid anions oxoanions oxoanion oxoanion ChEBI oxoacid anions ChEBI oxoanions ChEBI chebi_ontology carbon oxoacids oxoacids of carbon carbon oxoacid carbon oxoacids ChEBI oxoacids of carbon ChEBI A substance that inhibits or prevents the proliferation of neoplasms. chebi_ontology anticancer agent anticancer agents antineoplastic antineoplastic agents cytostatic antineoplastic agent anticancer agent ChEBI anticancer agents ChEBI antineoplastic ChEBI antineoplastic agents ChEBI cytostatic ChEBI A xenobiotic (Greek, xenos "foreign"; bios "life") is a compound that is foreign to a living organism. Principal xenobiotics include: drugs, carcinogens and various compounds that have been introduced into the environment by artificial means. CHEBI:10074 CHEBI:27333 KEGG:C06708 Wikipedia:Xenobiotic Xenobiotic xenobiotic xenobiotics chebi_ontology xenobiotic compounds xenobiotic Xenobiotic KEGG_COMPOUND xenobiotic IUPAC xenobiotics IUPAC xenobiotic compounds ChEBI pnictogen hydride chebi_ontology pnictogen hydrides pnictogen hydride pnictogen hydride ChEBI pnictogen hydrides ChEBI Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin). chebi_ontology leptons lepton leptons ChEBI Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). chebi_ontology baryons baryon baryons ChEBI Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. fermion chebi_ontology fermions fermion fermion IUPAC fermions ChEBI Particle of integer spin quantum number following Bose-Einstein statistics. Bosons are named after Satyendra Nath Bose. boson chebi_ontology bosons boson boson IUPAC bosons ChEBI A subatomic particle known to have substructure (i.e. consisting of smaller particles). chebi_ontology composite particles composite particle composite particles ChEBI Hadron is a subatomic particle which experiences the strong force. chebi_ontology hadrons hadron hadrons ChEBI A nucleus or any of its constituents in any of their energy states. nuclear particle chebi_ontology nuclear particle nuclear particle IUPAC Any molecular entity consisting of more than one atom. chebi_ontology polyatomic entities polyatomic entity polyatomic entities ChEBI An ion consisting of more than one atom. chebi_ontology polyatomic ions polyatomic ion polyatomic ions ChEBI Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. carbonyl compounds chebi_ontology carbonyl compound carbonyl compounds IUPAC Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. oxo compounds chebi_ontology organic oxo compounds organic oxo compound oxo compounds IUPAC organic oxo compounds ChEBI chebi_ontology inorganic ions inorganic ion inorganic ions ChEBI chebi_ontology inorganic cations inorganic cation inorganic cations ChEBI A monoatomic or polyatomic species having one or more elementary charges of the proton. CHEBI:23058 CHEBI:3473 KEGG:C01373 Cation cation chebi_ontology Kation Kationen cationes cations cation Cation KEGG_COMPOUND cation ChEBI cation IUPAC Kation ChEBI Kationen ChEBI cationes ChEBI cations ChEBI An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound chebi_ontology organochalcogen compounds organochalcogen compound organochalcogen compound ChEBI organochalcogen compounds ChEBI An organochalcogen compound containing at least one carbon-oxygen bond. PMID:17586126 organooxygen compound chebi_ontology organooxygen compounds organooxygen compound PMID:17586126 Europe PMC organooxygen compound ChEBI organooxygen compounds ChEBI amino-acid anion chebi_ontology amino acid anions amino-acid anions amino-acid anion amino-acid anion ChEBI amino acid anions ChEBI amino-acid anions ChEBI chebi_ontology organic hydrides organic hydride organic hydrides ChEBI mononuclear parent hydrides chebi_ontology mononuclear hydride mononuclear hydrides mononuclear parent hydride mononuclear parent hydrides IUPAC mononuclear hydride ChEBI mononuclear hydrides IUPAC chebi_ontology elemental copper An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid). CHEBI:13800 CHEBI:13801 CHEBI:22209 CHEBI:2426 KEGG:C00174 Acid acid chebi_ontology Saeure Saeuren acide acido acids acid Acid KEGG_COMPOUND acid IUPAC Saeure ChEBI Saeuren ChEBI acide IUPAC acido ChEBI acids ChEBI A molecular entity consisting of two or more chemical elements. chebi_ontology chemical compound heteroatomic molecular entities heteroatomic molecular entity chemical compound ChEBI heteroatomic molecular entities ChEBI An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom. 0 CNOR3 42.01680 41.99799 [*]C(=O)N([*])[*] CHEBI:35354 CHEBI:35355 carboxamides chebi_ontology carboxamides primary carboxamide carboxamide carboxamides IUPAC carboxamides ChEBI primary carboxamide ChEBI An EC 2.7.* (P-containing group transferase) inhibitor that interferes with the action of protein kinases. chebi_ontology protein kinase inhibitors protein kinase inhibitor protein kinase inhibitors ChEBI A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid. carboacyl groups carboxylic acyl group chebi_ontology carboxylic acyl groups carboacyl group carboacyl groups IUPAC carboxylic acyl group IUPAC carboxylic acyl groups IUPAC chebi_ontology mesylate salt mesylate salts methanesulfonate salts methanesulfonate salt mesylate salt ChEBI mesylate salts ChEBI methanesulfonate salts ChEBI Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. chebi_ontology heterocyclic organonitrogen compounds organonitrogen heterocyclic compounds organonitrogen heterocyclic compound heterocyclic organonitrogen compounds ChEBI organonitrogen heterocyclic compounds ChEBI Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure). chebi_ontology diazines Any protein kinase inhibitor that interferes with the action of tyrosine kinase. Wikipedia:Tyrosine-kinase_inhibitor chebi_ontology TKI inhibitor TKI inhibitors protein tyrosine kinase inhibitor protein tyrosine kinase inhibitors tyrosine kinase inhibitors tyrphostin tyrphostins tyrosine kinase inhibitor TKI inhibitor ChEBI TKI inhibitors ChEBI protein tyrosine kinase inhibitor ChEBI protein tyrosine kinase inhibitors ChEBI tyrosine kinase inhibitors ChEBI tyrphostin ChEBI tyrphostins ChEBI An analogue of imatinib where the piperidine N-methyl group is replaced by 2-aminoethyl. 0 C30H34N8O InChI=1S/C30H34N8O/c1-22-4-9-26(19-28(22)36-30-33-13-10-27(35-30)25-3-2-12-32-20-25)34-29(39)24-7-5-23(6-8-24)21-38-17-15-37(14-11-31)16-18-38/h2-10,12-13,19-20H,11,14-18,21,31H2,1H3,(H,34,39)(H,33,35,36) GYQHZALGPJRESJ-UHFFFAOYSA-N 522.64428 522.28556 Cc1ccc(NC(=O)c2ccc(CN3CCN(CCN)CC3)cc2)cc1Nc1nccc(n1)-c1cccnc1 4-{[4-(2-aminoethyl)piperazin-1-yl]methyl}-N-{4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl}benzamide chebi_ontology linkable imatinib analogue 4-{[4-(2-aminoethyl)piperazin-1-yl]methyl}-N-{4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl}benzamide IUPAC A molecular entity capable of donating a hydron to an acceptor (Bronsted base). Bronsted acid chebi_ontology Bronsted-Saeure acide de Bronsted donneur d'hydron hydron donor Bronsted acid Bronsted acid IUPAC Bronsted-Saeure ChEBI acide de Bronsted IUPAC donneur d'hydron IUPAC hydron donor IUPAC A molecular entity capable of accepting a hydron from a donor (Bronsted acid). Bronsted base chebi_ontology Bronsted-Base accepteur d'hydron base de Bronsted hydron acceptor Bronsted base Bronsted base IUPAC Bronsted-Base ChEBI accepteur d'hydron IUPAC base de Bronsted IUPAC hydron acceptor IUPAC A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct. Lewis base chebi_ontology Lewis-Base base de Lewis donneur d'une paire d'electrons electron donor Lewis base Lewis base IUPAC Lewis-Base ChEBI base de Lewis IUPAC donneur d'une paire d'electrons ChEBI electron donor ChEBI Any compound having a pyrimidine as part of its structure. CHEBI:13681 CHEBI:26448 chebi_ontology pyrimidines 0 HO 17.00734 17.00274 *O[H] CHEBI:24706 CHEBI:43171 PDBeChem:OH HYDROXY GROUP hydroxy hydroxy group chebi_ontology -OH hydroxyl hydroxyl group hydroxy group HYDROXY GROUP PDBeChem hydroxy IUPAC hydroxy group UniProt -OH IUPAC hydroxyl ChEBI hydroxyl group ChEBI A benzamide obtained by formal condensation of the carboxy group of 4-[(4-methylpiperazin-1-yl)methyl]benzoic acid with the primary aromatic amino group of 4-methyl-N(3)-[4-(pyridin-3-yl)pyrimidin-2-yl]benzene-1,3-diamine. Used (as its mesylate salt) for treatment of chronic myelogenous leukemia and gastrointestinal stromal tumours. 0 C29H31N7O InChI=1S/C29H31N7O/c1-21-5-10-25(18-27(21)34-29-31-13-11-26(33-29)24-4-3-12-30-19-24)32-28(37)23-8-6-22(7-9-23)20-36-16-14-35(2)15-17-36/h3-13,18-19H,14-17,20H2,1-2H3,(H,32,37)(H,31,33,34) KTUFNOKKBVMGRW-UHFFFAOYSA-N 493.60270 493.25901 CN1CCN(Cc2ccc(cc2)C(=O)Nc2ccc(C)c(Nc3nccc(n3)-c3cccnc3)c2)CC1 CHEBI:305376 CHEBI:38918 CHEBI:45781 Beilstein:7671333 CAS:152459-95-5 DrugBank:DB00619 Drug_Central:1423 HMDB:HMDB0014757 KEGG:D08066 LINCS:LSM-1023 PDBeChem:STI PMID:14660054 PMID:14715630 PMID:15073101 PMID:15170967 PMID:15722647 PMID:15794712 PMID:15966213 PMID:16122278 PMID:16826359 PMID:16983347 PMID:17190842 PMID:17410337 PMID:17457302 PMID:17717205 PMID:18193246 PMID:18216472 PMID:18337118 PMID:18344535 PMID:18376233 PMID:18407734 PMID:18420270 PMID:18423008 PMID:18548219 PMID:18623899 PMID:18780518 PMID:18809244 PMID:19020005 PMID:19052981 PMID:19077095 PMID:19097599 PMID:19182535 PMID:19242505 PMID:19415889 PMID:19527930 PMID:19591692 PMID:19693287 PMID:19749465 PMID:19810774 PMID:19853594 PMID:19920908 PMID:22891806 PMID:23075630 PMID:23183914 PMID:23313020 PMID:23394269 PMID:23480638 PMID:23503753 PMID:23536338 PMID:23574742 PMID:23580311 PMID:23587588 Patent:EP564409 Patent:US5521184 Reaxys:7671333 Wikipedia:Imatinib 4-[(4-methylpiperazin-1-yl)methyl]-N-{4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl}benzamide chebi_ontology 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE STI 571 alpha-(4-methyl-1-piperazinyl)-3'-((4-(3-pyridyl)-2-pyrimidinyl)amino)-p-toluidide imatinib imatinib PMID:17190842 Europe PMC PMID:17410337 Europe PMC PMID:17457302 Europe PMC PMID:17717205 Europe PMC PMID:18193246 Europe PMC PMID:18216472 Europe PMC PMID:18337118 Europe PMC PMID:18344535 Europe PMC PMID:18376233 Europe PMC PMID:18407734 Europe PMC PMID:18420270 Europe PMC PMID:18423008 Europe PMC PMID:18548219 Europe PMC PMID:18623899 Europe PMC PMID:18780518 Europe PMC PMID:18809244 Europe PMC PMID:19020005 Europe PMC PMID:19052981 Europe PMC PMID:19077095 Europe PMC PMID:19097599 Europe PMC PMID:19182535 Europe PMC PMID:19242505 Europe PMC PMID:19415889 Europe PMC PMID:19527930 Europe PMC PMID:19591692 Europe PMC PMID:19693287 Europe PMC PMID:19749465 Europe PMC PMID:19810774 Europe PMC PMID:19853594 Europe PMC PMID:19920908 Europe PMC PMID:22891806 Europe PMC PMID:23075630 Europe PMC PMID:23183914 Europe PMC PMID:23313020 Europe PMC PMID:23394269 Europe PMC PMID:23480638 Europe PMC PMID:23503753 Europe PMC PMID:23536338 Europe PMC PMID:23574742 Europe PMC PMID:23580311 Europe PMC PMID:23587588 Europe PMC Reaxys:7671333 Reaxys 4-[(4-methylpiperazin-1-yl)methyl]-N-{4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl}benzamide IUPAC 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE PDBeChem STI 571 ChemIDplus alpha-(4-methyl-1-piperazinyl)-3'-((4-(3-pyridyl)-2-pyrimidinyl)amino)-p-toluidide ChemIDplus imatinib ChemIDplus Beilstein:7671333 Beilstein CAS:152459-95-5 ChemIDplus Drug_Central:1423 DrugCentral PMID:14660054 Europe PMC PMID:14715630 Europe PMC PMID:15073101 Europe PMC PMID:15170967 Europe PMC PMID:15722647 Europe PMC PMID:15794712 Europe PMC PMID:15966213 Europe PMC PMID:16122278 Europe PMC PMID:16826359 Europe PMC PMID:16983347 Europe PMC 0 O 15.99940 15.99491 O=* CHEBI:29353 CHEBI:44607 PDBeChem:O OXO GROUP oxo chebi_ontology =O oxo group OXO GROUP PDBeChem oxo IUPAC =O IUPAC A liquid that can dissolve other substances (solutes) without any change in their chemical composition. Wikipedia:Solvent chebi_ontology Loesungsmittel solvant solvents solvent Loesungsmittel ChEBI solvant ChEBI solvents ChEBI chebi_ontology N-alkylpiperazines N-alkylpiperazine N-alkylpiperazines ChEBI 0 CHO2 45.01744 44.99765 *C(=O)O CHEBI:23025 CHEBI:41420 PDBeChem:FMT CARBOXY GROUP carboxy chebi_ontology -C(O)OH -CO2H -COOH carboxyl group carboxy group CARBOXY GROUP PDBeChem carboxy IUPAC -C(O)OH IUPAC -CO2H ChEBI -COOH IUPAC carboxyl group ChEBI chebi_ontology N-methylpiperazines N-methylpiperazine N-methylpiperazines ChEBI Organic derivatives of sulfonic acid in which the sulfo group is linked directly to carbon of an alkyl group. CHEBI:13809 CHEBI:33553 chebi_ontology alkanesulfonic acids alkylsulfonic acids alkanesulfonic acid alkanesulfonic acids ChEBI alkylsulfonic acids ChEBI chebi_ontology Schwefeloxide oxides of sulfur sulfur oxides sulfur oxide Schwefeloxide ChEBI oxides of sulfur ChEBI sulfur oxides ChEBI chebi_ontology non-polar solvent Esters or salts of methanesulfonic acid. chebi_ontology methanesulfonates 0 H2O3S InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3) LSNNMFCWUKXFEE-UHFFFAOYSA-N 82.08008 81.97247 OS(O)=O CHEBI:26837 CHEBI:9344 CAS:7782-99-2 Gmelin:1458 KEGG:C00094 KNApSAcK:C00019662 PDBeChem:SO3 UM-BBD_compID:c0348 Sulfurous acid dihydrogen trioxosulfate dihydroxidooxidosulfur sulfurous acid trioxosulfuric acid chebi_ontology H2SO3 S(O)(OH)2 Sulfite [SO(OH)2] acide sulfureux acido sulfuroso schweflige Saeure sulphurous acid sulfurous acid CAS:7782-99-2 ChemIDplus Gmelin:1458 Gmelin UM-BBD_compID:c0348 UM-BBD Sulfurous acid KEGG_COMPOUND dihydrogen trioxosulfate IUPAC dihydroxidooxidosulfur IUPAC sulfurous acid IUPAC trioxosulfuric acid IUPAC H2SO3 IUPAC S(O)(OH)2 IUPAC Sulfite KEGG_COMPOUND [SO(OH)2] IUPAC acide sulfureux ChEBI acido sulfuroso ChEBI schweflige Saeure ChemIDplus sulphurous acid ChemIDplus +1 Cu InChI=1S/Cu/q+1 VMQMZMRVKUZKQL-UHFFFAOYSA-N 63.54600 62.92905 [Cu+] CHEBI:23379 CHEBI:49551 CAS:17493-86-6 Gmelin:15189 PDBeChem:CU1 copper(1+) copper(1+) ion copper(I) cation chebi_ontology COPPER (I) ION Cu(+) copper cation copper(1+) ion copper(I) cation cuprous ion copper(1+) CAS:17493-86-6 ChemIDplus CAS:17493-86-6 NIST Chemistry WebBook Gmelin:15189 Gmelin copper(1+) IUPAC copper(1+) ion IUPAC copper(I) cation IUPAC COPPER (I) ION PDBeChem Cu(+) IUPAC Cu(+) UniProt copper cation NIST_Chemistry_WebBook copper(1+) ion ChEBI copper(I) cation ChEBI cuprous ion ChemIDplus 0 H InChI=1S/H YZCKVEUIGOORGS-UHFFFAOYSA-N 1.00794 1.00783 [H] CHEBI:24634 CHEBI:49636 WebElements:H hydrogen chebi_ontology 1H H Wasserstoff hidrogeno hydrogen hydrogene hydrogen atom hydrogen IUPAC 1H IUPAC H IUPAC Wasserstoff ChEBI hidrogeno ChEBI hydrogen ChEBI hydrogene ChEBI A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. chebi_ontology organic amino compounds organic amino compound organic amino compounds ChEBI chebi_ontology onium compound Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families. onium cations chebi_ontology onium cations onium ion onium ions onium cation onium cations IUPAC onium cations ChEBI onium ion ChEBI onium ions ChEBI Any molecular entity that contains carbon. CHEBI:25700 CHEBI:33244 chebi_ontology organic compounds organic entity organic molecular entities organic molecular entity organic compounds ChEBI organic entity ChEBI organic molecular entities ChEBI A role played by a chemical compound which is known to induce a process of carcinogenesis by corrupting normal cellular pathways, leading to the acquistion of tumoral capabilities. chebi_ontology agente carcinogeno cancerigene cancerogene carcinogen carcinogene carcinogenic agents carcinogeno carcinogens carcinogenic agent agente carcinogeno ChEBI cancerigene ChEBI cancerogene ChEBI carcinogen ChEBI carcinogene ChEBI carcinogenic agents ChEBI carcinogeno ChEBI carcinogens ChEBI A chemical compound, or part thereof, which causes the onset of an allergic reaction by interacting with any of the molecular pathways involved in an allergy. Wikipedia:Allergen chebi_ontology alergeno allergene allergenic agent allergen alergeno ChEBI allergene ChEBI allergenic agent ChEBI A role is particular behaviour which a material entity may exhibit. chebi_ontology role A poison that interferes with the functions of the nervous system. CHEBI:50911 Wikipedia:Neurotoxin chebi_ontology agente neurotoxico nerve poison nerve poisons neurotoxic agent neurotoxic agents neurotoxicant neurotoxins neurotoxin agente neurotoxico ChEBI nerve poison ChEBI nerve poisons ChEBI neurotoxic agent ChEBI neurotoxic agents ChEBI neurotoxicant ChEBI neurotoxins ChEBI A compound formally derived from ammonia by replacing three hydrogen atoms by organyl groups. chebi_ontology tertiary amino compounds tertiary amino compound tertiary amino compounds ChEBI A role played by the molecular entity or part thereof within a chemical context. chebi_ontology chemical role CHEBI:25556 CHEBI:7594 KEGG:C06061 chebi_ontology Nitrogenous compounds nitrogen compounds nitrogen molecular entities nitrogen molecular entity Nitrogenous compounds KEGG_COMPOUND nitrogen compounds ChEBI nitrogen molecular entities ChEBI Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s). chebi_ontology organodiyl groups organodiyl group organodiyl groups ChEBI chebi_ontology organic divalent group chebi_ontology organic univalent group A biological role played by the molecular entity or part thereof within a biochemical context. chebi_ontology biochemical role A role played by the molecular entity or part thereof which causes the development of a pathological process. chebi_ontology etiopathogenetic agent etiopathogenetic role aetiopathogenetic role etiopathogenetic agent ChEBI etiopathogenetic role ChEBI chebi_ontology physiological role Any substance introduced into a living organism with therapeutic or diagnostic purpose. CHEBI:33293 CHEBI:33294 chebi_ontology farmaco medicament pharmaceuticals pharmaceutical farmaco ChEBI medicament ChEBI pharmaceuticals ChEBI A cyclic compound having as ring members atoms of at least two different elements. Heterocyclic compound chebi_ontology compuesto heterociclico compuestos heterociclicos heterocycle heterocyclic compounds heterocyclic compound Heterocyclic compound KEGG_COMPOUND compuesto heterociclico IUPAC compuestos heterociclicos IUPAC heterocycle ChEBI heterocyclic compounds ChEBI A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons. chebi_ontology nucleophile nucleophiles nucleophilic reagents nucleophilic reagent nucleophile ChEBI nucleophiles ChEBI nucleophilic reagents ChEBI A metal cation with a valence of two. chebi_ontology a divalent metal cation divalent metal cation a divalent metal cation UniProt An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one. chebi_ontology a monovalent cation monovalent inorganic cation a monovalent cation UniProt An alkanesulfonate in which the carbon at position 1 is attached to at least two hydrogens. -1 CH2O3SR 94.09000 93.97246 [H]C([H])([*])S([O-])(=O)=O KEGG:C15521 MetaCyc:Alkanesulfonates chebi_ontology 1,1-di-unsubstituted alkanesulfonate 1,1-di-unsubstituted alkanesulfonates 1,1-diunsubstituted alkanesulfonates 1,1-diunsubstituted alkanesulfonate 1,1-di-unsubstituted alkanesulfonate ChEBI 1,1-di-unsubstituted alkanesulfonates ChEBI 1,1-diunsubstituted alkanesulfonates ChEBI An amide in which the amide linkage is bonded directly to an aromatic system. chebi_ontology aromatic amides aromatic amide aromatic amides ChEBI Any organic salt prepared using an organosulfonic acid as the acid component. chebi_ontology organosulfonate salts organosulphonate salt organosulphonate salts organosulfonate salt organosulfonate salts ChEBI organosulphonate salt ChEBI organosulphonate salts ChEBI An inorganic cation with a valency of two. chebi_ontology divalent inorganic cation An organic molecular entity containing a single carbon atom (C1). chebi_ontology one-carbon compounds one-carbon compound one-carbon compounds ChEBI Any organic molecular entity that is acidic and contains carbon in covalent linkage. chebi_ontology organic acids organic acid organic acids ChEBI An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of three. chebi_ontology trivalent inorganic cation Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism. Wikipedia:Poison chebi_ontology poisonous agent poisonous agents poisonous substance poisonous substances poisons toxic agent toxic agents toxic substance toxic substances poison poisonous agent ChEBI poisonous agents ChEBI poisonous substance ChEBI poisonous substances ChEBI poisons ChEBI toxic agent ChEBI toxic agents ChEBI toxic substance ChEBI toxic substances ChEBI Any substance that induces the process of apoptosis (programmed cell death) in multi-celled organisms. chebi_ontology Type I cell-death inducer Type I cell-death inducers Type I programmed cell-death inducer Type I programmed cell-death inducers apoptosis inducers apoptosis inducer Type I cell-death inducer ChEBI Type I cell-death inducers ChEBI Type I programmed cell-death inducer ChEBI Type I programmed cell-death inducers ChEBI apoptosis inducers ChEBI An enzyme inhibitor that inhibits the action of a transferase (EC 2.*) Wikipedia:Transferase chebi_ontology EC 2 inhibitor EC 2 inhibitors EC 2.* (transferase) inhibitors EC 2.* inhibitor EC 2.* inhibitors transferase inhibitor transferase inhibitors EC 2.* (transferase) inhibitor EC 2 inhibitor ChEBI EC 2 inhibitors ChEBI EC 2.* (transferase) inhibitors ChEBI EC 2.* inhibitor ChEBI EC 2.* inhibitors ChEBI transferase inhibitor ChEBI transferase inhibitors ChEBI Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. chebi_ontology organic compound organic compounds organic molecules organic molecule organic compound ChEBI organic compounds ChEBI organic molecules ChEBI Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms. chebi_ontology eukaryotic metabolites eukaryotic metabolite eukaryotic metabolites ChEBI Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals. CHEBI:77721 CHEBI:77743 chebi_ontology animal metabolites animal metabolite animal metabolites ChEBI Any animal metabolite produced during a metabolic reaction in mammals. CHEBI:77464 CHEBI:77744 chebi_ontology mammalian metabolites mammalian metabolite mammalian metabolites ChEBI Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus). chebi_ontology Mus musculus metabolite Mus musculus metabolites mouse metabolites mouse metabolite Mus musculus metabolite ChEBI Mus musculus metabolites ChEBI mouse metabolites ChEBI Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae). CHEBI:76949 CHEBI:76951 chebi_ontology S. cerevisiae metabolite S. cerevisiae metabolites S. cerevisiae secondary metabolite S. cerevisiae secondary metabolites Saccharomyces cerevisiae metabolites Saccharomyces cerevisiae secondary metabolites baker's yeast metabolite baker's yeast metabolites baker's yeast secondary metabolite baker's yeast secondary metabolites Saccharomyces cerevisiae metabolite S. cerevisiae metabolite ChEBI S. cerevisiae metabolites ChEBI S. cerevisiae secondary metabolite ChEBI S. cerevisiae secondary metabolites ChEBI Saccharomyces cerevisiae metabolites ChEBI Saccharomyces cerevisiae secondary metabolites ChEBI baker's yeast metabolite ChEBI baker's yeast metabolites ChEBI baker's yeast secondary metabolite ChEBI baker's yeast secondary metabolites ChEBI Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea. chebi_ontology prokaryotic metabolites prokaryotic metabolite prokaryotic metabolites ChEBI A transferase inhibitor that inhibits the action of a phosphorus-containing group transferase (EC 2.7.*.*). chebi_ontology EC 2.7.* (P-containing group transferase) inhibitors EC 2.7.* (phosphorus-containing group transferase) inhibitor EC 2.7.* (phosphorus-containing group transferase) inhibitors EC 2.7.* inhibitor EC 2.7.* inhibitors phosphorus-containing group transferase (EC 2.7.*) inhibitor phosphorus-containing group transferase (EC 2.7.*) inhibitors phosphorus-containing group transferase inhibitor phosphorus-containing group transferase inhibitors EC 2.7.* (P-containing group transferase) inhibitor EC 2.7.* (P-containing group transferase) inhibitors ChEBI EC 2.7.* (phosphorus-containing group transferase) inhibitor ChEBI EC 2.7.* (phosphorus-containing group transferase) inhibitors ChEBI EC 2.7.* inhibitor ChEBI EC 2.7.* inhibitors ChEBI phosphorus-containing group transferase (EC 2.7.*) inhibitor ChEBI phosphorus-containing group transferase (EC 2.7.*) inhibitors ChEBI phosphorus-containing group transferase inhibitor ChEBI phosphorus-containing group transferase inhibitors ChEBI Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*). Wikipedia:Hydrolase chebi_ontology EC 3.* (hydrolase) inhibitors EC 3.* inhibitor EC 3.* inhibitors EC 3.*.*.* inhibitor EC 3.*.*.* inhibitors hydrolase (EC 3.*) inhibitor hydrolase (EC 3.*) inhibitors hydrolase inhibitor hydrolase inhibitors EC 3.* (hydrolase) inhibitor EC 3.* (hydrolase) inhibitors ChEBI EC 3.* inhibitor ChEBI EC 3.* inhibitors ChEBI EC 3.*.*.* inhibitor ChEBI EC 3.*.*.* inhibitors ChEBI hydrolase (EC 3.*) inhibitor ChEBI hydrolase (EC 3.*) inhibitors ChEBI hydrolase inhibitor ChEBI hydrolase inhibitors ChEBI Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*). chebi_ontology EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors EC 3.5.* inhibitor EC 3.5.* inhibitors EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor ChEBI EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors ChEBI EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor ChEBI EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors ChEBI EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors ChEBI EC 3.5.* inhibitor ChEBI EC 3.5.* inhibitors ChEBI An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*). chebi_ontology EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors EC 3.5.1.* inhibitor EC 3.5.1.* inhibitors non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors ChEBI EC 3.5.1.* inhibitor ChEBI EC 3.5.1.* inhibitors ChEBI non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor ChEBI non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors ChEBI Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds. CHEBI:75765 CHEBI:76947 chebi_ontology fungal metabolites fungal metabolite fungal metabolites ChEBI Any prokaryotic metabolite produced during a metabolic reaction in bacteria. CHEBI:75760 CHEBI:76970 chebi_ontology bacterial metabolite Any bacterial metabolite produced during a metabolic reaction in Escherichia coli. chebi_ontology E.coli metabolite E.coli metabolites Escherichia coli metabolites Escherichia coli metabolite E.coli metabolite ChEBI E.coli metabolites ChEBI Escherichia coli metabolites ChEBI Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens). CHEBI:75770 CHEBI:77123 chebi_ontology H. sapiens metabolite H. sapiens metabolites Homo sapiens metabolite Homo sapiens metabolites human metabolite H. sapiens metabolite ChEBI H. sapiens metabolites ChEBI Homo sapiens metabolite ChEBI Homo sapiens metabolites ChEBI An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4). Wikipedia:Amidase chebi_ontology EC 3.5.1.4 (amidase) inhibitors EC 3.5.1.4 inhibitor EC 3.5.1.4 inhibitors N-acetylaminohydrolase inhibitor N-acetylaminohydrolase inhibitors acylamidase inhibitor acylamidase inhibitors acylamide amidohydrolase inhibitor acylamide amidohydrolase inhibitors amidase (EC 3.5.1.4) inhibitor amidase (EC 3.5.1.4) inhibitors amidase inhibitor amidase inhibitors amidohydrolase inhibitor amidohydrolase inhibitors deaminase inhibitor deaminase inhibitors fatty acylamidase inhibitor fatty acylamidase inhibitors EC 3.5.1.4 (amidase) inhibitor EC 3.5.1.4 (amidase) inhibitors ChEBI EC 3.5.1.4 inhibitor ChEBI EC 3.5.1.4 inhibitors ChEBI N-acetylaminohydrolase inhibitor ChEBI N-acetylaminohydrolase inhibitors ChEBI acylamidase inhibitor ChEBI acylamidase inhibitors ChEBI acylamide amidohydrolase inhibitor ChEBI acylamide amidohydrolase inhibitors ChEBI amidase (EC 3.5.1.4) inhibitor ChEBI amidase (EC 3.5.1.4) inhibitors ChEBI amidase inhibitor ChEBI amidase inhibitors ChEBI amidohydrolase inhibitor ChEBI amidohydrolase inhibitors ChEBI deaminase inhibitor ChEBI deaminase inhibitors ChEBI fatty acylamidase inhibitor ChEBI fatty acylamidase inhibitors ChEBI Any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants. chebi_ontology dietary component dietary components food components food component dietary component ChEBI dietary components ChEBI food components ChEBI Any minor or unwanted substance introduced into the environment that can have undesired effects. chebi_ontology environmental contaminants environmental contaminant environmental contaminants ChEBI A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure. Wikipedia:Refrigerant chebi_ontology refrigerants refrigerant refrigerants ChEBI Any inorganic anion with a valency of two. chebi_ontology divalent inorganic anions divalent inorganic anion divalent inorganic anions ChEBI Any inorganic anion with a valency of one. chebi_ontology monovalent inorganic anions monovalent inorganic anion monovalent inorganic anions ChEBI Any metal which causes the onset of an allergic reaction. chebi_ontology allergenic metal allergenic metals metal allergens metal allergen allergenic metal ChEBI allergenic metals ChEBI metal allergens ChEBI A cell that will develop into a neuron often after a migration phase. CL:0000337 BTO:0000930 FMA:70563 neuroblast cell neuroblast (sensu Vertebrata) A cell that will develop into a neuron often after a migration phase. GOC:NV http://en.wikipedia.org/wiki/Neuroblast A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CALOHA:TS-2086 FMA:63368 cell stem cell A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. GOC:tfm MESH:A11.872 A stem cell that self-renews as well as give rise to a single mature cell type. FMA:70569 unipotent stem cell unipotential stem cell cell single fate stem cell A stem cell that self-renews as well as give rise to a single mature cell type. GOC:tfm A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. BTO:0000725 CALOHA:TS-0448 FMA:70337 FMA:86475 VHOG:0001485 HSC blood forming stem cell hemopoietic stem cell cell colony forming unit hematopoietic Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell true A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. GOC:add GOC:dsd GOC:tfm PMID:19022770 http://en.wikipedia.org/wiki/Hematopoietic_stem_cell A stem cell that can give rise to multiple lineages of cells. FMA:84789 multi-fate stem cell multifate stem cell multipotent cell multipotent stem cell cell multi fate stem cell A stem cell that can give rise to multiple lineages of cells. GOC:add A oligopotent progenitor cell committed to the lymphoid lineage. CL:0000044 CLP common lymphocyte precursor common lymphocyte progenitor common lymphoid precursor cell ELP committed lymphopoietic stem cell early lymphocyte progenitor lymphoid stem cell lymphopoietic stem cell CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. common lymphoid progenitor true A oligopotent progenitor cell committed to the lymphoid lineage. GOC:add GOC:dsd GOC:tfm PMID:10407577 PMID:16551251 A precursor cell with a limited number of potential fates. BTO:0000125 FMA:84782 blast cell cell define using PATO mulit-potent or oligopotent? non-terminally differentiated cell A precursor cell with a limited number of potential fates. SANBI:mhl A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. CL:0000804 CL:0000812 BTO:0000782 CALOHA:TS-1001 FMA:62870 VHOG:0001479 T lymphocyte T-cell T-lymphocyte cell immature T cell mature T cell T cell true A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. GOC:add GOC:tfm ISBN:0781735149 Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. BTO:0003811 FBbt:00005125 FMA:67313 WBbt:0005113 cell interneuron Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. GOC:tfm MESH:A08.663.358 A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. This cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. CL:0002452 BTO:0002625 BTO:0003298 FMA:70546 BMSC bone marrow stromal cells colony-forming unit-fibroblast marrow stromal cells cell CFU-F MSC mesenchymal precursor cell mesenchymal progenitor cells mesenchymal stem cell mesenchymal stromal cell mesenchymal stromal cells stem cells, mesenchymal Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell true A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. This cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. FB:ma GOC:dsd PMCID:PMC2613570 PMID:10102814j PMID:16923606 PMID:17986482 PMID:19960544 http://en.wikipedia.org/wiki/Mesenchymal_stem_cell http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells marrow stromal cells PMID:11378515 MSC PMID:11378515 mesenchymal progenitor cells MESH:D044982 mesenchymal stromal cells stem cells, mesenchymal MESH:D044982 A cell whose function is determined by the generation or the reception of an electric signal. cell electrically active cell A cell whose function is determined by the generation or the reception of an electric signal. FB:ma A cell with a single nucleus. cell single nucleate cell A cell with a single nucleus. FB:ma GOC:tfm cell eukaryotic cell A cell whose function is determined by its response to an electric signal. cell electrically responsive cell A cell whose function is determined by its response to an electric signal. FB:ma A cell that initiates an electrical signal and passes that signal to another cell. cell electrically signaling cell A cell that initiates an electrical signal and passes that signal to another cell. FB:ma The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. BTO:0000938 CALOHA:TS-0683 FBbt:00005106 FMA:54527 VHOG:0001483 WBbt:0003679 nerve cell cell These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. MESH:A08.663 MESH:D009474 http://en.wikipedia.org/wiki/Neuron A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. BTO:0000775 CALOHA:TS-0583 FMA:62863 VHOG:0001535 cell Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) lymphocyte true A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. GOC:add ISBN:0683073696 ISBN:0781735149 cell animal cell A mesenchymal stem cell capable of developing into blood vessel endothelium. angioblast chondroplast cell These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell true A mesenchymal stem cell capable of developing into blood vessel endothelium. GOC:dsd GOC:tfm PMID:12768659 A stem cell that can give rise to cell types of the body other than those of the germ-line. CALOHA:TS-2086 FMA:63368 cell somatic stem cell true A stem cell that can give rise to cell types of the body other than those of the germ-line. GO:0048103 An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. BTO:0000751 CALOHA:TS-0549 FMA:62852 immune cell leucocyte white blood cell cell leukocyte true An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. GOC:add GOC:tfm ISBN:978-0-323-05290-0 A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage. pro-T lymphocyte progenitor T cell DN1 cell DN1 thymocyte TN1 cell cell pro-T cell true A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage. GOC:add ISBN:0781735149 A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. BTO:0000725 CALOHA:TS-0448 MPP hemopoietic progenitor cell cell Markers differ between mouse and human. hematopoietic multipotent progenitor cell true A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. GOC:add GOC:tfm PMID:19022770 A progenitor cell restricted to the lymphoid lineage. lymphoid progenitor cell BTO:0004731 CALOHA:TS-2025 FMA:70338 cell Note that this is a class of cell types, not an identified single cell type. lymphoid lineage restricted progenitor cell true A progenitor cell restricted to the lymphoid lineage. GOC:add GOC:tfm A leukocyte with a single non-segmented nucleus in the mature form. BTO:0000878 CALOHA:TS-0768 FMA:86713 mononuclear leukocyte peripheral blood mononuclear cell cell mononuclear cell true A leukocyte with a single non-segmented nucleus in the mature form. GOC:add A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 FMA:70366 FMA:83598 haematopoietic cell haemopoietic cell hemopoietic cell cell hematopoietic cell A cell of a hematopoietic lineage. GOC:add GO_REF:0000031 A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. tmeehan 2010-01-06T03:43:27Z cell hematopoietic oligopotent progenitor cell, lineage-negative A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. GOC:tfm PMID:19022770 A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. tmeehan 2010-01-06T03:43:20Z cell hematopoietic lineage restricted progenitor cell true A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. GOC:tfm PMID:19022770 A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. tmeehan 2010-01-06T03:43:27Z cell This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell true A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. GOC:tfm PMID:19022770 A cell containing at least one nucleus. tmeehan 2010-09-07T03:32:33Z FMA:67513 cell nucleate cell A cell containing at least one nucleus. GOC:tfm A cell that is part of the nervous system. tmeehan 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 cell neural cell A cell that is part of the nervous system. GOC:tfm ISBN:0618947256 A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. tmeehan 2010-09-15T03:01:54Z CL:1000406 CALOHA:TS-2096 FMA:63875 cell connective tissue cell true A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. GOC:tfm ISBN:0618947256 A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). tmeehan 2010-09-24T09:44:42Z BTO:0001268 FMA:72300 WBbt:0008378 cell somatic cell A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). GOC:tfm ISBN:0721662544 Any hematopoietic cell that is a precursor of some other hematopoietic cell type. hematopoietic precursor cell Any hematopoietic cell that is a precursor of some other hematopoietic cell type. GOC:dos A cell that, by division or terminal differentiation, can give rise to other cell types. Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell A cell that, by division or terminal differentiation, can give rise to other cell types. GOC:dos An interneuron of the hippocampus. FMA:84777 cl hippocampal interneuron An interneuron of the hippocampus. GOC:pr quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] BFO:0000019 quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] PATO:0000125 mass PATO:0002193 charge material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] BFO:0000040 material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] A particle smaller than an atom. CHEBI:36342 chebi_ontology subatomic particles subatomic particle subatomic particles ChEBI 1 A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. This atom is closely related to ChEBI's atom, but not exactly equivalent to. atom A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. CHEBI:33252 nucleus chebi_ontology Atomkern Kern noyau noyau atomique nuclei nucleo nucleo atomico nucleus atomi Some people may be uncomfortable calling every proton an atomic nucleus This is equivalent to CHEBI:33252 atomic nucleus nucleus IUPAC Atomkern ChEBI Kern ChEBI noyau IUPAC noyau atomique ChEBI nuclei ChEBI nucleo IUPAC nucleo atomico ChEBI nucleus atomi ChEBI A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. CHEBI:23367 molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet This molecular entity is different than ChEBI's 'molecular entity'. We would like to have cardinality restrictions on the logic, but there are some technical limitations. molecular entity molecular entity IUPAC entidad molecular IUPAC entidades moleculares IUPAC entite moleculaire IUPAC molecular entities IUPAC molekulare Entitaet ChEBI CHEBI:16541 CHEBI:36080 PR:000000001 protein PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity that has a plasma membrane and results from cellular division. cell and encapsulating structures CALOHA:TS-2035 CL:0000000 FMA:68646 GO:0005623 KUPO:0000002 NIF_Subcellular:sao1813327414 VHOG:0001533 WBbt:0004017 Wikipedia:Cell_(biology) XAO:0003012 cell cellular_component CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:0000013 CL:0000003 cell in vivo cell To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). native cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:mah A material entity consisting of at least two macromolecular entities derived from a cell as parts, and that has a function for the cell. Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. Overlaps with some cellular components from GO subcellular structure organism animal fungus plant virus A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism CARO:0001010 GC_ID:1 NCBITaxon:1 OBI:0100026 ncbi_taxonomy all "Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'. Includes virus - we will later have a class for cellular organisms. organism all organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI OBI:0000245 Should revisit if we can place outside of material entity - a collection of roles. organization processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples A material entity processed by human activity with an intent to produce PERSON: Alan Ruttenberg OBI:0000047 processed material entity BFO:0000041 immaterial entity BFO:0000017 realizable BFO:0000015 process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) OBI:0000011 completely executed planned process A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. janelomax 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 GO:0008150 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process A biological process is an evolved process 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. biological process 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. GO:0005554 GO:0003674 molecular function molecular_function 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. This is the same as GO molecular function gene product or complex activity 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 CHEBI:24867 chebi_ontology monoatomic ions monoatomic ion monoatomic ions ChEBI A chemical entity constituting the smallest component of an element having the chemical properties of the element. CHEBI:22671 CHEBI:23907 CHEBI:33250 atom chebi_ontology atome atomo atoms atomus element elements uncharged atom atom IUPAC atome IUPAC atomo IUPAC atoms ChEBI atomus ChEBI element ChEBI elements ChEBI 0 Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. -1 0.000548579903 0.0 CHEBI:10545 COB:0000010 KEGG:C05359 PMID:21614077 Wikipedia:Electron electron chebi_ontology Elektron beta beta(-) beta-particle e e(-) e- negatron nucleic acid polymer PMID:21614077 Europe PMC electron ChEBI electron IUPAC electron KEGG_COMPOUND Elektron ChEBI beta IUPAC beta(-) ChEBI beta-particle IUPAC e IUPAC e(-) UniProt e- KEGG_COMPOUND negatron IUPAC PCO:0000000 collection of organisms BFO:0000029 site The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group OBI:0001909 conclusion based on data IAO:0000030 Pier: 'data, information or knowledge'. OR 'representation information A process in which includes the components of an environmental system as participants. ENVO:02500000 This is a convenience class for organisation and should not be used for annotation. environmental process An environmental system which includes both living and non-living components. LTER:173 ENVO:01001110 This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here. ecosystem An environmental system which includes both living and non-living components. https://en.wikipedia.org/wiki/Ecosystem LTER:173 https://vocab.lternet.edu/vocab/vocab/index.php?tema=173&/ecosystems A material part of an astronomical body. ENVO:01000813 envoAstro envoPolar geophysical entity IAO:0000033 directive information entity gene product 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. GO:0043234 GO:0032991 macromolecular complex macromolecule complex protein containing complex protein complex protein-protein complex cellular_component 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. This is not covalently bonded, which conflicts with changes to the parent definition. protein-containing macromolecular complex 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 IAO:0000005 objective specification action specification IAO:0000104 plan specification A complex of two or more molecular entities that are not covalently bound. complex of molecular entities >=2 parts (not we cannot use cardinality with transitive properties) A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. Should we create agent? planned process IAO:0000310 document IAO:0000027 data item 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. GO:0005634 NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus cellular_component cell nucleus 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 horsetail nucleus GOC:al GOC:mah GOC:vw PMID:15030757 assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method OBI:0000070 assay data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors OBI:0200000 data transformation investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS study OBI:0000066 investigation material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived OBI:0000094 material processing BFO:0000016 disposition BFO:0000034 function plan The plan of researcher X to perform an experiment according to a protocol. A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived OBI:0000260 plan BFO:0000023 role CARO:0010004 GC_ID:1 NCBITaxon:131567 ncbi_taxonomy biota cellular organism biota OBI:0000067 evaluant role http://purl.obolibrary.org/obo/IAO_0000015 Pier 'representational entity' This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc information representation http://purl.obolibrary.org/obo/IAO_0000109 measurement datum physical information carrier sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] BFO:0000020 characteristic https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions. tmeehan 2010-05-25T01:36:34Z cell neutrophillic cytoplasm Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions. GOC:tfm A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. tmeehan 2009-12-23T10:53:24Z cell increased nucleus size A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. GOC:tfm https://en.wikipedia.org/wiki/Geographic_feature macroscopic spatial feature envoPolar This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass. geographic feature An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. FTT:78 TGN:50001 man-made feature manmade feature anthropogenic geographic feature An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. ORCID:0000-0002-4366-3088 A geographical feature associated with water. FTT:131 FTT:280 FTT:711 FTT:761 FTT:824 FTT:825 FTT:826 FTT:827 FTT:828 FTT:829 Geonames:H.OVF fluvial feature envoPolar hydrographic feature A geographical feature associated with water. MA:ma fluvial feature ADL:FTT A marine water body which is constitutes the majority of an astronomical body's hydrosphere. LTER:695 EcoLexicon:ocean FTT:1019 FTT:943 Geonames:H.OCN SWEETRealm:Ocean TGN:21102 https://en.wikipedia.org/wiki/Ocean Ocean ocean ocean region envoMarine envoPolar ocean LTER:695 https://vocab.lternet.edu/vocab/vocab/index.php?tema=695&/oceans Ocean NASA:earthrealm ocean Geonames:feature ocean region ADL:FTT A large expanse of saline water usually connected with an ocean. EcoLexicon:sea FTT:233 FTT:830 Geonames:H.SEA TGN:21103 https://en.wikipedia.org/wiki/Sea Sea sea channel closed sea marginal sea open sea open sound open water envoMarine envoPolar sea A large expanse of saline water usually connected with an ocean. https://en.wikipedia.org/wiki/Sea Sea NASA:earthrealm sea ADL:FTT sea Geonames:feature closed sea USGS:SDTS marginal sea USGS:SDTS open sea USGS:SDTS open sound USGS:SDTS open water USGS:SDTS A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L). ENVO saline hydrographic feature A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L). https://en.wikipedia.org/wiki/Salinity A lake whose water contains a considerable concentration of dissolved salts. FTT:221 FTT:907 Geonames:H.LKN Geonames:H.LKSN TGN:21116 https://en.wikipedia.org/wiki/Saline_lake salt lake salina soda lake saline lake A lake whose water contains a considerable concentration of dissolved salts. MA:ma salt lake USGS:SDTS salina USGS:SDTS A body of water or other liquid of considerable size contained in a depression on a landmass. LTER:278 EcoLexicon:lake FTT:221 FTT:704 FTT:909 Geonames:H.LK Geonames:H.LKS SPIRE:Lake_or_pond SWEETRealm:Lake TGN:21114 TGN:21115 catch basin open water tarn broad llyn loch lochan lough mere mortlake pasteuer lake envoPolar lake A body of water or other liquid of considerable size contained in a depression on a landmass. https://en.wikipedia.org/wiki/Lake LTER:278 https://vocab.lternet.edu/vocab/vocab/index.php?tema=278&/lakes catch basin USGS:SDTS open water USGS:SDTS tarn ADL:FTT lochan ADL:FTT mortlake USGS:SDTS pasteuer lake USGS:SDTS Place or area with clustered or scattered buildings and a permanent human population. place FTT:1097 FTT:33 Geonames:P.PPL Geonames:P.PPLS TGN:22201 TGN:83002 https://en.wikipedia.org/wiki/Populated_place inhabited place populated place populated places settlement ENVO inhabited region populated locality populated place Place or area with clustered or scattered buildings and a permanent human population. USGS:http://mapping.usgs.gov/www/ti/GNIS/gnis_users_guide_appendixc.html place USGS:SDTS inhabited place Getty:TGN populated place Geonames:feature populated places Geonames:feature settlement USGS:SDTS An accumulation of water of varying size. hydrographic feature EcoLexicon:waterbody FTT:131 FTT:280 FTT:827 SWEETRealm:BodyOfWater TGN:21100 TGN:21101 https://en.wikipedia.org/wiki/Water_body aquatic feature bodies of water body of water waterbody https://en.wikipedia.org/wiki/ The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water. water body An accumulation of water of varying size. https://en.wikipedia.org/wiki/Body_of_water hydrographic feature ADL:FTT bodies of water Getty:TGN body of water ADL:FTT body of water Getty:TGN A construction that has been assembled by deliberate human effort. "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference constructed feature human construction A construction that has been assembled by deliberate human effort. MA:ma A permanent walled and roofed construction. FTT:42 Geonames:S.BLDG LTER:76 TGN:51011 https://en.wikipedia.org/wiki/Building BUILDING building building A permanent walled and roofed construction. USGS:SDTS BUILDING USGS:SDTS building Geonames:feature An excavation in the Earth for the purpose of extracting earth materials. EcoLexicon:mine FTT:14 FTT:968 Geonames:L.MNA Geonames:S.MN TGN:54211 TGN:54212 mine An excavation in the Earth for the purpose of extracting earth materials. USGS:SDTS https://en.wikipedia.org/wiki/Mine A landform that extends above the surrounding terrain in a limited area. EcoLexicon:mountain FTT:1000 FTT:118 FTT:460 FTT:548 FTT:713 FTT:896 FTT:993 Geonames:T.MT Geonames:T.MTS SWEETRealm:Mountain TGN:21430 TGN:21434 https://en.wikipedia.org/wiki/Mountain Mountain mountains envoPolar A mountain is generally steeper than a hill, but there is no universally accepted standard definition for the height of a mountain or a hill although a mountain usually has an identifiable summit. The USGS had previously defined mountains as localised elevations of more than 300 meters; however, the organisation has accepted there are no technical definitions in the US. In ENVO, we primarily use the UNEP-WCMC classification to be compliant with SDG monitoring, but we can host other classifications on request: http://www.fao.org/sustainable-development-goals/indicators/1542/en/ mountain A landform that extends above the surrounding terrain in a limited area. https://en.wikipedia.org/wiki/Mountain#United_Kingdom https://www.unep-wcmc.org/resources-and-data/mountain-watch--environmental-change-sustainable-development-in-mountains https://www.usgs.gov/faqs/what-difference-between-mountain-hill-and-peak-lake-and-pond-or-river-and-creek Mountain NASA:earthrealm mountains Geonames:feature A rounded elevation of limited extent rising above the surrounding land with local relief of less than 300m. EcoLexicon:hill FTT:118 FTT:468 FTT:713 FTT:799 FTT:896 Geonames:T.HLL Geonames:T.HLLS SWEETRealm:Hill TGN:21437 TGN:21438 https://en.wikipedia.org/wiki/Hill ENVO cerro foothill hill hillock hills knoll mount mountain hill A rounded elevation of limited extent rising above the surrounding land with local relief of less than 300m. Geonames:feature foothill ADL:FTT foothill USGS:SDTS hill Geonames:feature hillock USGS:SDTS hills Geonames:feature knoll USGS:SDTS mount USGS:SDTS mountain ADL:FTT A region of general uniform slope, comparatively level, and of considerable extent. EcoLexicon:plain FTT:707 FTT:874 FTT:926 Geonames:T.PLN SWEETRealm:Plain TGN:21461 https://en.wikipedia.org/wiki/Plain PLAIN Plain plain interfluve llanos outwash plain plain A region of general uniform slope, comparatively level, and of considerable extent. USGS:SDTS PLAIN USGS:SDTS Plain NASA:earthrealm plain Geonames:feature interfluve ADL:FTT llanos ADL:FTT outwash plain USGS:SDTS An area of flat, low-lying land adjacent to a coast and separated from the interior by other features. EcoLexicon:coastal_plain EcoLexicon:coastal_zone FTT:240 FTT:499 FTT:500 FTT:501 FTT:502 FTT:503 FTT:504 SWEETRealm:CoastalPlain https://en.wikipedia.org/wiki/Coastal_plain ENVO coastal plain An area of flat, low-lying land adjacent to a coast and separated from the interior by other features. https://en.wikipedia.org/wiki/Coastal_plain A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of water. EcoLexicon:beach EcoLexicon:to_beach FTT:237 FTT:239 Geonames:T.BCH Geonames:T.BCHS SWEETRealm:Beach TGN:21482 https://en.wikipedia.org/wiki/Beach Beach beach berm lagoon beach beach beaches foreshore flats rivage strand beach A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of water. https://en.wikipedia.org/wiki/Beach Beach NASA:earthrealm beach berm USGS:SDTS lagoon beach USGS:SDTS beach Geonames:feature beaches Geonames:feature foreshore flats USGS:SDTS rivage USGS:SDTS strand ADL:FTT strand USGS:SDTS A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a sea. https://en.wikipedia.org/wiki/Strand strand sea beach A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a sea. https://en.wikipedia.org/wiki/Beach A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a lake. ENVO lacustrine beach A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a lake. MA:ma A part of an astronomical body associated with a volcano - an opening, or rupture, in that body's surface or crust - which allows hot, molten rock, ash and gases to escape from deep below the surface. FTT:591 TGN:21407 volcanic landform volcanic feature A part of an astronomical body associated with a volcano - an opening, or rupture, in that body's surface or crust - which allows hot, molten rock, ash and gases to escape from deep below the surface. https://en.wikipedia.org/wiki/Volcano volcanic landform Getty:TGN A region rendered barren or partially barren by environmental extremes, especially by low rainfall. EcoLexicon:desert FTT:1 FTT:188 Geonames:T.DSRT LTER:147 SWEETRealm:Desert TGN:21201 https://en.wikipedia.org/wiki/Desert arid region envoPolar desert area A region rendered barren or partially barren by environmental extremes, especially by low rainfall. USGS:SDTS arid region ADL:FTT A depression which has been formed as a result of erosion by water or ice and which is low-lying, bordered by higher ground, and especially elongate. EcoLexicon:valley FTT:158 FTT:166 FTT:418 FTT:761 FTT:811 FTT:949 Geonames:T.GRGE Geonames:T.VAL Geonames:T.VALS SWEETRealm:Valley TGN:21425 TGN:21451 TGN:21452 TGN:21453 chasm coulee dale glacial gorge glacial trough gulch gully median valley shelf valley glen goe gorge graben hollow lavaka moat ravine re-entrant seachannel strath trench vale water gap Valleys are typically located between hills our mountains. valley A depression which has been formed as a result of erosion by water or ice and which is low-lying, bordered by higher ground, and especially elongate. ADL:FTT https://en.wikipedia.org/wiki/Valley chasm USGS:SDTS coulee USGS:SDTS dale USGS:SDTS glacial gorge USGS:SDTS glacial trough USGS:SDTS gulch USGS:SDTS gully Getty:TGN gully USGS:SDTS median valley ADL:FTT median valley Geonames:feature shelf valley Geonames:feature glen ADL:FTT glen USGS:SDTS goe USGS:SDTS gorge Geonames:feature gorge USGS:SDTS graben USGS:SDTS hollow ADL:FTT hollow Getty:TGN hollow USGS:SDTS moat USGS:SDTS ravine USGS:SDTS re-entrant USGS:SDTS seachannel USGS:SDTS strath USGS:SDTS trench USGS:SDTS water gap USGS:SDTS EcoLexicon:fan EcoLexicon:platform EcoLexicon:ravine FTT:1020 FTT:1137 FTT:1176 FTT:1193 FTT:1194 FTT:1195 FTT:1196 FTT:5 FTT:810 FTT:984 Geonames:FRKU Geonames:FRSU Geonames:MDVU Geonames:PLFU Geonames:RAVU Geonames:RMPU Geonames:U.BSNU Geonames:U.EDGU Geonames:U.ESCU Geonames:U.FANU Geonames:U.FLTU Geonames:U.FURU Geonames:U.GAPU Geonames:U.GLYU Geonames:U.HOLU Geonames:U.LDGU Geonames:U.LEVU Geonames:U.PLNU Geonames:U.PLTU Geonames:U.PNLU Geonames:U.PRVU Geonames:U.RDGU Geonames:U.RDSU Geonames:U.RISU Geonames:U.SDLU Geonames:U.SHVU Geonames:U.SILU Geonames:U.SPRU Geonames:U.TERU Geonames:U.VALU Geonames:U.VLSU TGN:23001 TGN:23116 TGN:23117 TGN:23118 TGN:23135 TGN:23162 TGN:23181 TGN:23182 TGN:23183 TGN:23184 TGN:23188 TGN:23192 TGN:23193 TGN:23194 TGN:23195 TGN:23196 TGN:23211 TGN:23212 TGN:23301 TGN:23411 TGN:23412 TGN:23413 TGN:23415 TGN:23421 TGN:23423 TGN:23424 TGN:23431 TGN:23453 TGN:23461 TGN:23463 TGN:23467 TGN:23550 basin escarpment fan flat fork forks furrow gap gully hole hole (seafloor) ledge levee median valley moat (seafloor) pinnacle plain plateau platform province ramp ramp (seafloor) ravine ridge ridges rise rise (seafloor) saddle shelf edge undersea bank undersea basin undersea bench undersea cliff undersea fan undersea fork undersea fracture zone undersea furrow undersea gap undersea hole undersea ledge undersea levee undersea median valley undersea moat undersea peak undersea pinnacle undersea plain undersea platform undersea ramp undersea rise undersea saddle undersea shelf undersea shelf edge undersea shelf valley undersea sill undersea slope undersea spur undersea terrace undersea tongue undersea valley ENVO ocean floor feature seafloor feature sill spur subsea feature terrace tongue (seafloor) underwater feature valley valleys undersea feature basin Geonames:feature escarpment Geonames:feature fan Geonames:feature flat Geonames:feature fork Geonames:feature forks Geonames:feature furrow Geonames:feature gap Geonames:feature gully Geonames:feature hole Geonames:feature hole (seafloor) ADL:FTT ledge Geonames:feature levee Geonames:feature median valley Geonames:feature moat (seafloor) ADL:FTT pinnacle Geonames:feature plain Geonames:feature plateau Geonames:feature platform Geonames:feature province Geonames:feature ramp Geonames:feature ramp (seafloor) ADL:FTT ravine Geonames:feature ridge Geonames:feature ridges Geonames:feature rise Geonames:feature rise (seafloor) ADL:FTT saddle Geonames:feature shelf edge Geonames:feature undersea bank Getty:TGN undersea basin Getty:TGN undersea bench Getty:TGN undersea cliff Getty:TGN undersea fan Getty:TGN undersea fork Getty:TGN undersea fracture zone Getty:TGN undersea furrow Getty:TGN undersea gap Getty:TGN undersea hole Getty:TGN undersea ledge Getty:TGN undersea levee Getty:TGN undersea median valley Getty:TGN undersea moat Getty:TGN undersea peak Getty:TGN undersea pinnacle Getty:TGN undersea plain Getty:TGN undersea platform Getty:TGN undersea ramp Getty:TGN undersea rise Getty:TGN undersea saddle Getty:TGN undersea shelf Getty:TGN undersea shelf edge Getty:TGN undersea shelf valley Getty:TGN undersea sill Getty:TGN undersea slope Getty:TGN undersea spur Getty:TGN undersea terrace Getty:TGN undersea tongue Getty:TGN undersea valley Getty:TGN ocean floor feature ADL:FTT seafloor feature ADL:FTT sill Geonames:feature spur Geonames:feature subsea feature ADL:FTT terrace Geonames:feature tongue (seafloor) ADL:FTT underwater feature ADL:FTT valley Geonames:feature valleys Geonames:feature A vegetated area which is part of a tundra ecosystem. EcoLexicon:tundra FTT:151 FTT:152 Geonames:V.TUND LTER:605 TGN:21611 Arctic land TundraEcosystem envoPolar area of tundra A vegetated area which is part of a tundra ecosystem. Arctic land ADL:FTT https://en.wikipedia.org/wiki/Tundra TundraEcosystem NASA:earthrealm A valley that no longer has a surface flow of water. Typically found in either Karst (limestone) or chalk terrain. https://en.wikipedia.org/wiki/Dry_valley ENVO dry valley A valley that no longer has a surface flow of water. Typically found in either Karst (limestone) or chalk terrain. https://en.wikipedia.org/wiki/Dry_valley A ridge of rocks, lying near the surface of the sea, which may be visible at low tide, but is usually covered by water. EcoLexicon:reef FTT:202 FTT:203 FTT:729 Geonames:H.RF Geonames:U.RFSU Geonames:U.RFU SPIRE:Reef TGN:21479 https://en.wikipedia.org/wiki/Reef REEF atoll reef bank reef barrier reef fringing reef shore reef submerged reef ledge reef reef flat reefs rocky reef A ridge of rocks, lying near the surface of the sea, which may be visible at low tide, but is usually covered by water. USGS:SDTS REEF USGS:SDTS atoll reef USGS:SDTS bank reef USGS:SDTS barrier reef ADL:FTT barrier reef USGS:SDTS fringing reef ADL:FTT fringing reef USGS:SDTS shore reef USGS:SDTS submerged reef USGS:SDTS ledge USGS:SDTS reef Geonames:feature reef flat USGS:SDTS reefs Geonames:feature A hydrographic feature characterized by the dominance of snow or ice. EcoLexicon:ice FTT:648 SWEETRealm:LandIce TGN:21410 glacer Ice LandIce glacial landform glacier feature envoPolar Likely to be depopulated and "glacial" made into a quality or similar. glacial feature A hydrographic feature characterized by the dominance of snow or ice. MA:ma glacer ADL:FTT Ice NASA:earthrealm LandIce NASA:earthrealm glacial landform Getty:TGN glacier feature ADL:FTT A glacier which covers an area of greater than 50,000 square kilometers. FTT:758 FTT:835 FTT:837 SWEETRealm:IceSheet TGN:21147 https://en.wikipedia.org/wiki/Ice_sheet Arctic pack ICE FIELD bay ice continental glacier continental ice glacial tongue ice field ice mass island ice pack ice polar ice polar ice pack rock glacier shelf ice envoPolar This is not always classified as a glacier in the cryosphere community. ice sheet A glacier which covers an area of greater than 50,000 square kilometers. https://en.wikipedia.org/wiki/Ice_sheet Arctic pack USGS:SDTS ICE FIELD USGS:SDTS bay ice USGS:SDTS continental glacier USGS:SDTS continental ice USGS:SDTS glacial tongue USGS:SDTS ice field ADL:FTT ice mass ADL:FTT island ice USGS:SDTS pack ice USGS:SDTS polar ice USGS:SDTS polar ice pack USGS:SDTS rock glacier USGS:SDTS shelf ice USGS:SDTS This is not always classified as a glacier in the cryosphere community. https://github.com/Vocamp/Virtual-Hackahon-on-Glacier-topic An ice mass which is of sufficient mass that the action of gravity upon it overcomes the frictional forces holding it in place, causing it to deform and flow towards lower elevation. http://orcid.org/0000-0002-3410-4655 glacial feature EcoLexicon:glacier FTT:648 FTT:756 Geonames:H.GLCR TGN:21141 http://sweetontology.net/realmCryo/Glacier Glacier glacier RockGlacier rock glacier envoPolar The definition of glacier is highly variable. Two main issues exist: 1) Whether or not a mass of ice must currently show movement to be considered a glacier or not and 2) What is the relationship between ice sheets and glaciers (i.e., which is the parent in a parent/child relationship or whether they are distinct terms). glacier An ice mass which is of sufficient mass that the action of gravity upon it overcomes the frictional forces holding it in place, causing it to deform and flow towards lower elevation. https://en.wikipedia.org/wiki/Glacier glacial feature ADL:FTT Glacier NASA:earthrealm glacier Geonames:feature RockGlacier NASA:earthrealm rock glacier USGS:SDTS The definition of glacier is highly variable. Two main issues exist: 1) Whether or not a mass of ice must currently show movement to be considered a glacier or not and 2) What is the relationship between ice sheets and glaciers (i.e., which is the parent in a parent/child relationship or whether they are distinct terms). https://orcid.org/0000-0003-4808-4736 Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years. EcoLexicon:permafrost LTER:408 https://en.wikipedia.org/wiki/Permafrost Permafrost envoPolar Ice is not always present, as may be in the case of nonporous bedrock, but it frequently occurs and it may be in amounts exceeding the potential hydraulic saturation of the ground material. permafrost Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years. https://en.wikipedia.org/wiki/Permafrost Permafrost NASA:earthrealm Aragonite structures produced by living organisms, found in shallow, marine waters with little nutrients in the water. LTER:127 EcoLexicon:coral_reef FTT:202 FTT:547 FTT:729 Geonames:H.RFC LTER:127 https://en.wikipedia.org/wiki/Coral_reef CoralReef coral reef barrier reef fringing reef reef coral reef Aragonite structures produced by living organisms, found in shallow, marine waters with little nutrients in the water. https://en.wikipedia.org/wiki/Coral_reef LTER:127 https://vocab.lternet.edu/vocab/vocab/index.php?tema=127&/coral-reefs CoralReef NASA:earthrealm coral reef ADL:FTT coral reef Geonames:feature coral reef USGS:SDTS fringing reef ADL:FTT fringing reef USGS:SDTS reef USGS:SDTS A hill of sand built by eolian processes. mount ridge sandy area EcoLexicon:dune FTT:238 FTT:241 FTT:652 Geonames:T.DUNE LTER:171 SWEETRealm:Dune TGN:21419 TGN:21505 https://en.wikipedia.org/wiki/Dune Dune dune sand dune interdune trough sand hill dune A hill of sand built by eolian processes. https://en.wikipedia.org/wiki/Dune mount USGS:SDTS ridge USGS:SDTS sandy area ADL:FTT sandy area Geonames:feature sandy area Getty:TGN Dune NASA:earthrealm dune Geonames:feature sand dune USGS:SDTS interdune trough ADL:FTT sand hill USGS:SDTS A landform elevated above the surrounding area. LTER:177 SWEETRealm:Elevation https://en.wikipedia.org/wiki/Elevation elevation A landform elevated above the surrounding area. MA:ma A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes. EcoLexicon:landform EcoLexicon:landforms FTT:754 FTT:96 SWEETRealm:Landform TGN:21400 TGN:21401 geological feature physiographic feature solid astronomical body part A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes. https://en.wikipedia.org/wiki/Landform geological feature ADL:FTT Broken rock that appears at the bottom of crags, mountain cliffs or valley shoulders. EcoLexicon:scree FTT:1078 FTT:96 Geonames:T.TAL SWEETRealm:Talus TGN:21508 https://en.wikipedia.org/wiki/Scree ENVO TALUS talus slope scree Broken rock that appears at the bottom of crags, mountain cliffs or valley shoulders. https://en.wikipedia.org/wiki/Scree TALUS USGS:SDTS talus slope Geonames:feature talus slope Getty:TGN The zone of an ocean below 200m, in which photosynthesis cannot occur due to the lack of light. EcoLexicon:aphotic_zone SWEETRealm:AphoticZone https://en.wikipedia.org/wiki/Aphotic_zone AphoticZone envoMarine envoPolar marine aphotic zone The zone of an ocean below 200m, in which photosynthesis cannot occur due to the lack of light. https://en.wikipedia.org/wiki/Ocean AphoticZone NASA:earthrealm The zone of the ocean below the bathypelagic zone, with its lowest boundary at about 6000m. envoMarine marine abyssalpelagic zone The zone of the ocean below the bathypelagic zone, with its lowest boundary at about 6000m. https://en.wikipedia.org/wiki/Ocean A flat or very gently sloping areas of the deep ocean basin floor. EcoLexicon:abyssal_plain FTT:4 SPIRE:Abyssal TGN:23302 https://en.wikipedia.org/wiki/Abyssal_plain Abyssalplain ENVO abyssal feature abyssal plain A flat or very gently sloping areas of the deep ocean basin floor. https://en.wikipedia.org/wiki/Abyssal_plain Abyssalplain NASA:earthrealm abyssal feature ADL:FTT An opening, or rupture, in the Earth's surface or crust, which allows hot, molten rock, ash and gases to escape from deep below the surface. mount EcoLexicon:volcano FTT:592 Geonames:T.VLC TGN:21406 https://en.wikipedia.org/wiki/Volcano Volcano volcano volcano An opening, or rupture, in the Earth's surface or crust, which allows hot, molten rock, ash and gases to escape from deep below the surface. https://en.wikipedia.org/wiki/Volcano mount USGS:SDTS Volcano NASA:earthrealm volcano Geonames:feature A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section. https://en.wikipedia.org/wiki/Glacial_valley ENVO valley envoPolar glacial valley A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section. MA:ma valley USGS:SDTS The general region of indefinite width that extends from the sea inland to the first major change in terrain features. EcoLexicon:coast EcoLexicon:sea_coast FTT:500 Geonames:L.CST SPIRE:Coastal SPIRE:Littoral SWEETRealm:CoastalRegion TGN:21483 https://en.wikipedia.org/wiki/Coast coast line coastal area coastline sea coast The general region of indefinite width that extends from the sea inland to the first major change in terrain features. USGS:SDTS coastal area USGS:SDTS coastline USGS:SDTS That part of the land in immediate contact with a body of water including the area between high and low water lines. coastal zone EcoLexicon:shore FTT:240 FTT:503 FTT:504 Geonames:T.SHOR SWEETRealm:Shore TGN:21481 https://en.wikipedia.org/wiki/Shore SHORE shore shoreface beach face foreshore inshore rivage seashore strand shore That part of the land in immediate contact with a body of water including the area between high and low water lines. USGS:SDTS coastal zone ADL:FTT SHORE USGS:SDTS shore Geonames:feature shoreface USGS:SDTS beach face USGS:SDTS foreshore USGS:SDTS inshore USGS:SDTS rivage USGS:SDTS seashore USGS:SDTS strand USGS:SDTS A landform sunken or depressed below the surrounding area. Clarify that this pertains to the planetary crust and create superclass for general topological depressions. https://github.com/EnvironmentOntology/envo/issues/486 EcoLexicon:depression FTT:175 FTT:215 FTT:216 Geonames:T.DPR Geonames:T.PAN Geonames:T.PANS SWEETRealm:Depression TGN:21454 TGN:21497 TGN:21521 barrier basin depression non tidal basin pan pan (geologic) pans tidal basin depression A landform sunken or depressed below the surrounding area. https://en.wikipedia.org/wiki/Depression_%28geology%29 barrier basin USGS:SDTS depression Geonames:feature non tidal basin USGS:SDTS pan Geonames:feature pan Getty:TGN pan (geologic) ADL:FTT pans Geonames:feature tidal basin USGS:SDTS An abiotic mesoscopic feature made of the mineral material of the crust of the Earth. FTT:1010 FTT:145 Geonames:T.RK Geonames:T.RKS TGN:21444 piece of rock An abiotic mesoscopic feature made of the mineral material of the crust of the Earth. MA:ma grain of sand A piece of rock that is two millimeters (2mm) in its largest dimension (about 1/12 of an inch) and no more than 75 millimeters (about 3 inches). piece of gravel A piece of rock that is two millimeters (2mm) in its largest dimension (about 1/12 of an inch) and no more than 75 millimeters (about 3 inches). https://en.wikipedia.org/wiki/Gravel ENVO grain of desert sand ENVO grain of beach sand ENVO grain of acid dune sand ENVO grain of sea sand ENVO grain of rocky sand https://en.wikipedia.org/wiki/Coastal_dune ENVO coastal dune The solid surface that underlies an ocean. FTT:1020 https://en.wikipedia.org/wiki/Ocean_floor ocean bed ocean floor feature ocean floor The solid surface that underlies an ocean. MA:ma ocean floor feature ADL:FTT 2 A biome is an ecosystem to which resident ecological communities have evolved adaptations. LTER:809 EcoLexicon:biome major habitat type EcosytemType There has been some concern raised (see Issue #143) about the usefulness of the assertion that organisms have evolved within a given biome. They may have evolved adaptations elsewhere and demonstrating one or the other is often not feasible. Consider relabelling to "environmental system determined by an ecological community" or similar. biome A biome is an ecosystem to which resident ecological communities have evolved adaptations. DOI:10.1186/2041-1480-4-43 https://en.wikipedia.org/wiki/Biome LTER:809 https://vocab.lternet.edu/vocab/vocab/index.php?tema=809&/biomes major habitat type WWF:Biome EcosytemType NASA:earthrealm A biome which is primarily or completely situated on a landmass. LTER:798 SPIRE:Terrestrial terrestrial realm terrestrial biome A biome which is primarily or completely situated on a landmass. https://en.wikipedia.org/wiki/Biome#Terrestrial_biomes An aquatic biome which is determined by a marine water body. SPIRE:Marine marine realm envoPolar This biome includes open-ocean and unprotected coastal ecosystems, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt. marine biome An aquatic biome which is determined by a marine water body. ISBN:978-0-618-45504-1 MA:ma https://en.wikipedia.org/wiki/Ocean A mountain or a hill. EcoLexicon:dome FTT:118 FTT:460 SWEETRealm:Dome TGN:21439 https://en.wikipedia.org/wiki/Mount MOUNT cerrito cerro dome hill hillock hummock inselberg knob knoll koppje monadnock mountain rise mount A mountain or a hill. USGS:SDTS MOUNT USGS:SDTS cerrito USGS:SDTS cerro ADL:FTT cerro USGS:SDTS dome USGS:SDTS hill USGS:SDTS hillock USGS:SDTS hummock Getty:TGN hummock USGS:SDTS inselberg USGS:SDTS knob USGS:SDTS knoll USGS:SDTS koppje USGS:SDTS monadnock USGS:SDTS mountain ADL:FTT rise USGS:SDTS That part of the land in immediate contact with a sea, including the intertidal zone. EcoLexicon:seashore FTT:504 shore sea shore That part of the land in immediate contact with a sea, including the intertidal zone. MA:ma The portion of the ground surface which lies below water. BOTTOM EcoLexicon:bed FTT:804 SWEETRealm:Bottom https://en.wikipedia.org/wiki/Stream_bed submerged bed The portion of the ground surface which lies below water. USGS:SDTS BOTTOM USGS:SDTS A beach which is armoured with pebbles or small to medium sized cobbles. https://en.wikipedia.org/wiki/Shingle_beach pebble beach ENVO shingle beach A beach which is armoured with pebbles or small to medium sized cobbles. https://en.wikipedia.org/wiki/Shingle_beach Incorporated populated place. urban area EcoLexicon:city FTT:430 FTT:483 FTT:484 FTT:485 SWEETRealm:City TGN:83020 TGN:83040 TGN:83043 https://en.wikipedia.org/wiki/City ENVO city Incorporated populated place. ADL:FTT urban area ADL:FTT A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids. EcoLexicon:rock FTT:1010 FTT:145 Geonames:T.RK Geonames:T.RKS SWEETRealm:Rock TGN:21444 https://en.wikipedia.org/wiki/Rock From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure. rock A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids. MA:ma https://en.wikipedia.org/wiki/Rock_(geology) Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. The various 'has part' and 'has quality' relations may not hold true for all soils; however, I have yet to find counter examples. Require input from a pedologist or similar. [pbuttigieg] regolith LTER:535 SPIRE:Soil SWEETRealm:Soil https://en.wikipedia.org/wiki/Soil 'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the 'solid geology'. Soil is commonly referred to as "earth" or "dirt"; technically, the term "dirt" should be restricted to displaced soil.' https://en.wikipedia.org/wiki/Soil " The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants. The lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth's surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm." Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280 soil Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. https://en.wikipedia.org/wiki/Soil A significant accumulation of water which is part of a marine biome. body of marine water marine waterbody Ideas like "significant" are fuzzy and need to be modelled more accurately. The definition is a candidate for review. marine water body A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land. EcoLexicon:slope SWEETRealm:Slope https://en.wikipedia.org/wiki/Slope flank side slope A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land. MA:ma The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth. EcoLexicon:air LTER:18 SWEETRealm:Air https://en.wikipedia.org/wiki/Air envoPolar air The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth. https://en.wikipedia.org/wiki/Air An environmental material primarily composed of dihydrogen oxide in its liquid form. water EcoLexicon:water LTER:617 https://en.wikipedia.org/wiki/Water liquid water An environmental material primarily composed of dihydrogen oxide in its liquid form. MA:ma Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid. EcoLexicon:sediment EcoLexicon:sedimentation LTER:492 LTER:493 SWEETRealm:Sediment https://en.wikipedia.org/wiki/Sediment envoPolar It is recommended to use a combination of sediment terms to describe a more specific sediment type. sediment Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid. https://en.wikipedia.org/wiki/Sediment Minute solid particles with diameters less than 500 micrometers. Occurs in and may be deposited from, the atmosphere. EcoLexicon:dust SWEETRealm:Dust https://en.wikipedia.org/wiki/Dust envoPolar dust Minute solid particles with diameters less than 500 micrometers. Occurs in and may be deposited from, the atmosphere. https://en.wikipedia.org/wiki/Dust Water which contains a significant concentration of dissolved salts. EcoLexicon:saltwater SWEETRealm:SalineWater SWEETRealm:SaltWater https://en.wikipedia.org/wiki/Saline_water salt water The threshold salt concentration for classifying water as saline varies, but typically begins at about 1,000 to 3,000 parts salt per million parts water or 0.1–0.3% salt by weight. saline water Rock formed from molten magma. EcoLexicon:igneous_rock SWEETRealm:IgneousRock https://en.wikipedia.org/wiki/Igneous_rock ENVO igneous rock Rock formed from molten magma. https://en.wikipedia.org/wiki/Rock_%28geology%29 An igneous rock that results from the crystallization of a magma below the surface of the Earth. SWEETRealm:IntrusiveRock https://en.wikipedia.org/wiki/Plutonic_rock ENVO intrusive rock plutonic rock An igneous rock that results from the crystallization of a magma below the surface of the Earth. https://en.wikipedia.org/wiki/Plutonic_rock An igneous rock that results from magma reaching the surface either as lava or fragmental ejecta. EcoLexicon:volcanic_rock SWEETRealm:VolcanicRock https://en.wikipedia.org/wiki/Volcanic_rock ENVO Due to the general suggestion that volcanic rock simply comes from a volcanic process, it's not immediately clear whether this is interchangeable with igneous rock. volcanic rock An igneous rock that results from magma reaching the surface either as lava or fragmental ejecta. https://en.wikipedia.org/wiki/Rock_%28geology%29 A rock formed by deposition of either clastic sediments, organic matter, or chemical precipitates (evaporites), followed by compaction of the particulate matter and cementation during diagenesis. EcoLexicon:sedimentary_rock SWEETRealm:SedimentaryRock https://en.wikipedia.org/wiki/Sedimentary_rock ENVO sedimentary rock A rock formed by deposition of either clastic sediments, organic matter, or chemical precipitates (evaporites), followed by compaction of the particulate matter and cementation during diagenesis. https://en.wikipedia.org/wiki/Rock_%28geology%29 A rock formed by subjecting any rock type (including previously-formed metamorphic rock) to different temperature and pressure conditions than those in which the original rock was formed. These temperatures and pressures are always higher than those at the Earth's surface and must be sufficiently high so as to change the original minerals into other mineral types or else into other forms of the same minerals (e.g. by recrystallisation). EcoLexicon:metamorphic_rock SWEETRealm:MetamorphicRock https://en.wikipedia.org/wiki/Metamorphic_rock ENVO metamorphic rock A rock formed by subjecting any rock type (including previously-formed metamorphic rock) to different temperature and pressure conditions than those in which the original rock was formed. These temperatures and pressures are always higher than those at the Earth's surface and must be sufficiently high so as to change the original minerals into other mineral types or else into other forms of the same minerals (e.g. by recrystallisation). https://en.wikipedia.org/wiki/Rock_%28geology%29 A biome which is determined by a water body and which has ecological climax communities adapted to life in or on water. LTER:41 aquatic biome Sediment that accumulates in the flat or very gently sloping areas of the deep ocean basin floor. The three main types of deep marine sediment, also known as pelagic sediment, are siliceous oozes, calcareous oozes, and red clays. EcoLexicon:marine_sediment EcoLexicon:marine_sedimentation SWEETRealm:MarineSediment https://en.wikipedia.org/wiki/Marine_sediment deep marine sediments ENVO pelagic sediment {alternative name} envoPolar deep marine sediment Sediment that accumulates in the flat or very gently sloping areas of the deep ocean basin floor. The three main types of deep marine sediment, also known as pelagic sediment, are siliceous oozes, calcareous oozes, and red clays. https://en.wikipedia.org/wiki/Marine_sediment#_note-8 Sediment which has increased levels of one or more chemical compounds. chemically enriched sediment ENVO sea sand ENVO beach sand A clastic rock with a particle size of 4 to 64 millimeters based on the Krumbein phi scale of sedimentology. EcoLexicon:pebble SWEETRealm:Pebble https://en.wikipedia.org/wiki/Pebble ENVO pebble A clastic rock with a particle size of 4 to 64 millimeters based on the Krumbein phi scale of sedimentology. https://en.wikipedia.org/wiki/Pebble A rock or rock fragment with a particle size between 64 and 256 mm. EcoLexicon:cobble SWEETRealm:Cobble cobble A rock or rock fragment with a particle size between 64 and 256 mm. https://en.wikipedia.org/wiki/Cobble Water which has physicochemical properties that have been determined by the processes occuring in a sea or ocean. When we have more classes representing the various processes which make seawater seawater, we can further axiomatise this class. EcoLexicon:sea_water LTER:701 SWEETRealm:SeaWater https://en.wikipedia.org/wiki/Sea_water ocean water seawater This definition refers to water that is actually in a sea or ocean. This water may have a wide range of salinity levels. sea water Coastal sea water is sea water that is adjacent to a coast. coastal water coastal ocean water coastal oceanic water coastal seawater envoPolar The limits of what qualifies as "adjacent to" vary greatly. This should be defined on a data level and is left intentionally fuzzy here. The label is "coastal sea water" rather than "coastal water" as some large lakes are often said to have coasts. coastal sea water https://en.wikipedia.org/wiki/Coal_mine ENVO coal mine ENVO sandy beach coal mine waste ENVO coal refuse coal mine waste material A power plant is a building which contains one or more generators which convert mechanical energy into electrical energy through the relative motion between a magnetic field and a conductor. The energy source harnessed to turn the generator varies widely. SWEETRealm:PowerPlant https://en.wikipedia.org/wiki/Power_plant generating plant generating station power station powerhouse ENVO power plant A power plant is a building which contains one or more generators which convert mechanical energy into electrical energy through the relative motion between a magnetic field and a conductor. The energy source harnessed to turn the generator varies widely. https://en.wikipedia.org/wiki/Power_station A material which is not the desired output of a process and which is typically the input of a process which removes it from its producer (e.g. a disposal process). This seems more like a role than a material. Anything can be waste. Thus, a "waste" role or disposition will be created and this class can then be populated by inference: any environmental material which has [role,disposition] waste will be considered a waste material. EcoLexicon:waste SWEETRealm:Waste https://en.wikipedia.org/wiki/Waste ENVO waste material Industrial wastes are liquid, solid and gaseous wastes originating from the manufacture of specific products. This will become a defined class, with subclasses added through inference based on material having a 'waste role' and being associated with industrial entities. industrial waste ENVO industrial waste material Industrial wastes are liquid, solid and gaseous wastes originating from the manufacture of specific products. ISBN:978-92-1-161386-5 http://stats.oecd.org/glossary/detail.asp?ID=1340 A structural basin that is below sea level. EcoLexicon:ocean_basin https://en.wikipedia.org/wiki/Ocean_basin envoPolar This class is defined in its geological sense: https://en.wikipedia.org/wiki/ Hydrologically, an oceanic basin may be anywhere on Earth that is covered by seawater, but geologically ocean basins are large geologic basins that are below sea level. Geologically, there are other undersea geomorphological features such as the continental shelves, the deep ocean trenches, and the undersea mountain ranges (for example, the mid-Atlantic ridge) which are not considered to be part of the ocean basins; while hydrologically, oceanic basins include the flanking continental shelves and shallow, epeiric seas. ocean basin A structural basin that is below sea level. https://en.wikipedia.org/wiki/Ocean_basin A group of hydrous aluminium phyllosilicate (phyllosilicates being a subgroup of silicate minerals) minerals (see clay minerals), that are typically less than 2 micrometres in diameter. Clay consists of a variety of phyllosilicate minerals rich in silicon and aluminium oxides and hydroxides which include variable amounts of structural water. EcoLexicon:clay SWEETRealm:Clay https://en.wikipedia.org/wiki/Clay clay A group of hydrous aluminium phyllosilicate (phyllosilicates being a subgroup of silicate minerals) minerals (see clay minerals), that are typically less than 2 micrometres in diameter. Clay consists of a variety of phyllosilicate minerals rich in silicon and aluminium oxides and hydroxides which include variable amounts of structural water. https://en.wikipedia.org/wiki/Clay A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. manufactured good manufactured product A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. https://en.wikipedia.org/wiki/Manufactured_product A portion of enriched soil is a portion of soil with elevated levels of some material entity. ENVO This could be demoted to an inferred class if issues with double inheritance arise. enriched soil An industrial building is a building within which goods are produced and, optionally, stored or within which services are rendered. It's possible that this will become an inferred class in the future. The United Nations' International Standard Industrial Classification should be referred to when expanding this branch. ISIC can also be used to identify processes. See http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=27&Lg=1. industrial building An industrial building is a building within which goods are produced and, optionally, stored or within which services are rendered. https://en.wikipedia.org/wiki/Industry Soil which has little to no water content and in which minerals and other soluble chemical entities have either bonded or become adsorbed to sold particles due to insufficient water availability. dry soil ENVO acid dune sand ENVO rocky sand Sand which is part of a desert. desert sand A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. portion of environmental material Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. environmental material A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. DOI:10.1186/2041-1480-4-43 MA:ma ORCID:0000-0002-4366-3088 URL:http://ontology.buffalo.edu/smith/articles/niches.html A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings. EcoLexicon:surface http://sweetontology.net/reprSpaceGeometry/Surface https://en.wikipedia.org/wiki/Surface This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here. surface layer A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings. URL:http://www.merriam-webster.com/dictionary/surface Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets. EcoLexicon:aerosol SWEETRealm:Aerosol envoAtmo Should connect to PATO as "quality of an aerosol" aerosol Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets. https://en.wikipedia.org/wiki/Aerosol Anthropogenic material in or on which organisms may live. ENVO anthropogenic environmental material Anthropogenic material in or on which organisms may live. MA:ma Silt is granular material of a size somewhere between sand and clay whose mineral origin is quartz and feldspar. EcoLexicon:silt SWEETRealm:Silt https://en.wikipedia.org/wiki/Silt https://en.wikipedia.org/wiki/ In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity. silt Silt is granular material of a size somewhere between sand and clay whose mineral origin is quartz and feldspar. https://en.wikipedia.org/wiki/Silt A naturally occurring granular material composed of finely divided rock and mineral particles. EcoLexicon:sand LTER:484 SWEETRealm:Sand https://en.wikipedia.org/wiki/Sand ENVO sand A naturally occurring granular material composed of finely divided rock and mineral particles. https://en.wikipedia.org/wiki/Sand Gravel is an environmental material which is composed of pieces of rock that are at least two millimeters (2mm) in its largest dimension and no more than 75 millimeters. EcoLexicon:gravel SWEETRealm:Gravel https://en.wikipedia.org/wiki/Gravel The logical def is a little off here - it should really suggest that a gravel is composed of many "pieces" of gravel. gravel Gravel is an environmental material which is composed of pieces of rock that are at least two millimeters (2mm) in its largest dimension and no more than 75 millimeters. https://en.wikipedia.org/wiki/Gravel The marine pelagic biome (pelagic meaning open sea) is that of the marine water column, from the surface to the greatest depths. ORCID:0000-0002-4366-3088 2010-03-15T11:17:06Z ENVO envoPolar marine pelagic biome The marine pelagic biome (pelagic meaning open sea) is that of the marine water column, from the surface to the greatest depths. ISBN:978-0-7506-3384-0 The marine benthic biome (benthic meaning 'bottom') encompasses the seafloor and includes such areas as shores, littoral or intertidal areas, marine coral reefs, and the deep seabed. ORCID:0000-0002-4366-3088 2010-03-15T11:17:06Z SPIRE:Benthic envoPolar marine benthic biome The marine benthic biome (benthic meaning 'bottom') encompasses the seafloor and includes such areas as shores, littoral or intertidal areas, marine coral reefs, and the deep seabed. ISBN:978-0-7506-3384-0 ORCID:0000-0002-4366-3088 The marine bathyal zone biome comprises regions of the marine benthic biome between approximately 200 m and 3000 m depth. This zone generally coincides with the continental slope. ORCID:0000-0002-4366-3088 2010-03-15T11:18:40Z marine bathyal zone biome The marine bathyal zone biome comprises regions of the marine benthic biome between approximately 200 m and 3000 m depth. This zone generally coincides with the continental slope. ISBN:978-0-444-82619-0 ORCID:0000-0002-4366-3088 The marine abyssal zone biome comprises regions of the marine benthic biome between approximately 2500 m and 6000 m depth. This zone generally coincides with the continental rise and the abyssal plain. ORCID:0000-0002-4366-3088 2010-03-15T11:18:40Z marine abyssal zone biome The marine abyssal zone biome comprises regions of the marine benthic biome between approximately 2500 m and 6000 m depth. This zone generally coincides with the continental rise and the abyssal plain. ISBN:978-0-444-82619-0 ORCID:0000-0002-4366-3088 The marine hadal zone biome describes sea floor deeper than 6000 m such as that of the oceanic trenches. ORCID:0000-0002-4366-3088 2010-03-15T11:18:40Z marine hadal zone biome The marine hadal zone biome describes sea floor deeper than 6000 m such as that of the oceanic trenches. ISBN:978-0-444-82619-0 ORCID:0000-0002-4366-3088 A biome expressed by strips or ridges of rocks, sand, or coral that rises to or near the surface of a body of marine water. ORCID:0000-0002-4366-3088 2010-03-15T11:18:40Z ENVO marine reef biome A biome expressed by strips or ridges of rocks, sand, or coral that rises to or near the surface of a body of marine water. ISBN:978-0-618-45504-1 ORCID:0000-0002-4366-3088 The neritic epipelagic zone biome comprises the marine water column above a continental shelf. ORCID:0000-0002-4366-3088 2010-03-15T11:19:19Z ENVO neritic pelagic zone biome The neritic epipelagic zone biome comprises the marine water column above a continental shelf. ISBN:978-0-444-82619-0 ISBN:978-0-7506-3384-0 ORCID:0000-0002-4366-3088 The oceanic epipelagic zone biome comprises the marine water column offshore, beyond a continental shelf. ORCID:0000-0002-4366-3088 2010-03-15T11:19:19Z ENVO oceanic pelagic zone biome The oceanic epipelagic zone biome comprises the marine water column offshore, beyond a continental shelf. ISBN:978-0-444-82619-0 ISBN:978-0-7506-3384-0 ORCID:0000-0002-4366-3088 The oceanic sea surface microlayer (SML) biome comprises the top 1000 micrometers of the marine surface waters occurring offshore, away from a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath. ORCID:0000-0002-4366-3088 2010-03-15T11:21:03Z ENVO oceanic sea surface microlayer biome The oceanic sea surface microlayer (SML) biome comprises the top 1000 micrometers of the marine surface waters occurring offshore, away from a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath. ORCID:0000-0002-4366-3088 https://en.wikipedia.org/wiki/Sea_surface_microlayer The neritic sea surface microlayer (SML) biome comprises the top 1000 micrometers of marine surface waters occurring above a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath. ORCID:0000-0002-4366-3088 2010-03-15T11:22:09Z ENVO neritic sea surface microlayer biome The neritic sea surface microlayer (SML) biome comprises the top 1000 micrometers of marine surface waters occurring above a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath. ORCID:0000-0002-4366-3088 https://en.wikipedia.org/wiki/Sea_surface_microlayer A prominent or distinctive aspect, quality, or characteristic of environments occurring within the marine water column. ORCID:0000-0002-4366-3088 2010-03-16T12:10:50Z envoPolar marine pelagic feature A prominent or distinctive aspect, quality, or characteristic of environments occurring within the marine water column. ISBN:978-0-618-45504-1 ORCID:0000-0002-4366-3088 A marine biome which is determined by an ocean. ORCID:0000-0002-4366-3088 2010-03-15T11:23:23Z envoPolar Ocean biomes are determined by major bodies of saline water, principal components of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas. More than half of this area is over 3,000 metres (9,800 ft) deep. Average oceanic salinity is around 35 parts per thousand (ppt) (3.5%), and nearly all seawater has a salinity in the range of 30 to 38 ppt. ocean biome A marine biome which is determined by an ocean. ORCID:0000-0002-4366-3088 https://en.wikipedia.org/wiki/Ocean The marine coral reef biome comprises constructional wave-resistant entities which are primarily built by corals and are often cemented together. The growth of these structures is aided by zooxanthellae, algae that are symbiotic with the reef-building corals. ORCID:0000-0002-4366-3088 2010-03-15T11:27:06Z ENVO marine coral reef biome The marine coral reef biome comprises constructional wave-resistant entities which are primarily built by corals and are often cemented together. The growth of these structures is aided by zooxanthellae, algae that are symbiotic with the reef-building corals. ISBN:978-0-7506-3384-0 ORCID:0000-0002-4366-3088 Particulate material is an environmental material which is composed of microscopic portions of solid or liquid material suspended in another environmental material. Subclasses should be assigned by inference. envoAtmo envoPolar particulate matter A prominent or distinctive aspect, quality, or characteristic of environments occurring on or along marine benthic environments. ORCID:0000-0002-4366-3088 2010-03-16T12:27:00Z marine benthic feature A prominent or distinctive aspect, quality, or characteristic of environments occurring on or along marine benthic environments. ISBN:978-0-618-45504-1 ORCID:0000-0002-4366-3088 ORCID:0000-0002-4366-3088 2010-03-20T06:43:45Z ENVO marine reef Environmental material derived from living organisms and composed primarily of one or more biomacromolecules. ORCID:0000-0002-4366-3088 2010-03-20T08:40:04Z EcoLexicon:organic_material biomass organic material Environmental material derived from living organisms and composed primarily of one or more biomacromolecules. ISBN:978-0-618-45504-1 ORCID:0000-0002-4366-3088 A shrubland biome is a terrestrial biome which includes, across its entire spatial extent, dense groups of shrubs. ORCID:0000-0002-4366-3088 2013-04-07T14:26:46Z Preliminary definition. shrubland biome A desert biome is a terrestrial biome which loses more liquid water by evapotranspiration than is supplied by precipitation and includes communities adapted to these conditions. ORCID:0000-0002-4366-3088 2013-04-07T14:26:46Z SPIRE:Desert_or_dune wwfBiome Preliminary definition. desert biome A terrestrial biome which comprises a tundra ecosystem that has reached its climax community. ORCID:0000-0002-4366-3088 2013-04-07T14:26:46Z SPIRE:Tundra envoPolar wwfBiome Preliminary definition. tundra biome An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system. ORCID:0000-0002-4366-3088 2013-04-07T14:35:18Z envoPolar A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional. environmental condition An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system. DOI:10.1186/2041-1480-4-43 A tropical condition is an environmental condition in which an environmental system receives high yearly solar irradiance per unit area and, on Earth, the Sun reaches a subsolar point at least once during the solar year. This results in a hot and moist year-round climate at low elevations, which have a monthly average temperature above 18 degrees Celsius. ORCID:0000-0002-4366-3088 2013-04-07T14:36:47Z EcoLexicon:the_tropics SPIRE:Tropical tropical A tropical condition is an environmental condition in which an environmental system receives high yearly solar irradiance per unit area and, on Earth, the Sun reaches a subsolar point at least once during the solar year. This results in a hot and moist year-round climate at low elevations, which have a monthly average temperature above 18 degrees Celsius. https://en.wikipedia.org/wiki/Tropical A temperate condition is an environmental condition in which an environmental system receives less solar irradiance than those with subpolar conditions, but greater than those with subtropical conditions. ORCID:0000-0002-4366-3088 2013-04-07T14:36:47Z SPIRE:Temperate tepid climate This class' definition is less satisfactory than the other latitudinal conditoins. temperate A temperate condition is an environmental condition in which an environmental system receives less solar irradiance than those with subpolar conditions, but greater than those with subtropical conditions. https://en.wikipedia.org/wiki/Temperate_climate tepid climate https://en.wikipedia.org/wiki/Temperate_climate A montane shrubland biome is a shrubland biome which occurs in regions elevated above sea level and which has community structure determined by elevation-dependent environmental conditions. ORCID:0000-0002-4366-3088 2013-04-07T14:40:32Z wwfBiome Preliminary definition. montane shrubland biome An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity. ORCID:0000-0002-4366-3088 2013-04-07T14:45:22Z anthrome human biome Preliminary definition. anthropogenic terrestrial biome An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity. http://www.eoearth.org/view/article/150128/ An environmental condition in which annual precipitation is less than half of annual potential evapotranspiration. ORCID:0000-0002-4366-3088 2013-04-24T13:28:18Z EcoLexicon:aridity envoPolar arid Lava is a mixture of molten or semi-molten rock, volatiles, and solids which has extruded beyond a planetary crust. PLB 2013-05-05T16:52:47Z EcoLexicon:lava SWEETRealm:Lava ENVO Some use 'lava' to refer to rock that is formed when lava cools. This is not the intended meaning of this class. See 'igneous rock' or similar. lava Lava is a mixture of molten or semi-molten rock, volatiles, and solids which has extruded beyond a planetary crust. https://en.wikipedia.org/wiki/Lava A polar condition is an environmental condition in which an environmental system receives low, yearly solar irradiance per unit area, resulting in colder climatic conditions. ORCID:0000-0002-4366-3088 2013-05-08T07:49:36Z SPIRE:Polar SWEETRealm:Polarization frigid envoPolar On Earth, polar conditions are such that every month has average temperature lower than 10 degrees Celsius. Note that this class refers to a climatic rather than a positional condition. polar A polar condition is an environmental condition in which an environmental system receives low, yearly solar irradiance per unit area, resulting in colder climatic conditions. https://en.wikipedia.org/wiki/Polar_climate frigid https://en.wikipedia.org/wiki/Polar_climate A system which has the disposition to environ one or more material entities. 2013-09-23T16:04:08Z EcoLexicon:environment environment In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. environmental system A system which has the disposition to environ one or more material entities. DOI:10.1186/2041-1480-4-43 A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure. Look for "mineral" in a chemical or geochemical ontology to formalise the composed primarily of link. From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure. ORCID:0000-0002-4366-3088 2013-10-05T12:37:41Z LTER:341 mineral material A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure. https://en.wikipedia.org/wiki/Mineral Water vapour is a vapour which is the gas phase of water. ORCID:0000-0002-4366-3088 2013-10-10T07:58:18Z aqueous vapor aqueous vapour water vapor ENVO Perhaps a better relation between water vapour and water can be found in or added to RO? water vapour Water vapour is a vapour which is the gas phase of water. https://en.wikipedia.org/wiki/Water_vapor aqueous vapor https://en.wikipedia.org/wiki/Water_vapor aqueous vapour https://en.wikipedia.org/wiki/Water_vapor water vapor https://en.wikipedia.org/wiki/Water_vapor An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body. ORCID:0000-0002-4366-3088 2013-10-10T08:14:50Z LTER:48 atmosphere An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body. https://en.wikipedia.org/wiki/Atmosphere https://en.wikipedia.org/wiki/Physical_geography Atmospheric water vapour is water vapour that is part of an atmosphere. ORCID:0000-0002-4366-3088 2013-10-10T08:22:07Z atmospheric water vapor ENVO envoPolar atmospheric water vapour Atmospheric water vapour is water vapour that is part of an atmosphere. https://en.wikipedia.org/wiki/Water_vapor atmospheric water vapor https://en.wikipedia.org/wiki/Water_vapor A structural basin is a geological depression formed by tectonic warping of previously flat lying rock strata. ORCID:0000-0002-4366-3088 2013-10-12T16:30:32Z structural basin A structural basin is a geological depression formed by tectonic warping of previously flat lying rock strata. https://en.wikipedia.org/wiki/Structural_basin A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions. ORCID:0000-0002-4366-3088 2013-10-12T17:21:09Z envoPolar Unlike biomes, ecoregions are geographically defined entities. ENVO's sister project, GAZ, contains terms for instances of ecoregions (e.g. Beringia lowland tundra). Requests for new terms should be directed to GAZ. ENVO will only contain this top-level class. The class' definition is preliminary and will be aligned to BFO. ecoregion A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions. DOI:10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2 URL:http://worldwildlife.org/biomes Ice is water frozen into a solid state. It can appear transparent or opaque bluish-white color, depending on the presence of impurities or air inclusions. The addition of other materials such as soil may further alter its appearance. ORCID:0000-0002-4366-3088 2013-10-13T12:01:28Z LTER:262 ice envoPolar water ice Ice is water frozen into a solid state. It can appear transparent or opaque bluish-white color, depending on the presence of impurities or air inclusions. The addition of other materials such as soil may further alter its appearance. https://en.wikipedia.org/wiki/Ice ice http://www.eionet.europa.eu/gemet/concept/4131 Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration. ORCID:0000-0002-4366-3088 2013-10-13T18:32:46Z envoPolar ENVO contains this top-level class, but all instances will be in GAZ. The definition is preliminary and will be aligned to BFO. https://en.wikipedia.org/wiki/ Ecozones correspond to the floristic kingdoms of botany or zoogeographic regions of zoology. Ecozones are characterized by the evolutionary history of the organisms they contain. They are distinct from biomes, also known as major habitat types, which are divisions of the Earth's surface based on life form, or the adaptation of plants and animals to climatic, soil, and other conditions. Biomes are characterized by similar climax vegetation. Each ecozone may include a number of different biomes. A tropical moist broadleaf forest in Central America, for example, may be similar to one in New Guinea in its vegetation type and structure, climate, soils, etc., but these forests are inhabited by plants and animals with very different evolutionary histories. ecozone Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration. https://en.wikipedia.org/wiki/ecozone A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface. ORCID:0000-0002-4366-3088 2013-10-15T16:42:02Z envoPolar Preliminary definition. layer A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface. Wiktionary:layer A layer which is part of a lake. ORCID:0000-0002-4366-3088 2013-10-15T16:57:43Z ENVO envoPolar Note that this class does not contain metalimnion as a subclass. The metaliminon is classified as a thermocline. lake layer A mass of water ice. Class should be populated by inference and asserted subclasses redistributed. ORCID:0000-0002-4366-3088 2013-10-15T19:49:11Z accumulation of ice ice accumulation http://sweetontology.net/phenCryo/Accumulation envoPolar ice mass A layer that is part of a marine water body. ORCID:0000-0002-4366-3088 envoMarine envoPolar marine layer A layer that is part of a marine water body. ORCID:0000-0002-4366-3088 An endolithic environment is an environment that exists within solid rock. endolithic environment An environmental system which has its properties and dynamics determined by saline water. Water (saline) envoEmpo envoOmics envoPolar saline water environment Water (saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environment which has a lower temperature than some local or global average. envoPolar The definition of the deprecated 'cold temperature habitat' class, which this class was derived from, quotes an upper threshold of 15 degrees Celsius for 'coldness'. cold environment An anthropogenic environment is an environmental system which is the product of human activity. Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic. anthropogenic environment An environment whose dynamics are strongly influenced by water. aquatic environment A rocky slope is a slope which has a surface primarily composed of rock. rocky slope A marine environment and enviroment which is determined by a marine water body. envoPolar marine environment A marine environment and enviroment which is determined by a marine water body. NM:nm An environmental system determined by seawater. ocean water environment envoPolar sea water environment The atmospheric boundary layer is the lowest layer of an atmosphere which is strongly influenced by its contact with a planetary surface with strong vertical mixing and in which physical quantities such as flow velocity, temperature, and moisture display rapid fluctuations (turbulence). planetary boundary layer envoPolar atmospheric boundary layer A planetary surface is a surface layer where the solid or liquid material of a planet comes into contact with an atmosphere or outer space. a useful class: this can be used to define sub-terrestrial and sub-marine entities planetary surface A layer in a water mass, itself composed primarily of water. envoPolar This class will eventually be populated by inference, and its asserted subclasses removed. aquatic layer A gravelly slope is a slope which has a surface primarily composed of gravel. gravelly slope A hillside is a slope that is part of a hill. brae hillside A talus slope is a slope which has a surface layer composed of scree. scree slope talus slope A biome which is subject to polar climatic conditions. envoPolar This class is primarily for inference and, in general, should not be used directly by annotators. If you're an annotator, please consider using a more informative term such as 'tundra biome'. polar biome An altitudinal condition which inheres in a bearer by virtue of the bearer being located at an altitude between mid-altitude forests and the tree line. ORCID:0000-0002-4366-3088 LTER:350 envoPolar The exact level of the tree line varies with local climate, but typically the tree line is found where mean monthly soil temperatures never exceed 10.0 degrees C and the mean annual soil temperatures are around 6.7 degrees C. In the tropics, this region is typified by montane rain forest (above 3,000 ft) while at higher latitudes coniferous forests often dominate. montane An altitudinal condition which inheres in a bearer by virtue of the bearer being located at an altitude between mid-altitude forests and the tree line. https://en.wikipedia.org/wiki/Altitudinal_zonation The exact level of the tree line varies with local climate, but typically the tree line is found where mean monthly soil temperatures never exceed 10.0 degrees C and the mean annual soil temperatures are around 6.7 degrees C. In the tropics, this region is typified by montane rain forest (above 3,000 ft) while at higher latitudes coniferous forests often dominate. https://en.wikipedia.org/wiki/Altitudinal_zonation An altitudinal condition is an environmental condition in which ranges of factors such as temperature, humidity, soil composition, solar irradiation, and tree density vary with ranges in altitude. ORCID:0000-0002-4366-3088 envoPolar Depending on the latitude (and, to a lesser extent, other factors), the actual location of the zones where these conditions are in effect will change. altitudinal condition An altitudinal condition is an environmental condition in which ranges of factors such as temperature, humidity, soil composition, solar irradiation, and tree density vary with ranges in altitude. https://en.wikipedia.org/wiki/Altitudinal_zonation A portion of acidic water is a portion of water with a pH less than 7. acidic water An tundra climatic condition is a polar condition in which at least one month's average temperature exceeds 0 degrees Celsius. envoPolar tundra climatic condition An tundra climatic condition is a polar condition in which at least one month's average temperature exceeds 0 degrees Celsius. https://en.wikipedia.org/wiki/Polar_climate Snow is an environmental material which is primarily composed of flakes of crystalline water ice. envoPolar snow Snow is an environmental material which is primarily composed of flakes of crystalline water ice. http://www.eionet.europa.eu/gemet/concept/7769 https://en.wikipedia.org/wiki/Snow A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein. environmental area envoPolar Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition. environmental zone A building part is a construction which is part of a building. Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat. building part A disposition which is realised by an environmental system or system parts thereof. ORCID:0000-0002-4366-3088 This class and its subclasses are experimental and are being developed with NCEAS use cases in mind. environmental disposition A layer that is part of the atmosphere. ORCID:0000-0002-4366-3088 atmospheric layering envoPolar This could be made into an inferred class, rather than having asserted subclasses. atmospheric layer atmospheric layering GEMET:http://www.eionet.europa.eu/gemet/concept/627 A boundary layer is a layer of fluid in the immediate vicinity of a bounding surface where the effects of viscosity are significant enough to distort the surrounding non-viscous flow. ORCID:0000-0002-4366-3088 boundary layer boundary layer A boundary layer is a layer of fluid in the immediate vicinity of a bounding surface where the effects of viscosity are significant enough to distort the surrounding non-viscous flow. https://en.wikipedia.org/wiki/Boundary_layer boundary layer http://www.eionet.europa.eu/gemet/concept/976 A lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow. lentic water body Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase. condensation envoAtmo envoPolar "process" is included in the label to make it clear that we are not referring to the condensed material (e.g. water droplets, window fog) hydrological condensation process Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase. https://en.wikipedia.org/wiki/Condensation The long-term fluctuations in temperature, precipitation, wind, and all other aspects of the Earth's climate. External processes, such as solar-irradiance variations, variations of the Earth's orbital parameters (eccentricity, precession, and inclination), lithosphere motions, and volcanic activity, are factors in climatic variation. Internal variations of the climate system, e.g., changes in the abundance of greenhouse gases, also may produce fluctuations of sufficient magnitude and variability to explain observed climate change through the feedback processes interrelating the components of the climate system. envoPolar Definition vebatim from GEMET. Will need to be refined. Further, distinction between "climate change" and (one or many) "climate change process" will need to be discussed. Fluctuations are not processes, per se. climate change The long-term fluctuations in temperature, precipitation, wind, and all other aspects of the Earth's climate. External processes, such as solar-irradiance variations, variations of the Earth's orbital parameters (eccentricity, precession, and inclination), lithosphere motions, and volcanic activity, are factors in climatic variation. Internal variations of the climate system, e.g., changes in the abundance of greenhouse gases, also may produce fluctuations of sufficient magnitude and variability to explain observed climate change through the feedback processes interrelating the components of the climate system. GEMET:http://www.eionet.europa.eu/gemet/concept/1471 A volcanic eruption is a process during which lava, tephra (ash, lapilli, volcanic bombs and blocks), and assorted gases are expelled from a volcanic vent or fissure. environmental_hazards volcanic eruption A volcanic eruption is a process during which lava, tephra (ash, lapilli, volcanic bombs and blocks), and assorted gases are expelled from a volcanic vent or fissure. https://en.wikipedia.org/wiki/Types_of_volcanic_eruptions A landmass which is part of a planet. land ground planetary landmass A landmass which is part of a planet. Adpated from https://en.wikipedia.org/wiki/Planetary_surface Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. space envoAstro outer space Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. https://en.wikipedia.org/wiki/Outer_space A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle. crust This class is meant to be applicable accross planets. Earth's crust would be an instance. planetary crust A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle. https://en.wikipedia.org/wiki/Crust_(geology) A planetary structural layer is laminar part of a terrestrial planet or other rocky body large enough to have differentiation by density. Planetary layers have differing physicochemical properties and composition. Label should be improved to match definition. planetary structural layer A planetary mantle is a planetary layer which is an interior part of a terrestrial planet or other rocky body large enough to have differentiation by density. mantle This class is meant to be applicable accross planets. Earth's mantle would be an instance. planetary mantle A planetary mantle is a planetary layer which is an interior part of a terrestrial planet or other rocky body large enough to have differentiation by density. https://en.wikipedia.org/wiki/Mantle_(geology) A lithosphere is the outermost shell of a terrestrial-type planet or natural satellite that is defined by its rigid mechanical properties. Earth's lithosphere includes the crust and uppermost mantle. lithosphere A lithosphere is the outermost shell of a terrestrial-type planet or natural satellite that is defined by its rigid mechanical properties. https://en.wikipedia.org/wiki/Lithosphere Magma is a mixture of molten or semi-molten rock, volatiles, and solids that is found beneath the uppermost solid layer of a planetary body. Besides molten rock, magma may also contain suspended crystals, dissolved gas and sometimes gas bubbles. magma Magma is a mixture of molten or semi-molten rock, volatiles, and solids that is found beneath the uppermost solid layer of a planetary body. Besides molten rock, magma may also contain suspended crystals, dissolved gas and sometimes gas bubbles. https://en.wikipedia.org/wiki/Magma An explosive eruption is a volcanic process in which pressurised magma is violently expelled and froths into volcanic ash. Explosive eruptions can eject a cloud of rocks, dust, gas, and pyroclastic material which may then collapse, creating a pyroclastic flow of hot volcanic matter. environmental_hazards explosive eruption An explosive eruption is a volcanic process in which pressurised magma is violently expelled and froths into volcanic ash. Explosive eruptions can eject a cloud of rocks, dust, gas, and pyroclastic material which may then collapse, creating a pyroclastic flow of hot volcanic matter. https://en.wikipedia.org/wiki/Explosive_eruption A settlement with a high density of buildings and inhabitants. See also: http://www.ecotope.org/anthromes/v1/guide/urban/12_dense_settlements/default.aspx The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request. dense settlement Tephra is fragmental material produced by a volcanic eruption regardless of composition, fragment size or emplacement mechanism. tephra Tephra is fragmental material produced by a volcanic eruption regardless of composition, fragment size or emplacement mechanism. https://en.wikipedia.org/wiki/Tephra A role that is realized in some process wherein the bearer is discarded or not utilized further. This definition is preliminary. waste role A geological fracture is any separation in a geologic formation, such as a joint or a fault that divides a mass of rock into two or more pieces. fracture SWEETRealm:Fissure fissure geological fracture A geological fracture is any separation in a geologic formation, such as a joint or a fault that divides a mass of rock into two or more pieces. https://en.wikipedia.org/wiki/Fracture_(geology) fissure Genomes:fissure A mass of water. water mass A coast is the area where land meets the sea, ocean, or lake. Used for both marine and lake coasts. The boundary of the coast is fuzzy and it overlaps both the water body and land in quesiton. Compared to 'shore' coast A coast is the area where land meets the sea, ocean, or lake. https://en.wikipedia.org/wiki/Coast A tsunami is a process during which a series of waves is generated in a water body, typically an ocean or large lake, by the displacement of a large volume of water. Earthquakes, volcanic eruptions and other underwater explosions (including detonations of underwater nuclear devices), landslides, glacier calvings, meteorite impacts and other disturbances above or below water all have the potential to generate a tsunami. seismic sea wave tidal wave environmental_hazards tsunami A tsunami is a process during which a series of waves is generated in a water body, typically an ocean or large lake, by the displacement of a large volume of water. Earthquakes, volcanic eruptions and other underwater explosions (including detonations of underwater nuclear devices), landslides, glacier calvings, meteorite impacts and other disturbances above or below water all have the potential to generate a tsunami. https://en.wikipedia.org/wiki/Tsunami Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. precipitation "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet) hydrological precipitation process Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. https://en.wikipedia.org/wiki/Precipitation A meteotsunami is a tsunami caused by atmospheric processes and differences in air pressure. Ambiguity as to whether this label refers to the process or the material entities (the waves). The material entities are a type of severe storm surge. rissaga environmental_hazards meteotsunami A meteotsunami is a tsunami caused by atmospheric processes and differences in air pressure. https://en.wikipedia.org/wiki/Meteotsunami rissaga Language: Catalan Condensation is a process during which a gas undergoes a phase transition into a liquid. condensation process Condensation is a process during which a gas undergoes a phase transition into a liquid. https://en.wikipedia.org/wiki/Condensation An environmental system which can sustain and allow the growth of an ecological population. EcoLexicon:habitat LTER:238 SWEETRealm:Habitat https://en.wikipedia.org/wiki/Habitat A habitat's specificity to an ecological population differentiates it from other environment classes. habitat An environmental system which can sustain and allow the growth of an ecological population. EnvO:EnvO A process in which natural ecosystems present over an expanse of land are removed and replaced with anthropogenic ecosystems. An SDGIO request. Likely to be refined and revised. This looks like an aggregate class, subsuming a range of processes which can lead to degradation. These anthropogenic ecosystems may include urban or other built-up settlements or anthropogenic ecosystems used for activities such as forestry or agriculture. land consumption process A process in which natural ecosystems present over an expanse of land are removed and replaced with anthropogenic ecosystems. Adapted from EEA (1997) The concept of environmental space, Copenhagen, URL: http://www.eea.europa.eu/publications/92-9167-078-2/at_download/file An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. The range of entities that are considered "barren land" are not exhaustive, making axiomatisation risky at this stage. Barren Land (Rock/Sand/Clay) NLCD:31 envoPolar nlcd2011 According to the NLCD 2011, areas of barren land generally have less than 15% cover of vegetation. A specific threshold is not asserted in this definition. area of barren land An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. https://en.wikipedia.org/wiki/Exosphere https://en.wikipedia.org/wiki/Planetary_surface https://www.mrlc.gov/nlcd11_leg.php A part of an astronomical body which is primarily composed of a continuous volume of gaseous or aerosolised material held in shape by one or more environmental processes. This may not need to be in the atmosphere, also note that "meteor" will do much of the same work. envoAtmo Similar, in spirit, to landform. This class may need to be split into aerosols and 'pure' volumes of gas. aeroform A planned process during which a portion of environmental material is removed from a material entity. This should be an OBI planned process. Pending import. Created for SDGIO and intended to be a more general form of resource extraction process. material extraction process A process whereby a large volume of gas moves due to a disequilibrium of physical forces. wind envoAtmo envoPolar This class refers to all forms of "wind": from the familiar movement of air in the Earth's atmosphere to the solar wind. Use a subclass to be more precise. mass gaseous flow A process whereby a large volume of gas moves due to a disequilibrium of physical forces. https://en.wikipedia.org/wiki/Wind wind A mass gaseous flow which occurrs in a planet's atmosphere due to internal pressure disequilibria. envoAtmo envoPolar atmospheric wind A mass gaseous flow which occurrs in a planet's atmosphere due to internal pressure disequilibria. https://en.wikipedia.org/wiki/Wind A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. This class is to be populated by inference. gas gaseous environmental material A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. http://www.merriam-webster.com/dictionary/gas A material entity which is composed of a volume of unbound positive and negative particles in roughly equal numbers, conducts electricity, and possesses internal magnetic fields. An NTR for `quality of a plasma` has been posted on the PATO tracker: https://github.com/pato-ontology/pato/issues/88 plasma A material entity which is composed of a volume of unbound positive and negative particles in roughly equal numbers, conducts electricity, and possesses internal magnetic fields. http://www.merriam-webster.com/dictionary/plasma https://en.wikipedia.org/wiki/Plasma_%28physics%29 An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. celestial body envoAstro Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'. astronomical body An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. https://en.wikipedia.org/wiki/Astronomical_object A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals. envoAstro envoPolar Considerable debate on the definition of planet exists. planet A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals. http://solarsystem.nasa.gov/planets/whatisaplanet https://en.wikipedia.org/wiki/Planet 1 An object which is composed of one or more gravitationally bound structures that are associated with a position in space. celestial object envoAstro If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far. astronomical object An object which is composed of one or more gravitationally bound structures that are associated with a position in space. https://en.wikipedia.org/wiki/Astronomical_object An environmental material which is in a solid state. This is a defined class: its subclasses will not be asserted, but filled by inference. solid environmental material An environmental material which is in a liquid state. envoPolar This is a defined class: its subclasses will not be asserted, but filled by inference. liquid environmental material A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact. Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion. envoAstro envoPolar The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations. biosphere A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact. http://www.biology-online.org/dictionary/Biosphere https://en.wikipedia.org/wiki/Biosphere A cryosphere is that part of a planet which is primarily composed of water is in solid form. envoAstro envoPolar This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class. cryosphere A cryosphere is that part of a planet which is primarily composed of water is in solid form. https://en.wikipedia.org/wiki/Cryosphere An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet. envoAstro envoPolar This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class. hydrosphere An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet. https://en.wikipedia.org/wiki/Hydrosphere An astronomical body part which is composed of soil, subject to soil formation processes, and found on the surface of a lithosphere. envoAstro This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class. pedosphere An astronomical body part which is composed of soil, subject to soil formation processes, and found on the surface of a lithosphere. https://en.wikipedia.org/wiki/Pedosphere A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force. precipitation process A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force. https://en.wikipedia.org/wiki/Precipitation_%28chemistry%29 https://en.wikipedia.org/wiki/Precipitation A hydrological process in which irregular aggregates of snow fall to a planetary surface. snow fall environmental_hazards envoPolar snowfall An envirommental system which bridges two or more biomes and which includes ecological communities which blend these biomes' phylogenetic and phenotypic compositions. There are many subtypes of ecotone, some with sharp transitions and others with gradual, patchy transitions between communities. From Wikipedia:Ecotone - The word ecotone was coined from a combination of eco(logy) plus -tone, from the Greek tonos or tension – in other words, a place where ecologies are in tension. ecotone An envirommental system which bridges two or more biomes and which includes ecological communities which blend these biomes' phylogenetic and phenotypic compositions. ISBN:978-0-03-058414-5 https://en.wikipedia.org/wiki/Ecotone https://github.com/EnvironmentOntology/envo/issues/501 https://www.merriam-webster.com/dictionary/ecotone An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. non-anthropised environment non-anthropized environment In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised. natural environment An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. https://en.wikipedia.org/wiki/Anthropization https://en.wikipedia.org/wiki/Natural_environment A process during which a natural environmental system is altered by human action. anthropization An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action. anthropisation A process during which a natural environmental system is altered by human action. https://en.wikipedia.org/wiki/Anthropization An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action. https://en.wikipedia.org/wiki/Anthropization An ecotone which overlaps at least one biome which supports the growth and persistence of trees and at least one that does not. Before ceasing altogether, tree growth becomes sparse and trees appear stunted as conditions become less favourable along this ecotone. tree line tree-line treeline tree line ecotone An ecotone which overlaps at least one biome which supports the growth and persistence of trees and at least one that does not. Before ceasing altogether, tree growth becomes sparse and trees appear stunted as conditions become less favourable along this ecotone. https://en.wikipedia.org/wiki/Tree_line A planet that is composed primarily of silicate rocks or metals. rocky planet telluric planet Earth-like planet envoAstro terrestrial planet A planet that is composed primarily of silicate rocks or metals. https://en.wikipedia.org/wiki/Terrestrial_planet A process whereby a volume of liquid moves due to a disequilibrium of physical forces. envoPolar This class can refer to the flow of any material in a liquid phase. mass liquid flow A process whereby a volume of liquid moves due to a disequilibrium of physical forces. https://en.wikipedia.org/wiki/Wind A process during which a volume of water is transported due to a disequilibria in physical forces. environmental_hazards water flow process A part of an astronomical body which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology and which are within the gravitational sphere of influence of that body. envoAstro The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations. technosphere A part of an astronomical body which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology and which are within the gravitational sphere of influence of that body. http://dx.doi.org/10.1177/2053019616677743 http://www.yourdictionary.com/technosphere https://www.sciencedaily.com/releases/2016/11/161130085021.htm A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation. The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale. manufacturing process A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation. https://en.wikipedia.org/wiki/Manufacturing The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale. https://en.wikipedia.org/wiki/Manufacturing An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures. The nature of "structures" must be further specified. human-directed construction process An environmental system within which an environmental material strongly influences the system's composition and properties. Organisational class. Not intended for annotation. Subclasses describe environments which are usually permeated by an environmental material. They may also describe environments which are sufficiently close to a material, that their dynamics are strongly influenced by it (e.g. a patch of forest ecosystem neighbouring a uranium dump). environmental system determined by a material An environmental system which is determined by a living organism. host-associated environment envoEmpo envoOmics environmental system determined by an organism A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body. envoAtmo meteor A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body. https://cloudatlas.wmo.int/other-meteors.html A meteor which is primarily composed of water. envoAtmo hydrometeor A meteor which is primarily composed of water. https://cloudatlas.wmo.int/other-meteors.html A meteor which is primarily composed of rock. envoAtmo lithometeor A lake which has formed as the result of processes that are not or are only minimally driven by human activity. This class is to be filled by inference. natural lake A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium. Requires addition of waves for full axiomatisation. This should be linked to "subatomic particle" with an "or". Note that ENVO represents space as an environmental material (a hard vacuum with sparse material inclusions). environmental_hazards envoAstro radiation A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium. https://en.wikipedia.org/wiki/Radiation A radiation process during which waves (or their quanta, photons) of the electromagnetic field propagate (radiate) through space carrying electromagnetic energy. EM radiation environmental_hazards envoAstro Note that this class is concerned only with active radiative processes: static electric and magnetic fields are not inlcuded. All electromagnetic radiation carries radiant energy. electromagnetic radiation A radiation process during which waves (or their quanta, photons) of the electromagnetic field propagate (radiate) through space carrying electromagnetic energy. https://en.wikipedia.org/wiki/Electromagnetic_radiation An environmental system which has its properties and dynamics determined by soil. Soil (non-saline) envoEmpo envoOmics soil environment Soil (non-saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environmental system which has its properties and dynamics determined by sediment. envoEmpo envoOmics sediment environment An environmental system which has its properties and dynamics determined by an aerosol. envoEmpo envoOmics aerosol environment An environmental system which has its properties and dynamics determined by a saline aerosol. Aerosol (saline) envoEmpo envoOmics saline aerosol environment Aerosol (saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ seaspray or other aerosolized saline material (>5 psu) An environmental system which has its properties and dynamics determined by an aerosol with a low concentration of dissolved solutes. Aerosol (non-saline) envoEmpo envoOmics non-saline aerosol environment Aerosol (non-saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ aerosolized dust or liquid An environmental system determined by part of a living or dead plant, or a whole small plant. Plant corpus envoEmpo envoMeo envoOmics environment associated with a plant part or small plant Plant corpus http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An astronomical body which is composed of rocky or metallic materials and is considerably smaller than asteroids. envoAstro meteoroid An astronomical body which is composed of rocky or metallic materials and is considerably smaller than asteroids. https://en.wikipedia.org/wiki/Meteoroid A material which is composed primarily of one or more pure metals and which shows their properties. Far more axiomatisation can be done should the qualities of metals be added to PATO or a similar quality ontology. However, note that there are many exceptions to the typical qualities of the majority of metals. metal While this class allows for some degree of contamination by non-metal substances, the material represented should show at least some of the typical features of a pure metal: hardness (except for liquid metals), opacity, lustre, malleability, fusibility, ductile and good electrical and thermal conductivity. metallic material A material which is composed primarily of one or more pure metals and which shows their properties. https://en.wikipedia.org/wiki/Metal The disposition of an environmental system, particularly those influencing atmospheres, to manifest a cyclic pattern of weather over time. The current alignment of "climate" under BFO:disposition is drawing from its very useful etymology (Ancient Greek klima, meaning inclination). The climatic conditions currently used to axiomatise biomes (polar, tropical, etc) may be better placed under this class. Climate is commonly defined as the weather averaged, or otherwise summarised, over a period of time much longer than the duration of any phenomenon that constitutes weather. The standard averaging period is 30 years, but other periods may be used depending on the purpose. climate The disposition of an environmental system, particularly those influencing atmospheres, to manifest a cyclic pattern of weather over time. https://en.wikipedia.org/wiki/Climate Climate is commonly defined as the weather averaged, or otherwise summarised, over a period of time much longer than the duration of any phenomenon that constitutes weather. The standard averaging period is 30 years, but other periods may be used depending on the purpose. https://en.wikipedia.org/wiki/Climate A process during which microscopic solid or liquid objects are formed. particle formation particulate matter formation process A process during which microscopic solid or liquid objects are formed. https://en.wikipedia.org/wiki/Particulates An aerosol formation process which occurs in an atmosphere. atmospheric aerosol formation envoAtmo atmospheric aerosol formation An aerosol formation process which occurs in an atmosphere. https://en.wikipedia.org/wiki/Particulates A process during which an aerosol, consisting of solid particulates suspended in a gas, is formed in an atmosphere. formation of solid particles in an atmosphere envoAtmo formation of a solid aerosol in an atmosphere A process during which an aerosol, consisting of solid particulates suspended in a gas, is formed in an atmosphere. https://en.wikipedia.org/wiki/Particulates A process during which an aerosol, consisting of droplets of liquid suspended in gas, is formed in an atmosphere. formation of liquid droplets in an atmosphere formation of liquid particles in an atmosphere envoAtmo formation of a liquid aerosol in an atmosphere A process during which an aerosol, consisting of droplets of liquid suspended in gas, is formed in an atmosphere. https://en.wikipedia.org/wiki/Particulates An aerosol which has non-gaseous parts that are primarily composed of liquid droplets. SWEETRealm:Aerosol liquid aerosol envoAtmo aerosolised liquids An aerosol which has non-gaseous parts that are primarily composed of liquid droplets. https://en.wikipedia.org/wiki/Aerosol An aerosol which has non-gaseous parts that are primarily composed of solid particles. SWEETRealm:Aerosol solid aerosol envoAtmo aerosolised solids An aerosol which has non-gaseous parts that are primarily composed of solid particles. https://en.wikipedia.org/wiki/Aerosol A process during which microscopic solid particulates are formed from gaseous materials in an atmosphere. atmospheric formation of a solid aerosol formation of a solid aerosol in an atmosphere formation of a solid aerosol in the atmosphere formation of solid particles from gaseous material in an atmosphere envoAtmo formation of a solid aerosol from gaseous material in an atmosphere A process during which microscopic solid particulates are formed from gaseous materials in an atmosphere. https://en.wikipedia.org/wiki/Particulates A process during which microscopic liquid droplets are formed from gaseous materials in an atmosphere. atmospheric formation of a liquid aerosol formation of a liquid aerosol in an atmosphere formation of a liquid aerosol in the atmosphere formation of liquid droplets from gaseous material in an atmosphere formation of liquid particles from gaseous material in an atmosphere envoAtmo formation of a liquid aerosol from gaseous material in an atmosphere A process during which microscopic liquid droplets are formed from gaseous materials in an atmosphere. https://en.wikipedia.org/wiki/Particulates A process during which pieces of a planetary crust and uppermost mantle move. tectonic movement A process during which pieces of a planetary crust and uppermost mantle move. https://en.wikipedia.org/wiki/Plate_tectonics https://en.wikipedia.org/wiki/List_of_tectonic_plates A part of a lithosphere which is separated by other such parts by geographic faults or similar geomorphological discontinuities. tectonic plate A part of a lithosphere which is separated by other such parts by geographic faults or similar geomorphological discontinuities. https://en.wikipedia.org/wiki/List_of_tectonic_plates A geomorphological feature which is formed where two or more tectonic plates move towards, away from, or along one another, resulting in deformation of the lithosphere. tectonic plate boundary A geomorphological feature which is formed where two or more tectonic plates move towards, away from, or along one another, resulting in deformation of the lithosphere. https://en.wikipedia.org/wiki/Plate_tectonics An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure. This class is defined logically - any material that is frozen is considered a subclass. Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure. ice A terrestrial planet which has a surface dominated by hot deserts. dry planet envoAstro This class of planet is still mostly theoretical. desert planet A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water. An axiom to express that the planet has a 'substantial' proportion of its mass in the form of water wound enhance this class. aquaplanet panthalassic planet water world envoAstro While this planetary form is still mostly theoretical, strong candidates exist such as the extrasolar planet GJ 1214 b and ocean planet candidate Kepler-22b. ocean planet A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water. https://en.wikipedia.org/wiki/Ocean_planet A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice. cryoplanet envoAstro While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane. ice planet A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice. https://en.wikipedia.org/wiki/Ice_planet While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane. https://en.wikipedia.org/wiki/Ice_planet A planet which has a surface layer that nearly completely or completely covered by lava, and which has a substantial portion of its mass composed of lava. envoAstro This class of planets is still mostly theoretical, however, lava planets are thought plausible shortly after a terrestrial planet is formed, soon after a terrestrial planet has suffered a large collision event, or if a terrestrial planet is orbiting very close to its star, causing intense irradiation and tidal forces. Likely lava exoplanets include COROT-7b, Kepler-10b, Alpha Centauri Bb, and Kepler-78b. lava planet A planet which has a surface layer that nearly completely or completely covered by lava, and which has a substantial portion of its mass composed of lava. https://en.wikipedia.org/wiki/Lava_planet This class of planets is still mostly theoretical, however, lava planets are thought plausible shortly after a terrestrial planet is formed, soon after a terrestrial planet has suffered a large collision event, or if a terrestrial planet is orbiting very close to its star, causing intense irradiation and tidal forces. Likely lava exoplanets include COROT-7b, Kepler-10b, Alpha Centauri Bb, and Kepler-78b. https://en.wikipedia.org/wiki/Lava_planet A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms. Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities. geodiversity A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms. https://en.wikipedia.org/wiki/Geodiversity Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities. An ecosystem which has been causally isolated from a larger ecosystem within which it was previously embedded, such that the direct exchange of materials, resources, and energy between these systems is severely or entirely curtailed. Often, ecosystem fragments are unable to sustain themselves without human intervention and management as they are not large enough to perform self-sustaining functions (e.g. nutrient recycling) or hold sufficient ecological resources such as genetic diversity of populations. ecosystem fragment A process during which one or more parts of an ecosystem become causally isolated such that the direct flow or exchange of materials, resources, and energy between a given fragment and the remainder of the original system is severely curtailed or entirely halted. ecosystem fragmentation process A process during which one or more parts of an ecosystem become causally isolated such that the direct flow or exchange of materials, resources, and energy between a given fragment and the remainder of the original system is severely curtailed or entirely halted. https://en.wikipedia.org/wiki/Ecosystem_decay https://en.wikipedia.org/wiki/Habitat_fragmentation https://en.wikipedia.org/wiki/Population_fragmentation A process during which an ecosystem, its parts, or the processes it participates in are modified by human intervention to accomplish an objective. ecosystem management Umweltmaßnahme environmental management active ecosystem management process A process during which an ecosystem, its parts, or the processes it participates in are modified by human intervention to accomplish an objective. https://www.iucn.org/theme/protected-areas/about/protected-areas-categories/category-iv-habitatspecies-management-area Umweltmaßnahme https://orcid.org/0000-0002-9620-2832 www.awi.de/internas 1 A process during which an ecosystem fragment loses its system integrity, with many of its resident ecological populations 1) losing their habitats, 2) undergoing a loss of functional and phylogenetic diversity, and 3) undergoing a subsequent genetic destabilisation through inbreeding. This process may be caused by direct anthropisation (i.e. the fragmentation of ecosystems due to the establishment of cropland) or by more natural events such as forest fires or erosion of land bridges. ecosystem decay A process during which an ecosystem fragment loses its system integrity, with many of its resident ecological populations 1) losing their habitats, 2) undergoing a loss of functional and phylogenetic diversity, and 3) undergoing a subsequent genetic destabilisation through inbreeding. https://en.wikipedia.org/wiki/Ecosystem_decay Soil which has increased levels of molecules or ions capable of donating a hydron (proton or hydrogen ion) to other chemical entities, or, alternatively, capable of forming covalent bonds with other chemicals via the acceptance of an electron pair, resulting in a bulk pH measurement of less than 7. acidic soil Soil which has increased levels of molecules or ions capable of donating a hydron (proton or hydrogen ion) to other chemical entities, or, alternatively, capable of forming covalent bonds with other chemicals via the acceptance of an electron pair, resulting in a bulk pH measurement of less than 7. https://en.wikipedia.org/wiki/Acid The surface layer of a volume of water. EcoLexicon:surface_water SWEETRealm:SurfaceWater https://en.wikipedia.org/wiki/Surface_water surface of a body of water water body surface water surface The surface layer of a mass of sediment. surface of a sedimentary mass surface sediment sediment surface An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it. terrestrial environmental zone A terrestrial zone which is bounded by constructed, manufactured, or other anthropogenic material entities. anthropised terrestrial environmental zone An environmental zone which is bounded by material parts of a marine environment. This class will eventually be populated by inference alone, with its subclasses distributed in more process-linked hierarchies to improve semantic density. marine environmental zone A process during which sediments compact under pressure, expel connate fluids, and gradually become solid sedimentary rock. lithification A process during which sediments compact under pressure, expel connate fluids, and gradually become solid sedimentary rock. https://en.wikipedia.org/wiki/Lithification A natural environment which is located on a land mass. terrestrial natural environment A natural environment which is within a water body. aquatic natural environment A layer which is primarily composed of some liquid material. liquid layer A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid. solid layer A solid layer which is primarily composed of some water-based ice. water ice layer An environmental zone which is part of an atmosphere. atmospheric area atmospheric zone A vegetated area is a geographic feature which has ground cover dominated by plant communities. ORCID:0000-0002-4366-3088 envoPolar vegetated area A geographic feature which is primarily composed of a continuous volume of liquid water held in shape or sustained by an environmental process. Should create links to envrionmental process with new relation like "sustained_by" Similar, in spirit, to landform. hydroform Should create links to envrionmental process with new relation like "sustained_by" ORCID:0000-0002-4366-3088 A liquid surface layer which is in contact with air. liquid air-water interface layer A surface layer which is composed primarily of some liquid. liquid surface layer A surface layer which is composed primarily of solid environmental material. solid surface layer A body of water which is primarily composed of saline water. saline body of water This class has its subclasses populated by inference. saline water body A material transport process during which a volume of material is displaced due to a disequilibrium in physical forces and during which 1) the qualities that inhere in that volume and 2) the processes that are unfolding within it are largely unchanged. advective transport Advective processes are disjoint from diffusive processes. Typically, fluids are advected. advective transport process A material transport process during which a volume of material is displaced due to a disequilibrium in physical forces and during which 1) the qualities that inhere in that volume and 2) the processes that are unfolding within it are largely unchanged. https://en.wikipedia.org/wiki/Advection https://en.wikipedia.org/wiki/Intensive_and_extensive_properties An action of exogenic processes (such as water flow or wind) which remove environmental material from one location on the surface of an astronomical body, transporting it to another location where it is deposited. erosion An action of exogenic processes (such as water flow or wind) which remove environmental material from one location on the surface of an astronomical body, transporting it to another location where it is deposited. https://en.wikipedia.org/wiki/Erosion A landform which has been rendered barren or partially barren by environmental extremes, especially by low rainfall. desert A system which consists of an atmosphere, hydrosphere, cryosphere, land surface, and biosphere, forced or influenced by external processes. This class, from the IPCC report, is naturally focused on the Earth's climate. The report cites the Sun as the agent of the most important forcing processes. It also considers the direct effect of human activities on the climate system an external forcing climate system A system which consists of an atmosphere, hydrosphere, cryosphere, land surface, and biosphere, forced or influenced by external processes. https://github.com/EnvironmentOntology/envo/issues/604 https://www.ipcc.ch/ipccreports/tar/wg1/040.htm This class, from the IPCC report, is naturally focused on the Earth's climate. The report cites the Sun as the agent of the most important forcing processes. It also considers the direct effect of human activities on the climate system an external forcing https://www.ipcc.ch/ipccreports/tar/wg1/040.htm A process during which particles suspended in a gaseous medium are formed. new particle formation process envoAtmo aerosolised particle formation process A process during which particles suspended in a gaseous medium are formed. https://en.wikipedia.org/wiki/Aerosol https://en.wikipedia.org/wiki/Particulates A material transport process during which solid or liquid particles are directly introduced into a volume of gas. primary aerosol formation primary aerosol formation process A material transport process during which solid or liquid particles are directly introduced into a volume of gas. https://en.wikipedia.org/wiki/Aerosol https://en.wikipedia.org/wiki/Particulates An ecosystem which 1) typically has monthly average temperatures below 10 degrees Celsius 2) has a low evapotranspiration ratio 3) is dominated by treeless terrain, covered by communities of low-growing vegetation such as dwarf shrubs, sedges and grasses, mosses, and lichens, 4) contains areas of soil underlain by permafrost with a thin active layer and 5) occurs in both polar and alpine regions (i.e., both high latitudes and high altitudes), and 5) does not have permanent snow or ice cover. SPIRE:Tundra envoPolar Tundra ecosysems are often underlaid by permafrost, with the result that drainage is bad and the soil may be saturated for long periods. It does not have a permanent snow-ice cover. Productivity is low in this biome because of the extremes of climate. tundra ecosystem An ecosystem which 1) typically has monthly average temperatures below 10 degrees Celsius 2) has a low evapotranspiration ratio 3) is dominated by treeless terrain, covered by communities of low-growing vegetation such as dwarf shrubs, sedges and grasses, mosses, and lichens, 4) contains areas of soil underlain by permafrost with a thin active layer and 5) occurs in both polar and alpine regions (i.e., both high latitudes and high altitudes), and 5) does not have permanent snow or ice cover. This definition is a synthesis of the following sources: NSIDC Glossary accessed 2016, IPCC WGII AR5 2014, Van Everdingen International Permafrost Association 2005, AMS - glossary of meteorology, PhysicalGeography.net A bed which underlies a marine water body. marine bed Clay which is part of an abyssal plain. abyssal clay A mining process during which materials are extracted from benthic environments deep below the ocean surface, where no stellar radiation reaches.. deep seafloor mining deep-seafloor mining "The most valuable of the marine mineral resources is petroleum. About 15% of the world's oil is produced offshore, and extraction capabilities are advancing. One of the largest environmental impacts of deep sea mining are discharged sediment plumes which disperse with ocean currents and thus may negatively influence the marine ecosystem. Coal deposits known as extensions of land deposits , are mined under the sea floor in Japan and England." benthic deep-sea mining A mining process during which materials are extracted from benthic environments deep below the ocean surface, where no stellar radiation reaches.. https://en.wikipedia.org/wiki/Mining https://www.eionet.europa.eu/gemet/en/concept/14956 "The most valuable of the marine mineral resources is petroleum. About 15% of the world's oil is produced offshore, and extraction capabilities are advancing. One of the largest environmental impacts of deep sea mining are discharged sediment plumes which disperse with ocean currents and thus may negatively influence the marine ecosystem. Coal deposits known as extensions of land deposits , are mined under the sea floor in Japan and England." https://www.eionet.europa.eu/gemet/en/concept/14956 An anthropisation process during which terrestrial environments - natural or anthropised - or parts thereof are altered to facilitate human activities such as agriculture, settlement, or commerce. land conversion land development Further examples include subdividing real estate into lots, typically for the purpose of building homes and converting unused factories into condominia. land conversion process An anthropisation process during which terrestrial environments - natural or anthropised - or parts thereof are altered to facilitate human activities such as agriculture, settlement, or commerce. https://en.wikipedia.org/wiki/Land_development Further examples include subdividing real estate into lots, typically for the purpose of building homes and converting unused factories into condominia. https://en.wikipedia.org/wiki/Land_development An anthropogenic environmental process which includes all human activities undertaken in a natural, semi-natural, or anthropised environment. There are multiple systems of land use classification. This hierarchy aims to be generally applicable, but national systems can be added on request. land use process An anthropogenic environmental process which includes all human activities undertaken in a natural, semi-natural, or anthropised environment. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use A land use process during which materials of economic value are extracted from a planet, usually from an orebody, lode, vein, seam, reef or placer deposit. mining terrestrial mining A land use process during which materials of economic value are extracted from a planet, usually from an orebody, lode, vein, seam, reef or placer deposit. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use https://en.wikipedia.org/wiki/Mining https://www.eionet.europa.eu/gemet/en/concept/14837 A process during which an ecosystem - natural or anthropised - is changed by the actions of humans. anthropogenic ecosystem conversion process A planned process during which humans access and obtain resources, benefits, or services from a natural or anthropised ecosystem. planned environmental usage process A planned environmental usage process during which a non-renewable resource such as petroleum, natural gas, or water is extracted from an ecosystem. mining A planned environmental usage process during which a non-renewable resource such as petroleum, natural gas, or water is extracted from an ecosystem. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use https://en.wikipedia.org/wiki/Mining https://www.eionet.europa.eu/gemet/en/concept/14837 A mining process which occurs in a marine ecosystem. marine mining A planned environmental usage process during which an environment supports manufacturing facilities producing commodities that are sold with the expectation of recovering the total cost of production. This class includes environments used to support the facilities engaged with a broad variety of manufacturing activities from food and tobacco, to textiles, metals, vehicles, and chemicals. usage of an environment for industry A planned environmental usage process during which an environment supports manufacturing facilities producing commodities that are sold with the expectation of recovering the total cost of production. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use https://www.eionet.europa.eu/gemet/en/concept/4279 A mountain which is located on land and which is bounded by an atmosphere or outer space. terrestrial mountain A mountain that is part of a polar environment. envoPolar polar mountain A mountain that is part of a polar environment. https://www.unep-wcmc.org/resources-and-data/mountain-watch--environmental-change-sustainable-development-in-mountains A mountain that is part of a temperate environment. temperate mountain A mountain that is part of a temperate environment. https://www.unep-wcmc.org/resources-and-data/mountain-watch--environmental-change-sustainable-development-in-mountains A mountain that is part of a tropical environment. tropical mountain A mountain that is part of a tropical environment. https://www.unep-wcmc.org/resources-and-data/mountain-watch--environmental-change-sustainable-development-in-mountains body of liquid A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes. liquid astronomical body part A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes. https://en.wikipedia.org/wiki/Landform A part of an astronomical body which is primarily composed of a continuous volume of gaseous material, shaped by one or more environmental processes. gaseous astronomical body part A part of an astronomical body which is primarily composed of a continuous volume of gaseous material, shaped by one or more environmental processes. https://en.wikipedia.org/wiki/Landform A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space. 2018-10-04T16:55:57Z a useful class: this can be used to define sub-terrestrial and sub-marine entities surface of an astronomical body A solid surface layer which is that part of a glacier in contact with a planetary atmosphere, water body, or solid material partially surrounding that glacier. 2019-01-14T15:39:35Z glacier surface glacial surface layer A velocity quality which inheres in the surface layer of a glacier. 2019-01-14T15:42:21Z glacier surface layer velocity glacier surface velocity glacial surface layer velocity A material transformation process during which a material's viscosity increase either through a reduction in temperature, through chemical reactions, or other physical effects. 2019-01-14T18:47:32Z congelation congelation process Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question. material congelation process A material transformation process during which a material's viscosity increase either through a reduction in temperature, through chemical reactions, or other physical effects. https://en.wikipedia.org/wiki/Congelation Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question. https://en.wikipedia.org/wiki/Congelation Land which is below the freezing point of water. 2019-01-14T21:18:19Z http://sweetontology.net/realmCryo/FrozenGround frozen ground Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load. frozen land Land which is below the freezing point of water. https://orcid.org/0000-0003-4808-4736 Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load. https://orcid.org/0000-0003-4808-4736 Soil which is below the freezing point of water. 2019-01-14T21:26:59Z frozen soil An advective transport process during which a mass of ice is transported from one location to another. 2019-01-31T17:51:48Z mass ice flow A material congelation process during which a liquid turns into a solid when its temperature is lowered below its melting point. 2019-01-31T21:13:16Z freezing A material congelation process during which a liquid turns into a solid when its temperature is lowered below its melting point. https://en.wikipedia.org/wiki/Freezing A freezing process during which liquid water is transformed into water ice. 2019-01-31T21:16:46Z freezing of water into water ice A water surface that is part of a water body. 2019-02-27T21:22:13Z surface layer of a water body An ecoregion which is located on a landmass. 2019-03-05T17:40:44Z https://www.worldwildlife.org/biome-categories/terrestrial-ecoregions terrestrial ecoregion A surface layer of a water body which is part of an ocean or sea. 2019-03-06T01:22:01Z envoMarine At this level, the depth of this layer is ambiguous. Some methods (telemetry) measure only the first few centimeters of the sea or ocean surface. In situ methods often sample the first few meters. Subclasses can be created for such cases. sea surface layer A layer which is part of a cryosphere. 2019-04-09T13:05:25Z envoPolar cryospheric layer Permafrost which contains inclusions of water-based ice. 2019-04-09T13:45:40Z ice-bearing permafrost A material accumulation process during which the mass of snow on a surface increases. 2019-04-24T18:29:18Z http://sweetontology.net/phenCryo/Accumulation This term is used both as a process and as an amount of mass added. Semantically speaking these are two distinct concepts (e.g., accumulation results in accumulation_amount of ice or snow gain), though accumulation_amount would more likely be an attribute. The scope of this term varies depending on the definition. Some definitions constrain themselves snow or ice added to glaciers; while others also include ice fields, snow cover, and/or floating ice. How to resolve this depends on the scope desired. Some definitions include additional discussion of the the physics involved which would be useful for connecting glacier ontologies to atmospheric, hydrologic, etc. ontologies. This information should be captured no matter how the inconsistencies above are resolved. snow accumulation process A material accumulation process during which the mass of snow on a surface increases. A material accumulation process during which ice forms in an environmental material or an existing accumulation of ice increases in mass. 2019-04-24T18:48:53Z http://sweetontology.net/phenCryo/Accumulation ice accumulation process A material accumulation process during which ice forms in an environmental material or an existing accumulation of ice increases in mass. A material accumulation process during which a accumulation of snow and ice forms or increases in mass. 2019-04-24T18:59:45Z http://sweetontology.net/phenCryo/Accumulation snow and ice accumulation process A material accumulation process during which a accumulation of snow and ice forms or increases in mass. A object which is composed primarily of water-based snow and ice. 2019-04-24T19:08:03Z http://sweetontology.net/phenCryo/Accumulation mass of ice and snow A positional quality inhering in a bearer by virtue of the bearer being located within a glacier or ice sheet, between their summer surface or bed. 2019-04-24T19:51:34Z englacial An environmental system process which occurs within a glacier or ice sheet. 2019-04-24T19:59:58Z http://sweetontology.net/phenCryo/Englacial englacial process An environmental system process which occurs within a glacier or ice sheet. A process during which microscopic solid particulates are formed from liquid materials in an atmosphere. 2019-05-30T21:07:51Z atmospheric formation of a solid aerosol formation of a solid aerosol in an atmosphere formation of a solid aerosol in the atmosphere formation of solid particles from liquid material in an atmosphere envoAtmo formation of a solid aerosol from liquid material in an atmosphere A process during which microscopic solid particulates are formed from liquid materials in an atmosphere. https://en.wikipedia.org/wiki/Particulates That part of an atmosphere which is composed of gaseous material. 2019-06-02T07:52:47Z gaseous part of an atmosphere A solid material which does not have a regularly organised internal structure. 2019-06-02T11:07:47Z amorphous solid An aerosol that is suspended in an atmosphere. 2019-06-03T12:24:09Z atmospheric aerosol A material transformation process during which solid or liquid particles form and are suspended in a mass of air, thus creating an aerosol. 2019-06-24T13:43:29Z aerosol formation process An environmental process which involves glaciers or ice sheets. 2019-06-24T17:12:30Z Note that ice sheets and glaciers are confounded and confused in multiple communities and across multiple sources. glacial process Note that ice sheets and glaciers are confounded and confused in multiple communities and across multiple sources. A surface layer which is composed primarily of some liquid or gas. 2019-08-20T08:28:42Z fluid surface layer A surface layer which separates two portions of fluid with respect to either 1) a discontinuity of some fluid property or 2) some derivative of one of these properties in a direction normal to the interface. 2019-07-22T17:29:44Z fluid interface layer A surface layer which separates two portions of fluid with respect to either 1) a discontinuity of some fluid property or 2) some derivative of one of these properties in a direction normal to the interface. A layer which is composed primarily of some fluid. 2019-07-22T17:35:08Z fluid layer A fluid interface which separates two fluid masses with differing properties. 2019-07-22T17:43:32Z fluid front A fluid interface which separates two fluid masses with differing properties. A fluid front which is composed primarily of gaseous material and separates at least two gaseous masses. 2019-07-22T17:50:08Z gaseous front A gaseous front which separates two masses of air with different densities and is a principal cause of meteorological phenomena. 2019-07-22T17:57:21Z meteorological front envoAtmo This class refers to Earth's weather fronts. Other forms, not composed of air, are present on other planets and can be created on request. Note: "Since the temperature distribution is the most important regulator of atmospheric density, a front almost invariably separates air masses of different temperature. Along with the basic density criterion and the common temperature criterion, many other features may distinguish a front, such as a pressure trough, a change in wind direction, a moisture discontinuity, and certain characteristic cloud and precipitation forms." weather front A gaseous front which separates two masses of air with different densities and is a principal cause of meteorological phenomena. This class refers to Earth's weather fronts. Other forms, not composed of air, are present on other planets and can be created on request. Note: "Since the temperature distribution is the most important regulator of atmospheric density, a front almost invariably separates air masses of different temperature. Along with the basic density criterion and the common temperature criterion, many other features may distinguish a front, such as a pressure trough, a change in wind direction, a moisture discontinuity, and certain characteristic cloud and precipitation forms." An object which is composed of a continuous mass of air. 2019-08-20T07:54:32Z envoAtmo air mass A fluid surface layer which is composed primarily of some gaseous material. 2019-08-20T08:30:01Z gaseous surface layer A layer which separates two portions of environmental material which possess 1) differing compositions, 2) a discontinuity of some property, or 3) some derivative of some property in a direction normal to the interface. 2019-08-20T09:28:10Z interface layer An object which is composed primarily of an environmental material 2019-08-20T09:38:29Z This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. mass of environmental material An object which is composed primarily of a solid environmental material 2019-08-20T09:41:27Z This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. mass of solid material An object which is composed primarily of a fluid. 2019-08-20T09:42:35Z fluid mass This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. mass of fluid An object which is composed primarily of a gas. 2019-08-20T09:44:01Z gaseous mass This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. mass of gas An object which is composed primarily of a liquid. 2019-08-20T09:45:03Z liquid mass This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. mass of liquid An mass of environmental materials which has appreciable quantities of several individual materials, such that the removal of one would convert the mass into a different entity. 2019-08-20T09:47:10Z mass of compounded environmental materials A weather front which separates air masses of tropical and polar origin. 2019-08-20T13:46:42Z envoAtmo envoPolar polar front A weather front which separates air masses of tropical and polar origin. An environment which has a climate with continually high temperatures and with considerable precipitation, at least during part of the year. 2019-08-20T13:58:38Z tropical environment An environment which has a climate with continually high temperatures and with considerable precipitation, at least during part of the year. An environment which is located in a part of an astronomical body subject to polar climatic conditions. 2019-08-20T14:53:26Z polar environment An environment which is located in a part of an astronomical body subject to polar climatic conditions. An environment which is located in a part of an astronomical body subject to temperate climatic conditions. 2019-08-20T16:41:52Z temperate environment An environment which is located in a part of an astronomical body subject to temperate climatic conditions. 2019-09-05T05:47:26Z mass fluid flow An ecosystem in which the composition, structure, and function of resident ecological assemblages are primarily determined by a desert. 2019-10-17T08:21:08Z desert ecosystem A solid astronomical body part which is part of the landmass of that body. 2019-10-17T08:27:17Z part of a landmass A large continuous area of land, either surrounded by sea or contiguous with another landmass. 2019-10-17T08:31:26Z landmass A large continuous area of land, either surrounded by sea or contiguous with another landmass. A part of an astronomical body which is primarily composed of a continuous medium bearing liquid, gaseous, and solid material in varying quantities. 2019-10-17T08:36:00Z 2018-10-04T13:59:22Z ENVO:01001479 compound astronomical body part A part of an astronomical body which is primarily composed of a continuous medium bearing liquid, gaseous, and solid material in varying quantities. https://en.wikipedia.org/wiki/Landform A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water. 2019-10-21T10:42:26Z land A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water. 2019-10-21T11:05:45Z aquatic ecosystem 2019-10-21T11:06:11Z marine ecosystem 2019-10-21T11:09:58Z terrestrial ecosystem An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem. 2019-10-21T11:52:55Z ecosystem process A material entity which has been assembled through the intentional, instinctual, or deliberately programmed efforts of an organism or machine. 2019-10-29T14:50:34Z construction A biome which is subject to tropical climatic conditions. 2019-11-06T15:56:17Z tropical biome A biome which is subject to temperate climatic conditions. 2019-11-06T15:57:04Z temperate biome A biome which is subject to montane altitudinal conditions. 2019-11-06T16:00:33Z montane biome A biome which is subject to arid environmental conditions. 2019-11-06T16:06:47Z arid biome A process during which one entity loses energy to another entity. 2020-02-13T13:34:28Z energy transfer process A material accumulation process during which the volume of liquid entity increases. 2020-05-18T14:39:20Z liquid accumulation process Coastal water is a marine water body bordering a coast. envoPolar coastal water body Coastal water is a marine water body bordering a coast. https://en.wikipedia.org/wiki/Coastal A combustible black or brownish-black sedimentary rock usually occurring in rock strata in layers or veins called coal beds or coal seams. cjm coal A combustible black or brownish-black sedimentary rock usually occurring in rock strata in layers or veins called coal beds or coal seams. Dust which is derived from coal. cjm coal dust Dust which is derived from mineral material. cjm mineral dust Dust which is composed primarily of some metallic material. cjm metallic dust Dust which is derived from clay material. cjm clay dust cjm dust from plant parts A liquid or a gas. fluid fluid environmental material A liquid or a gas. https://github.com/EnvironmentOntology/envo/issues/940 A type of land degradation in which terrestrial ecosystem becomes increasingly dry, typically losing its bodies of water as well as vegetation and wildlife. desertification A type of land degradation in which terrestrial ecosystem becomes increasingly dry, typically losing its bodies of water as well as vegetation and wildlife. A process which occurs within an atmosphere. This class will be populated by inference and is primarily organisational. atmospheric process A process which diminishes the functioning of an ecosystem located on land. An SDGIO request. Likely to be refined and revised. This could include, for example, reducing soil health, pollinator activity, or an ecosystem's ability to sequester carbon. land degradation A process which diminishes the functioning of an ecosystem located on land. http://www.who.int/globalchange/ecosystems/desert/en/ https://en.wikipedia.org/wiki/Land_degradation A process during which humans apply technology to alter the magnitude, duration, rate, or impact of an environmental process. Relabel the obo foundry unique label to be generic process anthropogenic modulatory intervention process An environmental process which is driven by the action of humans. anthropogenic environmental process An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited. envoPolar planetary erosion An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited. https://en.wikipedia.org/wiki/Erosion An environmental process which has water - in any of its states - as a participant. This classes asserted subclasses will be moved away as it should be an inferred class. hydrological process Any water ice that is part of a glacier. It is suggested that users complement this term with ice terms that are more descriptive of the ice itself, rather than its location/parthood. http://orcid.org/0000-0002-3410-4655 envoPolar glacial ice Any water ice that is part of a glacier. https://en.wikipedia.org/wiki/Glacier A process during which the mass of one or more materials, present within a given site, increases. http://orcid.org/0000-0002-3410-4655 envoPolar Experimental class for structural purposes not recommended for annotation. A material accumulation process ends a material transport process. material accumulation process A process during which material is displaced from its original location and transported either to a new location or back to the original location. http://orcid.org/0000-0002-3410-4655 envoPolar Experimental class for structural purposes not recommended for annotation. material transport process A material transport process during which the snow and ice constituting a glacier, and anything contained within it, is transported down a slope by gravitation. http://orcid.org/0000-0002-3410-4655 glacial flow glacial movement envoPolar This must be differentiated from small ice masses simply falling or moving down slopes. In ENVO, this is a subclass of advective transport process, however, this may not be universally accepted by some which strictly limit advection to fluids. glacial transport process A depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed. The general semantics of depression and geographic basin are still to be worked out see https://github.com/EnvironmentOntology/envo/issues/486 http://orcid.org/0000-0002-3410-4655 envoPolar geographic basin A depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed. https://en.wikipedia.org/wiki/Basin A material transport process during which one or more environmental materials are transported by the action of wind. http://orcid.org/0000-0002-3410-4655 eolian æolian envoPolar aeolian transport process A material transport process during which one or more environmental materials are transported by the action of wind. https://en.wikipedia.org/wiki/Aeolian_processes Sediment which has been transported through the marine water column, settling on the seafloor. http://orcid.org/0000-0002-3410-4655 marine sediments envoPolar Particles of marine sediment are primarily generated by 1) processes in terrestrial systems and transported to the marine realm by the action of rivers or aeolian processes (amongst other routes) , 2) marine organisms, 3) chemical processes in seawater, or 4) cosmogeneous input. marine sediment Sediment which has been transported through the marine water column, settling on the seafloor. https://en.wikipedia.org/wiki/Pelagic_sediment#_note-8 A material accumulation process during which solid particles are pulled through a water body by gravitation or centrifugal force and which ends when they settle on a solid surface. http://orcid.org/0000-0002-3410-4655 envoPolar sedimentation in a water body A process during which a portion of some environmental material is converted into a different material or a collection of materials. A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies. http://orcid.org/0000-0002-3410-4655 envoPolar Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another. material transformation process A geographic feature which is primarily composed of a continuous mass of snow and/or ice. Place holder class. Also the axiom should be changed to something along the lines of 'primairly composed of’ some ‘environmental material’ and ‘has quality’ frozen once PATO:frozen is imported. http://orcid.org/0000-0002-3410-4655 envoPolar cryoform A mass of snow. http://orcid.org/0000-0002-3410-4655 accumulation of snow snow accumulation http://sweetontology.net/phenCryo/Accumulation envoPolar snow mass A surface layer which is composed primarily of soil. 2019-04-12T17:35:13Z envoNceas soil surface layer The generation of energy for use by humans cjm 2018-11-03T20:02:04Z anthropogenic generation of energy cjm 2018-11-03T20:04:34Z generation of energy from coal A disposition which is realized during the execution of work, the emission of heat, or the possession of mass. cjm 2018-11-03T20:22:18Z Consider replacing with PATO class; note that PATO class is not a disposition. This should likely go into OBO Core and also have a physicist look at it. energy Energy that it realized through motion. cjm 2018-11-03T20:25:57Z kinetic energy A power station which burns a fossil fuel such as coal, natural gas, or petroleum to produce electricity. cjm 2018-11-03T21:00:37Z fossil fuel power plant cjm 2018-11-03T21:01:16Z coal power plant A radiation process during which electromagnetic waves or their quanta are emitted at wavelengths between 10 nm and 400 nm. To be expanded to account for subtypes. UV radiation ENVO environmental_hazards ultraviolet radiation A radiation process during which electromagnetic waves or their quanta are emitted at wavelengths between 10 nm and 400 nm. https://en.wikipedia.org/wiki/Ultraviolet obsolete aggregate of governmental organizations An aggregate of geopoliticial entities. Examples include the group of states of the United States, the nations of North America, and so on. William R. Hogan taken over by GEO_0000000401 obsolete group of governmental organizations true subcontinental land mass 2 An aggregate of organizations that is not itself a governmental organization, has only governmental organizations as members, and has at least two governmental organizations as members. William R. Hogan aggregate of governmental organizations aggregate of contiguous land masses geographical entity of astronomical body A material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface). Mathias Brochhausen Matt Diller William R. Hogan Includes atmosphere, crust, geographical regions (e.g., the geographical region over which the state of Florida has jurisdiction), bodies of water, mountains, etc. Generally, an individual organism is a distinct object that is not a part of the Earth, although this requires more thought. But the intent is definitely for this class to NOT subsume organism universally. Human beings are contained within, but not part of, the Earth, for example. Note that despite the word 'planetary' in 'planetary surface', it refers generally to surface of dwarf planets, asteroids, moons, etc. We note that not all planets have a surface per se (e.g., gas giants such as Jupiter and Saturn). So only planets, natural satellites, etc. with a planetary surface (with or without a planetary boundary layer) have geographical entities. We note that the term 'geography' is also applied to the Earth's moon, Mars, Venus, and possibly even other moons and planets in our own solar system and beyond. Thus, we are attempting to define things generally enough that they could be reused for the geographical entities/features on the Moon, Mars, other planets, exoplanets, other natural satellites (a.k.a moons), asteroids, etc. geographical entity A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface. François Modave Mathias Brochhausen Matt Diller William R. Hogan geographical region continent land mass island An object aggregate of geographical entities aggregate of geographical entities aggregate of islands geopolitical organization Amanda Hicks geopoli organization A governmental organization with a defined territory on which it exercises internal and external sovereignty, a permanent population, a government, and the capacity to enter into relations with other sovereign states. William R. Hogan de facto sovereign state de facto state nation nation state http://en.wikipedia.org/wiki/Sovereign_state Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam". sovereign state An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii). Note: this definition was taken over from "geopolitical organization". Amanda Hicks IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization). "geopoli organization" is a label for a new and different class. governmental organization 2 An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common Amanda Hicks William R. Hogan http://purl.obolibrary.org/obo/omrse.owl aggregate of geopolitical organizations 2 An aggregate of governmental organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common William R. Hogan http://purl.obolibrary.org/obo/omrse.owl examples: all the sovereign states in North America, all the sovereign states with a GDP below or exceeding a particular quantity of money, all the sovereign states with a constitutional monarchy, all the sovereign states who belong to the U.N. (which is different than the U.N. itself), etc. aggregate of sovereign states planar angular measurement unit label plane angle measurement unit label The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton. mitochondrial inheritance biological_process mitochondrion inheritance The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton. GOC:mcc PMID:10873824 PMID:11389764 The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome. biological_process mitochondrial genome maintenance The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome. GOC:ai GOC:vw The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0019952 GO:0050876 Wikipedia:Reproduction reproductive physiological process biological_process reproduction 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 The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton. biological_process vacuole inheritance The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton. GOC:mcc PMID:10873824 PMID:14616069 Interacting selectively and non-covalently with transfer RNA. GO:0000946 base pairing with tRNA molecular_function tRNA binding Interacting selectively and non-covalently with transfer RNA. GOC:ai A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. microtubule cytoskeleton organisation microtubule dynamics biological_process microtubule cytoskeleton organization and biogenesis microtubule cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. GOC:mah microtubule cytoskeleton organisation GOC:mah microtubule dynamics GOC:dph GOC:tb microtubule cytoskeleton organization and biogenesis GOC:mah A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. nuclear interphase chromosome cellular_component nuclear chromosome A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. GOC:dph GOC:mah A chromosome found in the cytoplasm. cytoplasmic interphase chromosome cellular_component cytoplasmic chromosome A chromosome found in the cytoplasm. GOC:mah A chromosome found in the mitochondrion of a eukaryotic cell. NIF_Subcellular:sao1186327184 mitochondrial DNA mtDNA cellular_component mitochondrial genome mitochondrial chromosome A chromosome found in the mitochondrion of a eukaryotic cell. GOC:mah The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments. mitochondrial division biological_process mitochondrial proliferation mitochondrial fission The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments. PMID:11038192 Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GO:0007067 Wikipedia:Mitosis biological_process mitosis mitotic cell cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 Reactome:69278 The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. biological_process karyokinesis nuclear division The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. GOC:mah A ribosome contained within a subcellular membrane-bounded organelle. cellular_component organellar ribosome A ribosome contained within a subcellular membrane-bounded organelle. GOC:mah GOC:mcc A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases. cellular_component lytic vacuole A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases. GOC:krc The autophagic process in which mitochondria are delivered to a type of vacuole and degraded in response to changing cellular conditions. Wikipedia:Autophagy_(cellular)#Selective_autophagy Wikipedia:Mitophagy mitochondrion autophagy biological_process mitophagy autophagy of mitochondrion The autophagic process in which mitochondria are delivered to a type of vacuole and degraded in response to changing cellular conditions. GOC:autophagy PMID:15798367 PMID:19289147 PMID:23065344 mitochondrion autophagy GOC:autophagy Any phosphodiester bond hydrolysis involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule. biological_process cleavage during rRNA processing cleavage involved in rRNA processing Any phosphodiester bond hydrolysis involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule. GOC:curators cleavage during rRNA processing GOC:dph GOC:tb 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. proteasome 26S proteasome cellular_component proteasome complex 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 Wikipedia:Proteasome proteasome GOC:cjm The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. GO:0007335 Wikipedia:Karyogamy nuclear fusion nuclear fusion during karyogamy biological_process karyogamy The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. GOC:elh The developmental process in which the size or shape of a cell is generated and organized. GO:0007148 GO:0045790 GO:0045791 cellular morphogenesis biological_process cell morphogenesis The developmental process in which the size or shape of a cell is generated and organized. GOC:clt GOC:dph GOC:go_curators GOC:tb The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. biological_process cell morphogenesis involved in differentiation The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of RNA transcribed from the mitochondrial genome and occurring in the mitochondrion. biological_process mitochondrial RNA catabolic process The chemical reactions and pathways resulting in the breakdown of RNA transcribed from the mitochondrial genome and occurring in the mitochondrion. GOC:krc GOC:mah The chemical reactions and pathways resulting in the breakdown of mRNA transcribed from the mitochondrial genome and occurring in the mitochondrion. biological_process mitochondrial mRNA catabolic process The chemical reactions and pathways resulting in the breakdown of mRNA transcribed from the mitochondrial genome and occurring in the mitochondrion. GOC:krc GOC:mah The chemical reactions and pathways involving RNA transcribed from the mitochondrial genome and occurring in the mitochondrion. biological_process mitochondrial RNA metabolic process The chemical reactions and pathways involving RNA transcribed from the mitochondrial genome and occurring in the mitochondrion. GOC:krc GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome. biological_process regulation of mitochondrial RNA catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome. GOC:krc GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome. biological_process negative regulation of mitochondrial RNA catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome. GOC:krc GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome. biological_process positive regulation of mitochondrial RNA catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome. GOC:krc GOC:mah The conversion of a primary RNA molecule transcribed from a mitochondrial genome into one or more mature RNA molecules; occurs in the mitochondrion. biological_process mitochondrial RNA processing The conversion of a primary RNA molecule transcribed from a mitochondrial genome into one or more mature RNA molecules; occurs in the mitochondrion. GOC:krc GOC:mah Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. kchris 2010-08-10T11:00:02Z molecular_function The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA-binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". transcription regulatory region sequence-specific DNA binding Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. GOC:txnOH Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair. kchris 2010-10-21T04:08:56Z molecular_function regulatory region nucleic acid binding Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair. GOC:txnOH A process that results in a parallel arrangement of microtubules. microtubule bundling biological_process microtubule bundle formation A process that results in a parallel arrangement of microtubules. GOC:dph Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). translation initiation ternary complex assembly biological_process formation of translation initiation ternary complex Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). GOC:hjd The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein. hjd 2011-06-09T03:11:53Z biological_process Note that this term applies to translation performed by cytoplasmic ribosomes, which is distinct from translation performed by organellar ribosomes. For mitochondrial translation, consider GO:0032543 'mitochondrial translation' or its child terms. cytoplasmic translation The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein. GOC:hjd The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in the cytoplasm. hjd 2011-06-09T03:14:42Z biological_process cytoplasmic translational elongation The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in the cytoplasm. GOC:hjd The process preceding formation of the peptide bond between the first two amino acids of a protein in the cytoplasm. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. hjd 2011-06-09T03:15:48Z biological_process cytoplasmic translational initiation The process preceding formation of the peptide bond between the first two amino acids of a protein in the cytoplasm. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. GOC:hjd The process resulting in the release of a polypeptide chain from the ribosome in the cytoplasm, usually in response to a termination codon. hjd 2011-06-09T03:17:13Z biological_process cytoplasmic translational termination The process resulting in the release of a polypeptide chain from the ribosome in the cytoplasm, usually in response to a termination codon. GOC:hjd Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. Wikipedia:Immune_system biological_process 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). immune system process Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. GOC:add GO_REF:0000022 Any process that modulates the frequency, rate, or extent of an immune system process. biological_process regulation of immune system process Any process that modulates the frequency, rate, or extent of an immune system process. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. down regulation of immune system process down-regulation of immune system process downregulation of immune system process inhibition of immune system process biological_process negative regulation of immune system process Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. GOC:add Any process that activates or increases the frequency, rate, or extent of an immune system process. up regulation of immune system process up-regulation of immune system process upregulation of immune system process activation of immune system process stimulation of immune system process biological_process positive regulation of immune system process Any process that activates or increases the frequency, rate, or extent of an immune system process. GOC:add A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring. puberty biological_process reproductive developmental process developmental process involved in reproduction A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring. GOC:dph GOC:isa_complete puberty GOC:dph reproductive developmental process GOC:dph GOC:tb A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. organ system process biological_process system process A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. GOC:mtg_cardio A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. Wikipedia:Circulatory_system biological_process circulatory system process A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. GOC:mtg_cardio Interacting selectively and non-covalently with any nucleic acid. GO:0000496 base pairing molecular_function nucleic acid binding Interacting selectively and non-covalently with any nucleic acid. GOC:jl Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0043566 plasmid binding molecular_function microtubule/chromatin interaction structure specific DNA binding structure-specific DNA binding DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GOC:dph GOC:jl GOC:tb GOC:vw Interacting selectively and non-covalently with double-stranded DNA. dsDNA binding molecular_function double-stranded DNA binding Interacting selectively and non-covalently with double-stranded DNA. GOC:elh GOC:vw dsDNA binding GOC:elh A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons. https://github.com/geneontology/go-ontology/issues/15704 https://github.com/geneontology/go-ontology/issues/16534 kchris 2010-10-21T04:37:54Z GO:0000130 GO:0001071 GO:0001130 GO:0001131 GO:0001151 GO:0001199 GO:0001204 nucleic acid binding transcription factor activity transcription factor activity DNA binding transcription factor activity gene-specific transcription factor activity sequence-specific DNA binding transcription factor activity bacterial-type DNA binding transcription factor activity bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity bacterial-type RNA polymerase transcription enhancer sequence-specific DNA binding transcription factor activity bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity metal ion regulated sequence-specific DNA binding transcription factor activity sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding transcription factor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding transcription factor activity, bacterial-type RNA polymerase transcription enhancer sequence-specific binding transcription factor activity, metal ion regulated sequence-specific DNA binding molecular_function Curator guidance: Note that most DNA-binding transcription factors do not have enzymatic activity. The presence of specific domains known to be present in DNA-binding transcription factors (HOX, GATA etc) should be used to help decide whether a protein is a DNA binding transcription factor or a coregulator. If a protein has an enzymatic activity (for example, ubiquitin ligase, histone acetyl transferase) and no known DNA binding domain, consider annotating to GO:0003712 transcription coregulator activity. Special care should be taken with proteins containing Myb/SANT and ARID domains, since only a subset of proteins containing these domains are DNA-binding transcription factors for specific genes. DNA-binding transcription factor activity A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons. GOC:txnOH-2018 Interacting selectively and non-covalently with an RNA molecule or a portion thereof. GO:0000498 GO:0044822 Reactome:R-HSA-203922 base pairing with RNA molecular_function poly(A) RNA binding poly(A)-RNA binding poly-A RNA binding RNA binding Interacting selectively and non-covalently with an RNA molecule or a portion thereof. GOC:jl GOC:mah Reactome:R-HSA-203922 Exportin-5 recognizes 3' overhang of pre-miRNA Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns. GO:0000499 base pairing with mRNA molecular_function mRNA binding Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns. GOC:kmv GOC:pr SO:0000234 The action of a molecule that contributes to the structural integrity of the ribosome. GO:0003736 GO:0003737 GO:0003738 GO:0003739 GO:0003740 GO:0003741 GO:0003742 ribosomal protein molecular_function ribosomal RNA Note that this term may be used to annotate ribosomal RNAs as well as ribosomal proteins. structural constituent of ribosome The action of a molecule that contributes to the structural integrity of the ribosome. GOC:mah 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. Wikipedia:Enzyme enzyme activity molecular_function catalytic activity 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 enzyme activity GOC:dph GOC:tb Catalysis of the reaction: GTP + H2O = GDP + phosphate. https://github.com/geneontology/go-ontology/issues/19078 dph 2015-11-11T12:47:56Z GO:0061745 hydrolase activity, acting on acid anhydrides, acting on GTP, involved in cellular and subcellular movement RHEA:19669 Reactome:R-HSA-1445143 Reactome:R-HSA-1458485 Reactome:R-HSA-156923 Reactome:R-HSA-164381 Reactome:R-HSA-165055 Reactome:R-HSA-167415 Reactome:R-HSA-170666 Reactome:R-HSA-170685 Reactome:R-HSA-170686 Reactome:R-HSA-177501 Reactome:R-HSA-203973 Reactome:R-HSA-2130641 Reactome:R-HSA-2130725 Reactome:R-HSA-2584246 Reactome:R-HSA-380979 Reactome:R-HSA-392133 Reactome:R-HSA-392212 Reactome:R-HSA-418574 Reactome:R-HSA-418582 Reactome:R-HSA-421835 Reactome:R-HSA-428941 Reactome:R-HSA-432707 Reactome:R-HSA-5333615 Reactome:R-HSA-5389839 Reactome:R-HSA-5389842 Reactome:R-HSA-5419273 Reactome:R-HSA-5419279 Reactome:R-HSA-555065 Reactome:R-HSA-5623513 Reactome:R-HSA-5638006 Reactome:R-HSA-5658231 Reactome:R-HSA-5665809 Reactome:R-HSA-5672017 Reactome:R-HSA-5694527 Reactome:R-HSA-6807877 Reactome:R-HSA-6814833 Reactome:R-HSA-8847534 Reactome:R-HSA-8847883 Reactome:R-HSA-8849082 Reactome:R-HSA-8854173 Reactome:R-HSA-8854255 Reactome:R-HSA-8854329 Reactome:R-HSA-8854604 Reactome:R-HSA-8854612 Reactome:R-HSA-8868661 Reactome:R-HSA-8981353 Reactome:R-HSA-8982020 Reactome:R-HSA-8982021 Reactome:R-HSA-8982025 Reactome:R-HSA-983422 ARF small monomeric GTPase activity RHEB small monomeric GTPase activity Rab small monomeric GTPase activity Ran small monomeric GTPase activity Ras small monomeric GTPase activity Rho small monomeric GTPase activity Sar small monomeric GTPase activity dynamin GTPase activity heterotrimeric G-protein GTPase activity protein-synthesizing GTPase activity protein-synthesizing GTPase activity, elongation protein-synthesizing GTPase activity, initiation protein-synthesizing GTPase activity, termination signal-recognition-particle GTPase activity small monomeric GTPase activity tubulin GTPase activity molecular_function GTPase activity, coupled heterotrimeric G-protein GTPase, alpha-subunit heterotrimeric G-protein GTPase, beta-subunit heterotrimeric G-protein GTPase, gamma-subunit GTPase activity Catalysis of the reaction: GTP + H2O = GDP + phosphate. ISBN:0198547684 PMID:26832457 PMID:27218782 Reactome:R-HSA-1445143 RAB8A,10,13,14 hydrolyze GTP Reactome:R-HSA-1458485 RALA hydrolyzes GTP Reactome:R-HSA-156923 Hydrolysis of eEF1A:GTP Reactome:R-HSA-164381 G alpha (s) auto-inactivates by hydrolysing GTP to GDP Reactome:R-HSA-165055 Hydrolysis of Ran:GTP to Ran:GDP Reactome:R-HSA-167415 G-protein alpha subunit is inactivated Reactome:R-HSA-170666 Adenylate cyclase increases the GTPase activity of G alpha-olf Reactome:R-HSA-170685 Adenylaye cyclase increases the GTPase activity of G alpha-olf Reactome:R-HSA-170686 Adenylate cyclase increases the GTPase activity of Gi alpha Reactome:R-HSA-177501 Endocytosis (internalization) of clathrin-coated vesicle Reactome:R-HSA-203973 Vesicle budding Reactome:R-HSA-2130641 Translocation of TGN-lysosome vesicle to lysosome Reactome:R-HSA-2130725 Internalization of MHC II:Ii clathrin coated vesicle Reactome:R-HSA-2584246 GNAT1-GTP hydrolyses its bound GTP to GDP Reactome:R-HSA-380979 RHEB in mTORC1:RHEB:GTP hydrolyses GTP Reactome:R-HSA-392133 G alpha (z) auto-inactivates by hydrolysing GTP to GDP Reactome:R-HSA-392212 G alpha (i) auto-inactivates by hydrolysing GTP to GDP Reactome:R-HSA-418574 G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP Reactome:R-HSA-418582 G alpha (q) auto-inactivates by hydrolysing GTP to GDP Reactome:R-HSA-421835 trans-Golgi Network Vesicle Scission Reactome:R-HSA-428941 P2Y purinoceptor 1 activates MAP kinase p38 alpha Reactome:R-HSA-432707 trans-Golgi Network Lysosomal Vesicle Scission Reactome:R-HSA-5333615 80S:Met-tRNAi:mRNA:SECISBP2:Sec-tRNA(Sec):EEFSEC:GTP is hydrolysed to 80S:Met-tRNAi:mRNA:SECISBP2:Sec and EEFSEC:GDP by EEFSEC Reactome:R-HSA-5389839 39S subunit binds 28S subunit:mRNA:fMet-tRNA Reactome:R-HSA-5389842 TUFM hydrolyzes GTP and TUFM:GDP dissociates from 55S ribosome Reactome:R-HSA-5419273 Hydrolysis of GTP and dissociation of 28S and 39S subunits Reactome:R-HSA-5419279 Translocation of peptidyl-tRNA from A-site to P-site (and translocation of 55S ribosome by 3 bases along mRNA) Reactome:R-HSA-555065 Formation of clathrin coated vesicle Reactome:R-HSA-5623513 ASAP1 stimulates GTPase activity of ARF4 Reactome:R-HSA-5638006 ARL3 hydrolyzes GTP Reactome:R-HSA-5658231 RAS GAPs stimulate RAS GTPase activity Reactome:R-HSA-5665809 SRGAP2 stimulates RAC1 GTP-ase activity and ends FMNL1-mediated elongation of actin filaments Reactome:R-HSA-5672017 Rheb in the mTORC1 complex hydrolyses GTP Reactome:R-HSA-5694527 Loss of SAR1B GTPase Reactome:R-HSA-6807877 ARFGAPs stimulate ARF GTPase activity Reactome:R-HSA-6814833 TBC1D20 stimulates GTPase activity of RAB1, resulting in hydrolysis of GTP Reactome:R-HSA-8847534 RAB43 hydrolyses GTP Reactome:R-HSA-8847883 CYTH proteins stimulate ARF1 GTPase activity Reactome:R-HSA-8849082 ARHGAP35 stimulates RHOA GTPase activity Reactome:R-HSA-8854173 TBC RabGAPs accelerate GTP hydrolysis by RAB35 Reactome:R-HSA-8854255 TBC1D2A accelerates GTP hydrolysis by RAB7 Reactome:R-HSA-8854329 TBC1D15 accelerates GTP hydrolysis by RAB7 Reactome:R-HSA-8854604 TBC1D16 accelerates GTP hydrolysis by RAB4A Reactome:R-HSA-8854612 TBC1D25 accelerates GTP hydrolysis by RAB33B Reactome:R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission Reactome:R-HSA-8981353 RASA1 stimulates RAS GTPase activity Reactome:R-HSA-8982020 G alpha (i)i1/i2/i3 in G (i):RGS complex is inactivated Reactome:R-HSA-8982021 G alpha (z) in G alpha (z):RGS complex is inactivated Reactome:R-HSA-8982025 G alpha (q) in G (q):RGS complex is inactivated Reactome:R-HSA-983422 Disassembly of COPII coated vesicle Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain. GO:0016809 MetaCyc:RXN0-5195 Reactome:R-HSA-1168640 Reactome:R-HSA-1234159 Reactome:R-HSA-1236935 Reactome:R-HSA-1236970 Reactome:R-HSA-1251997 Reactome:R-HSA-1433374 Reactome:R-HSA-1504193 Reactome:R-HSA-174058 Reactome:R-HSA-174105 Reactome:R-HSA-174202 Reactome:R-HSA-174203 Reactome:R-HSA-174255 Reactome:R-HSA-180573 Reactome:R-HSA-180603 Reactome:R-HSA-187574 Reactome:R-HSA-188191 Reactome:R-HSA-193682 Reactome:R-HSA-209061 Reactome:R-HSA-211715 Reactome:R-HSA-2130282 Reactome:R-HSA-2213200 Reactome:R-HSA-264458 Reactome:R-HSA-353125 Reactome:R-HSA-3640874 Reactome:R-HSA-3928656 Reactome:R-HSA-450466 Reactome:R-HSA-4608855 Reactome:R-HSA-4641256 Reactome:R-HSA-4641260 Reactome:R-HSA-5358340 Reactome:R-HSA-5358460 Reactome:R-HSA-5362448 Reactome:R-HSA-5387392 Reactome:R-HSA-5607724 Reactome:R-HSA-5607731 Reactome:R-HSA-5610754 Reactome:R-HSA-5610757 Reactome:R-HSA-5610758 Reactome:R-HSA-5610760 Reactome:R-HSA-5635854 Reactome:R-HSA-5635868 Reactome:R-HSA-5658430 Reactome:R-HSA-5668481 Reactome:R-HSA-5668520 Reactome:R-HSA-5687112 Reactome:R-HSA-5693081 Reactome:R-HSA-6784628 Reactome:R-HSA-6784676 Reactome:R-HSA-68825 Reactome:R-HSA-68948 Reactome:R-HSA-69016 Reactome:R-HSA-69600 Reactome:R-HSA-74730 Reactome:R-HSA-75825 Reactome:R-HSA-8849797 Reactome:R-HSA-8850992 Reactome:R-HSA-8852354 Reactome:R-HSA-8854044 Reactome:R-HSA-8854071 Reactome:R-HSA-8866553 Reactome:R-HSA-8866858 Reactome:R-HSA-8934819 Reactome:R-HSA-8939801 Reactome:R-HSA-8952408 Reactome:R-HSA-8957265 Reactome:R-HSA-9008110 Reactome:R-HSA-9008475 Reactome:R-HSA-9009362 Reactome:R-HSA-9010096 Reactome:R-HSA-9011313 Reactome:R-HSA-9604642 Reactome:R-HSA-983150 Reactome:R-HSA-983158 endoprotease activity proteasome endopeptidase activity proteinase molecular_function elastase activity endopeptidase activity Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain. http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE Reactome:R-HSA-1168640 Ubiquitinated IkB is degraded Reactome:R-HSA-1234159 Proteasome proteolyzes ub-HIF-alpha Reactome:R-HSA-1236935 Proteasomal cleavage of substrate Reactome:R-HSA-1236970 Proteasomal clevage of exogenous antigen Reactome:R-HSA-1251997 Cleavage of ERBB4m80 by gamma-scretase complex Reactome:R-HSA-1433374 Processing of SCF isoform 1 Reactome:R-HSA-1504193 Ubiquitinated DVL is degraded by the proteasome Reactome:R-HSA-174058 Degradation of multiubiquitinated Cdh1 Reactome:R-HSA-174105 Degradation of multiubiquitinated cell cycle proteins Reactome:R-HSA-174202 Degradation of multiubiquitinated Securin Reactome:R-HSA-174203 SCF-mediated degradation of Emi1 Reactome:R-HSA-174255 Degradation multiubiquitinated Cyclin A Reactome:R-HSA-180573 Degradation of ubiquitinated CD4 Reactome:R-HSA-180603 Proteosome-mediated degradation of APOBEC3G Reactome:R-HSA-187574 Degradation of ubiquitinated p27/p21 by the 26S proteasome Reactome:R-HSA-188191 APC/C:Cdh1-mediated degradation of Skp2 Reactome:R-HSA-193682 gamma-secretase cleaves the p75NTR transmembrane domain Reactome:R-HSA-209061 Ubiquitinated and phosphorylated IKBA binds to and is degraded by the proteasome complex Reactome:R-HSA-211715 Proteasome mediated degradation of PAK-2p34 Reactome:R-HSA-2130282 Degradation of ubiquitinated beta catenin by the proteasome Reactome:R-HSA-2213200 Release of endostatin-like peptides Reactome:R-HSA-264458 Proteasome mediated degradation of COP1 Reactome:R-HSA-353125 26S proteosome degrades ODC holoenzyme complex Reactome:R-HSA-3640874 Ub-RibC-AXIN is degraded by the proteasome Reactome:R-HSA-3928656 gamma-secretase cleaves EPHB2 Reactome:R-HSA-450466 AUF1:mRNA complex is destroyed Reactome:R-HSA-4608855 PRICKLE1 is degraded by the proteasome Reactome:R-HSA-4641256 Ubiquitinated AXIN is degraded by the proteasome Reactome:R-HSA-4641260 Ubiquitinated DVL1 is degraded by the proteasome Reactome:R-HSA-5358340 Autoproteolytic cleavage of Hh precursors Reactome:R-HSA-5358460 HPE SHH variants don't undergo autoproteolytic cleavage Reactome:R-HSA-5362448 Hh C-terminal fragments are degraded by the proteasome Reactome:R-HSA-5387392 processing defective Hh variants are degraded by the proteasome Reactome:R-HSA-5607724 26S proteasome processes K48PolyUb-K21,22-p-S32,36-IkBA:NF-kB complex to form NF-kB complex Reactome:R-HSA-5607731 26S proteasome processes p-7S-p100:RELB to form p52:RELB Reactome:R-HSA-5610754 GLI3 is partially degraded by the proteasome to yield the GLI3 repressor Reactome:R-HSA-5610757 GLI2 is degraded by the proteasome Reactome:R-HSA-5610758 GLI1 is degraded by the proteasome after ubiquitination by beta-TrCP Reactome:R-HSA-5610760 GLI1 is degraded by the proteasome after ubiquitination by ITCH Reactome:R-HSA-5635854 GLI2,3 are degraded by the proteasome Reactome:R-HSA-5635868 ub-GLI is degraded by the proteasome Reactome:R-HSA-5658430 NF1 is degraded by the proteasome Reactome:R-HSA-5668481 Protesomal degradation of K48polyUb-TRAF3 Reactome:R-HSA-5668520 26Sproteasome degrades K48polyUb-NIK Reactome:R-HSA-5687112 MAPK6 is degraded by the 26S proteasome Reactome:R-HSA-5693081 FURIN cleaves 7K-BACE1 to 7K-BACE1(46-501) Reactome:R-HSA-6784628 PCSK6,FURIN mediate dissociation of 2 x LPL from GPIHBP1:HSPG:LPL dimer Reactome:R-HSA-6784676 PCSK5 mediates dissociation of 2 x LPL from GPIHBP1:HSPG:LPL dimer Reactome:R-HSA-68825 Ubiquitinated geminin is degraded by the proteasome Reactome:R-HSA-68948 Ubiquitinated Orc1 is degraded by the proteasome Reactome:R-HSA-69016 Ubiquitinated Cdc6 is degraded by the proteasome Reactome:R-HSA-69600 Proteolytic degradation of ubiquitinated-Cdc25A Reactome:R-HSA-74730 Insulin degradation Reactome:R-HSA-75825 Proteasome mediated degradation of Cyclin D1 Reactome:R-HSA-8849797 Membrane proteases cleave Profilaggrin producing Filaggrin Reactome:R-HSA-8850992 Proteasome degrades polyubiquitinated PTEN Reactome:R-HSA-8852354 GTSE1 facilitates proteasome-mediated degradation of TP53 Reactome:R-HSA-8854044 Proteasome degrades AURKA ubiquitinated by SCF-FBXL7 Reactome:R-HSA-8854071 Proteasome-mediated degradation of PolyUb-FBXL7 Reactome:R-HSA-8866553 misfolded CFTR is degraded by the 26S proteasome Reactome:R-HSA-8866858 CFTR F508del is degraded by the 26S proteasome Reactome:R-HSA-8934819 Cytoplasmic proteases cleave Profilaggrin producing Filaggrin Reactome:R-HSA-8939801 26S proteasome degrades PolyUb-RUNX2 Reactome:R-HSA-8952408 Polyubiquitinated RUNX3 is degraded by the proteasome Reactome:R-HSA-8957265 26S proteasome degrades TP73 polyubiquitinated by ITCH Reactome:R-HSA-9008110 Proteasome degrades polyubiquitinated RUNX2 Reactome:R-HSA-9008475 Proteasome degrades polyubiquitinated RUNX2 Reactome:R-HSA-9009362 Proteasome degrades PolyUb-RUNX2 Reactome:R-HSA-9010096 Gamma-secretase cleaves APP(672-770) to APP(672-711) and APP(672-713) Reactome:R-HSA-9011313 Proteasome degrades ubiquitinated ROBO3.1 Reactome:R-HSA-9604642 Proteasome degrades ubiquitinated NICD4 Reactome:R-HSA-983150 Proteasomal cleavage of substrate Reactome:R-HSA-983158 Trimming of peptides in ER elastase activity GOC:krc Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix. GO:0008026 Reactome:R-HSA-167097 Reactome:R-HSA-169461 Reactome:R-HSA-169468 Reactome:R-HSA-5690996 Reactome:R-HSA-75949 Reactome:R-HSA-9613490 Reactome:R-HSA-9613494 Reactome:R-HSA-9613497 Reactome:R-HSA-9613498 ATP-dependent helicase activity molecular_function Note that most helicases catalyze processive duplex unwinding. helicase activity Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix. GOC:jl Reactome:R-HSA-167097 HIV Promoter Opening: First Transition Reactome:R-HSA-169461 MCM8 mediated fork unwinding Reactome:R-HSA-169468 MCM2-7 mediated fork unwinding Reactome:R-HSA-5690996 ERCC2 and ERCC3 DNA helicases form an open bubble structure in damaged DNA Reactome:R-HSA-75949 RNA Polymerase II Promoter Opening: First Transition Reactome:R-HSA-9613490 Unwinding of DNA for the nascent HIV-1 transcript: Second Transition Reactome:R-HSA-9613494 Unwinding of DNA for the Nascent Transcript: Second Transition Reactome:R-HSA-9613497 Unwinding DNA for the nascent transcript Reactome:R-HSA-9613498 Unwinding of DNA for the nascent HIV-1 transcript Catalysis of the hydrolysis of ester linkages within nucleic acids. molecular_function Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', and 'DNA-(apurinic or apyrimidinic site) lyase activity ; GO:0003906' do not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. nuclease activity Catalysis of the hydrolysis of ester linkages within nucleic acids. ISBN:0198547684 Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid. GO:0004537 Reactome:R-HSA-211247 Reactome:R-HSA-5685994 Reactome:R-HSA-6785986 caspase-activated deoxyribonuclease activity molecular_function deoxyribonuclease activity Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah ISBN:0198547684 Reactome:R-HSA-211247 Cleavage of DNA by DFF40 Reactome:R-HSA-5685994 Long-range resection of DNA DSBs by EXO1 or DNA2 Reactome:R-HSA-6785986 DNA nucleases unhook the interstrand crosslink (ICL) Combining with a nuclear export signal (NES) on a cargo to be transported, to mediate transport of a the cargo through the nuclear pore, from the nuclear lumen to the cytoplasm. The cargo can be either a RNA or a protein. https://github.com/geneontology/go-ontology/issues/14336 GO:0008262 NES receptor importin-alpha export receptor activity molecular_function exportin activity importin-alpha binding nuclear export signal receptor activity Combining with a nuclear export signal (NES) on a cargo to be transported, to mediate transport of a the cargo through the nuclear pore, from the nuclear lumen to the cytoplasm. The cargo can be either a RNA or a protein. GOC:bf GOC:mah GOC:pg GOC:vw PMID:11743003 PMID:25802992 PMID:28713609 Wikipedia:Nuclear_transport importin-alpha export receptor activity GO:0008262 The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell. molecular_function structural molecule activity 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 The action of a molecule that contributes to the structural integrity of a cell wall. molecular_function structural constituent of cell wall The action of a molecule that contributes to the structural integrity of a cell wall. GOC:mah The action of a molecule that contributes to the structural integrity of a cytoskeletal structure. molecular_function structural constituent of cytoskeleton The action of a molecule that contributes to the structural integrity of a cytoskeletal structure. GOC:mah The action of a molecule that contributes to the structural integrity of the extracellular matrix. core extracellular matrix core matrisome extracellular matrix glycoprotein molecular_function Extracellular matrix glycoproteins may be annotated to this term. PMID:24443019 extracellular matrix structural constituent The action of a molecule that contributes to the structural integrity of the extracellular matrix. GOC:mah Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. GO:0005478 EC:7 Reactome:R-HSA-168313 Reactome:R-HSA-178215 molecular_function carrier 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. transporter activity 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 Reactome:R-HSA-168313 Virion-associated M2 protein mediated ion infusion Reactome:R-HSA-178215 SMAD7:SMURF1 complex is exported to the cytosol Enables the transfer of amines, including polyamines, from one side of a membrane to the other. Amines are organic compounds that are weakly basic in character and contain an amino (-NH2) or substituted amino group. GO:0005279 amine/amide/polyamine channel activity amine/polyamine transmembrane transporter activity amino acid-polyamine transmembrane transporter activity molecular_function amine transmembrane transporter activity Enables the transfer of amines, including polyamines, from one side of a membrane to the other. Amines are organic compounds that are weakly basic in character and contain an amino (-NH2) or substituted amino group. GOC:mtg_transport ISBN:0198506732 ISBN:0815340729 Enables the directed movement of lipids into, out of or within a cell, or between cells. Reactome:R-HSA-1369028 Reactome:R-HSA-1369052 Reactome:R-HSA-174786 Reactome:R-HSA-5682285 Reactome:R-HSA-5682311 Reactome:R-HSA-5683672 Reactome:R-HSA-5683714 Reactome:R-HSA-5688397 Reactome:R-HSA-6801250 Reactome:R-HSA-8848053 Reactome:R-HSA-8866329 lipophorin molecular_function apolipoprotein lipid transporter activity GO_REF:0000090 Enables the directed movement of lipids into, out of or within a cell, or between cells. GOC:ai Reactome:R-HSA-1369028 ABCAs mediate lipid efflux Reactome:R-HSA-1369052 ABCAs mediate lipid influx Reactome:R-HSA-174786 ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex Reactome:R-HSA-5682285 ABCA12 transports lipids from cytosol to extracellular region Reactome:R-HSA-5682311 Defective ABCA12 does not transport lipids from cytosol to extracellular region Reactome:R-HSA-5683672 Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body Reactome:R-HSA-5683714 ABCA3 transports PC, PG from ER membrane to lamellar body Reactome:R-HSA-5688397 Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body Reactome:R-HSA-6801250 TRIAP1:PRELID1, PRELID3A transports PA from the outer to the inner mitochondrial membrane Reactome:R-HSA-8848053 ABCA5 transports CHOL from lysosomal lumen to cytosol Reactome:R-HSA-8866329 MTTP lipidates APOB-100, forming a pre-VLDL Enables the transfer of organic acids from one side of a membrane to the other. Organic acids are acidic compound containing carbon in covalent linkage. molecular_function organic acid transmembrane transporter activity Enables the transfer of organic acids from one side of a membrane to the other. Organic acids are acidic compound containing carbon in covalent linkage. ISBN:0198506732 The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Wikipedia:Binding_(molecular) ligand molecular_function 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. binding 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 Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GO:0001948 GO:0045308 Reactome:R-HSA-170835 Reactome:R-HSA-170846 protein amino acid binding glycoprotein binding molecular_function protein binding 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 Reactome:R-HSA-170835 An anchoring protein, ZFYVE9 (SARA), recruits SMAD2/3 Reactome:R-HSA-170846 TGFBR2 recruits TGFBR1 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). GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity 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. cellular_component 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:sao1337158144 subcellular entity NIF_Subcellular:nlx_subcell_100315 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. Wikipedia:Extracellular extracellular cellular_component 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'. extracellular region 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 That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. NIF_Subcellular:sao1425028079 cellular_component intercellular space Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term. extracellular space That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. ISBN:0198547684 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. Wikipedia:Cell_wall cellular_component cell wall The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins. GOC:giardia ISBN:0198547684 PMID:15134259 Wikipedia:Microbial_cyst The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. Wikipedia:Intracellular internal to cell protoplasm cellular_component nucleocytoplasm protoplast intracellular The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 nucleocytoplasm GOC:mah protoplast GOC:mah The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). GO:0005636 Wikipedia:Nuclear_envelope cellular_component nuclear envelope The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). ISBN:0198547684 That part of the nuclear content other than the chromosomes or the nucleolus. NIF_Subcellular:sao661522542 Wikipedia:Nucleoplasm cellular_component nucleoplasm That part of the nuclear content other than the chromosomes or the nucleolus. GOC:ma ISBN:0124325653 A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription. janelomax 2013-08-28T12:11:37Z GO:0044797 GO:0044798 cellular_component cytoplasmic transcription factor complex nuclear transcription factor complex transcription factor complex transcription regulator complex 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 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Wikipedia:Chromosome interphase chromosome prophase chromosome cellular_component chromatid Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. ISBN:0198547684 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. NIF_Subcellular:sao1820400233 Wikipedia:Nucleolus cellular_component nucleolus 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 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. Wikipedia:Cytoplasm cellular_component cytoplasm All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. ISBN:0198547684 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. NIF_Subcellular:sao1860313010 Wikipedia:Mitochondrion mitochondria cellular_component 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.) mitochondrion 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 The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation. GO:0031980 NIF_Subcellular:sao1804523077 Wikipedia:Mitochondrial_matrix mitochondrial lumen mitochondrial stroma cellular_component mitochondrial matrix The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation. GOC:as ISBN:0198506732 A ribosome found in the mitochondrion of a eukaryotic cell; contains a characteristic set of proteins distinct from those of cytosolic ribosomes. 55S ribosome, mitochondrial cellular_component mitochondrial ribosome A ribosome found in the mitochondrion of a eukaryotic cell; contains a characteristic set of proteins distinct from those of cytosolic ribosomes. GOC:mah ISBN:0198506732 A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. NIF_Subcellular:sao585356902 Wikipedia:Lysosome cellular_component lysosome A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. GOC:mah ISBN:0198506732 A vacuole to which materials ingested by endocytosis are delivered. NIF_Subcellular:sao1720343330 Wikipedia:Endosome cellular_component endosome A vacuole to which materials ingested by endocytosis are delivered. ISBN:0198506732 PMID:19696797 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. Wikipedia:Vacuole cellular_component vacuolar carboxypeptidase Y vacuole 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 The volume enclosed within the vacuolar membrane. cellular_component vacuolar lumen The volume enclosed within the vacuolar membrane. ISBN:0198506732 A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism. GO:0019818 peroxisome vesicle NIF_Subcellular:sao499555322 Wikipedia:Peroxisome cellular_component peroxisomal peroxisome A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism. GOC:pm PMID:9302272 UniProtKB-KW:KW-0576 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). NIF_Subcellular:sao1036339110 Wikipedia:Endoplasmic_reticulum ER cellular_component endoplasmic reticulum 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 The volume enclosed by the membranes of the endoplasmic reticulum. GO:0016022 ER cisterna ER lumen cisternal lumen endoplasmic reticulum cisterna cellular_component endoplasmic reticulum lumen The volume enclosed by the membranes of the endoplasmic reticulum. ISBN:0198547684 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. Golgi NIF_Subcellular:sao451912436 Wikipedia:Golgi_apparatus Golgi complex Golgi ribbon cellular_component 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. Golgi apparatus 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 Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell. NIF_Subcellular:sao819927218 cellular_component Golgi vesicle vesicular component Note that this definition includes vesicles that are transiently associated with the Golgi. Golgi-associated vesicle Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell. GOC:mah vesicular component NIF_Subcellular:sao138219748 An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins. adiposome lipid body lipid particle cellular_component Note that this term does not refer to vesicles, but instead to structures in which lipids do not necessarily form bilayers. lipid droplet An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins. GOC:mah GOC:tb An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides. Wikipedia:Microtubule_organizing_center MTOC microtubule organising centre cellular_component microtubule organizing center An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides. GOC:vw ISBN:0815316194 PMID:17072892 PMID:17245416 Wikipedia:Microtubule_organizing_center The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. NIF_Subcellular:sao101633890 Wikipedia:Cytosol cellular_component cytosol The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GOC:hjd GOC:jl 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. GO:0033279 NIF_Subcellular:sao1429207766 Wikipedia:Ribosome free ribosome membrane bound ribosome cellular_component ribosomal RNA ribosome 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 free ribosome NIF_Subcellular:sao1139385046 membrane bound ribosome NIF_Subcellular:sao1291545653 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. Wikipedia:Cytoskeleton cellular_component cytoskeleton 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 Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. NIF_Subcellular:sao1846835077 Wikipedia:Microtubule microtubuli microtubulus neurotubule cellular_component microtubule Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. ISBN:0879693568 neurotubule NIF_Subcellular:sao248349196 A microtubule in the axoneme of a eukaryotic cilium or flagellum; an axoneme contains nine modified doublet microtubules, which may or may not surround a pair of single microtubules. cellular_component axonemal microtubule A microtubule in the axoneme of a eukaryotic cilium or flagellum; an axoneme contains nine modified doublet microtubules, which may or may not surround a pair of single microtubules. GOC:cilia ISBN:0815316194 Any microtubule in the nucleus of a cell. cellular_component nuclear microtubule Any microtubule in the nucleus of a cell. GOC:mah Any microtubule in the cytoplasm of a cell. non-spindle-associated astral microtubule cellular_component cytoplasmic microtubule Any microtubule in the cytoplasm of a cell. GOC:mah The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane cell membrane cellular membrane cytoplasmic membrane plasmalemma bacterial inner membrane inner endospore membrane plasma membrane lipid bilayer cellular_component plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. ISBN:0716731363 cellular membrane NIF_Subcellular:sao6433132645 plasma membrane lipid bilayer GOC:mah The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. integral to plasma membrane cellular_component integral component of plasma membrane The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. GOC:dos GOC:go_curators 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. GO:0072372 FMA:67181 NIF_Subcellular:sao787716553 Wikipedia:Cilium eukaryotic flagellum microtubule-based flagellum primary cilium cellular_component flagellum 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. cilium 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 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. GO:0035085 GO:0035086 Wikipedia:Axoneme ciliary axoneme cilium axoneme flagellar axoneme flagellum axoneme cellular_component 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. axoneme 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 The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. Wikipedia:Cell_cortex cellular_component cell periphery peripheral cytoplasm cell cortex The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. GOC:mah ISBN:0815316194 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. janelomax 2012-10-23T15:40:34Z GO:0044261 GO:0044723 Wikipedia:Carbohydrate_metabolism carbohydrate metabolism multicellular organismal carbohydrate metabolic process biological_process single-organism carbohydrate metabolic process carbohydrate metabolic process 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 The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage. organic acid metabolism biological_process organic acid metabolic process The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage. ISBN:0198506732 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. energy pathways biological_process intermediary metabolism metabolic energy generation generation of precursor metabolites and energy 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 intermediary metabolism GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates. regulation of carbohydrate metabolism biological_process regulation of carbohydrate metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates. GOC:go_curators Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0055134 cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb 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. GO:0055132 DNA metabolism cellular DNA metabolism biological_process DNA metabolic process 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 The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. DNA breakdown DNA catabolism DNA degradation biological_process DNA catabolic process The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. GOC:go_curators ISBN:0198506732 The cellular synthesis of RNA on a template of DNA. GO:0006350 GO:0061018 GO:0061022 cellular transcription transcription Wikipedia:Transcription_(genetics) DNA-dependent transcription cellular transcription, DNA-dependent transcription, DNA-dependent biological_process transcription regulator activity transcription, DNA-templated The cellular synthesis of RNA on a template of DNA. GOC:jl GOC:txnOH transcription, DNA-dependent GOC:txnOH Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0032583 GO:0045449 GO:0061019 transcriptional control regulation of cellular transcription, DNA-dependent regulation of transcription, DNA-dependent biological_process regulation of gene-specific transcription regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GOC:go_curators GOC:txnOH regulation of transcription, DNA-dependent GOC:txnOH Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. GO:0006365 35S primary transcript processing biological_process rRNA processing Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. GOC:curators Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. biological_process cleavage stimulation factor activity mRNA cleavage Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. GOC:mah The synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase. https://github.com/geneontology/go-ontology/issues/14854 transcription from mitochondrial promoter biological_process mitochondrial transcription The synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase. GOC:jl Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. GO:0006394 Wikipedia:Post-transcriptional_modification biological_process RNA processing Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. GOC:mah Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide. biological_process mRNA maturation mRNA processing Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide. GOC:mah The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established. tRNA metabolism biological_process tRNA metabolic process The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of 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. RNA breakdown RNA catabolism RNA degradation biological_process RNA catabolic process The chemical reactions and pathways resulting in the breakdown of 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 The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes. mRNA breakdown mRNA catabolism mRNA degradation biological_process mRNA decay mRNA catabolic process The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes. ISBN:0198506732 mRNA decay GOC:ascb_2010 GOC:dph GOC:tb A process in which RNA is transported to, or maintained in, a specific location. RNA localisation establishment and maintenance of RNA localization biological_process RNA localization A process in which RNA is transported to, or maintained in, a specific location. GOC:ai RNA localisation GOC:mah 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. GO:0006416 GO:0006453 GO:0043037 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis protein biosynthetic process protein formation protein synthesis protein translation biological_process translation 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 The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. GO:0006440 GO:0006454 biopolymerisation biopolymerization protein synthesis initiation translation initiation biological_process translational initiation The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. ISBN:019879276X The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. GO:0006442 GO:0006455 protein synthesis elongation translation elongation biological_process translational elongation The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. GOC:ems The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). GO:0006443 GO:0006456 protein synthesis termination translation termination translational complex disassembly biological_process translational termination The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). GOC:hjd ISBN:019879276X Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GO:0006445 regulation of protein anabolism regulation of protein biosynthesis regulation of protein formation regulation of protein synthesis biological_process regulation of translation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GOC:isa_complete Any process that modulates the frequency, rate or extent of translational initiation. biological_process regulation of translational initiation Any process that modulates the frequency, rate or extent of translational initiation. GOC:go_curators Any process that modulates the frequency, rate, extent or accuracy of translational elongation. biological_process regulation of translational elongation Any process that modulates the frequency, rate, extent or accuracy of translational elongation. GOC:go_curators Any process that modulates the frequency, rate or extent of translational termination. biological_process regulation of translational termination Any process that modulates the frequency, rate or extent of translational termination. GOC:go_curators The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. GO:0007022 GO:0007024 GO:0007025 Wikipedia:Protein_folding alpha-tubulin folding beta-tubulin folding chaperonin-mediated tubulin folding biological_process chaperone activity chaperonin ATPase activity co-chaperone activity co-chaperonin activity glycoprotein-specific chaperone activity non-chaperonin molecular chaperone ATPase activity protein complex assembly, multichaperone pathway protein folding 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 alpha-tubulin folding GOC:mah beta-tubulin folding GOC:mah chaperonin-mediated tubulin folding GOC:mah 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). protein modification process biological_process process resulting in protein modification protein tagging activity cellular protein modification process 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 protein modification process GOC:bf GOC:jl The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. Wikipedia:Proteolysis peptidolysis ATP-dependent proteolysis biological_process 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. proteolysis The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GOC:bf GOC:mah ATP-dependent proteolysis GOC:mah The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells. GO:0006519 amino acid and derivative metabolism amino acid metabolic process cellular amino acid and derivative metabolic process cellular amino acid metabolism biological_process cellular amino acid metabolic process The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells. ISBN:0198506732 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids. regulation of amino acid metabolism biological_process regulation of cellular amino acid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids. GOC:go_curators The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif. Wikipedia:Protein_targeting protein sorting along secretory pathway biological_process nascent polypeptide association Note that protein targeting encompasses the transport of the protein to the specified location, and may also include additional steps such as protein processing. protein targeting The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif. GOC:ma The process of directing proteins towards a membrane, usually using signals contained within the protein. protein membrane targeting protein-membrane targeting biological_process protein targeting to membrane The process of directing proteins towards a membrane, usually using signals contained within the protein. GOC:curators The process of directing proteins towards the lysosome using signals contained within the protein. protein-lysosome targeting biological_process protein targeting to lysosome The process of directing proteins towards the lysosome using signals contained within the protein. GOC:curators The process of directing proteins towards the vacuole, usually using signals contained within the protein. protein vacuolar targeting protein-vacuolar targeting protein-vacuole targeting vacuolar protein sorting biological_process protein targeting to vacuole The process of directing proteins towards the vacuole, usually using signals contained within the protein. GOC:curators vacuolar protein sorting GOC:vw The process of directing proteins towards the peroxisome, usually using signals contained within the protein. protein-peroxisome targeting biological_process protein targeting to peroxisome The process of directing proteins towards the peroxisome, usually using signals contained within the protein. GOC:ai The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein. GO:0043681 protein import into mitochondrion protein targeting to mitochondria protein-mitochondrial targeting biological_process mitochondrial protein import mitochondrial translocation protein targeting to mitochondrion The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein. GOC:mcc ISBN:0716731363 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. Wikipedia:Lipid_metabolism lipid metabolism biological_process lipid metabolic process 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 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. Wikipedia:Sulfur_metabolism sulfur metabolism sulphur metabolic process sulphur metabolism biological_process sulfur compound metabolic process 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 The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. phosphate metabolism biological_process phosphate metabolic process phosphate-containing compound metabolic process The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. GOC:ai The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. nitrogen compound metabolism biological_process nitrogen compound metabolic process The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. GOC:jl ISBN:0198506732 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. janelomax 2012-12-13T16:25:32Z GO:0015457 GO:0015460 GO:0044765 small molecule transport solute:solute exchange biological_process single-organism transport 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. transport 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 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. biological_process ion transport 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 Transport of substances into, out of or within a mitochondrion. mitochondrial alpha-ketoglutarate/malate transport mitochondrial aspartate/glutamate transport mitochondrial sodium/calcium ion exchange biological_process mitochondrial transport Transport of substances into, out of or within a mitochondrion. GOC:ai The transport of substances that occurs outside cells. biological_process extracellular transport The transport of substances that occurs outside cells. GOC:go_curators The directed extracellular movement of carbohydrates. biological_process extracellular carbohydrate transport The directed extracellular movement of carbohydrates. GOC:ai 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. biological_process lipid transport 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 The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GO:0032779 biological_process copper-induced intracellular protein transport intracellular protein transport The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GOC:mah copper-induced intracellular protein transport GOC:al A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GO:0016194 GO:0016195 Wikipedia:Exocytosis vesicle exocytosis biological_process nonselective vesicle exocytosis exocytosis A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GOC:mah ISBN:0716731363 PMID:22323285 The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi. GO:0048221 ER to Golgi transport ER to Golgi vesicle-mediated transport anterograde (ER to Golgi) transport anterograde transport, ER to Golgi anterograde transport, endoplasmic reticulum to Golgi anterograde vesicle-mediated transport, ER to Golgi anterograde vesicle-mediated transport, endoplasmic reticulum to Golgi endoplasmic reticulum to Golgi transport endoplasmic reticulum to Golgi vesicle-mediated transport rough ER to cis-Golgi transport rough ER to cis-Golgi vesicle-mediated transport rough endoplasmic reticulum to cis-Golgi transport rough endoplasmic reticulum to cis-Golgi vesicle-mediated transport biological_process endoplasmic reticulum to Golgi vesicle-mediated transport The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi. GOC:ascb_2009 GOC:dph GOC:jp GOC:tb ISBN:0716731363 The directed movement of substances from the Golgi to other parts of the cell, including organelles and the plasma membrane, mediated by small transport vesicles. post-Golgi transport biological_process post-Golgi vesicle-mediated transport The directed movement of substances from the Golgi to other parts of the cell, including organelles and the plasma membrane, mediated by small transport vesicles. GOC:ai GOC:mah The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis. Golgi to plasma membrane vesicle-mediated transport biological_process Golgi to plasma membrane transport The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis. ISBN:0716731363 The directed movement of substances from the Golgi to early sorting endosomes. Clathrin vesicles transport substances from the trans-Golgi to endosomes. GO:0048218 Golgi to endosome vesicle-mediated transport TGN to endosome transport trans-Golgi to endosome transport biological_process Golgi to endosome transport The directed movement of substances from the Golgi to early sorting endosomes. Clathrin vesicles transport substances from the trans-Golgi to endosomes. GOC:jl ISBN:0716731363 PMID:10873832 The directed movement of substances from the Golgi to the vacuole. Golgi to vacuole vesicle-mediated transport biological_process Golgi to vacuole transport The directed movement of substances from the Golgi to the vacuole. GOC:ai The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. biological_process vesicle targeting The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. GOC:mah PMID:17335816 Fusion of the membrane of a transport vesicle with its target membrane. biological_process vesicle fusion Fusion of the membrane of a transport vesicle with its target membrane. GOC:jid The directed movement of molecules between the nucleus and the cytoplasm. GO:0000063 nucleocytoplasmic shuttling biological_process Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed. nucleocytoplasmic transport The directed movement of molecules between the nucleus and the cytoplasm. GOC:go_curators 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. GO:0016238 Wikipedia:Autophagy_(cellular) biological_process autophagy 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 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. cellular component motion cellular component movement biological_process cell movement Note that in GO cellular components include whole cells (cell is_a cellular component). movement of cell or subcellular component 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 cellular component motion GOC:dph GOC:jl Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). biological_process response to abiotic stress response to biotic stress 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. response to stress Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:mah 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. jl 2013-12-19T15:25:51Z GO:1902589 organelle organisation single organism organelle organization biological_process organelle organization and biogenesis single-organism organelle organization organelle organization 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 single organism organelle organization GOC:TermGenie organelle organization and biogenesis GOC:dph GOC:jl GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GO:0048287 nuclear organisation nuclear organization biological_process nuclear morphology nuclear organization and biogenesis nucleus organization and biogenesis nucleus organization 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 nuclear organization and biogenesis GOC:mah nucleus organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope. nuclear envelope organisation biological_process nuclear envelope organization and biogenesis nuclear envelope organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope. GOC:dph GOC:ems GOC:jl GOC:mah nuclear envelope organisation GOC:mah nuclear envelope organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus. nucleolus organisation biological_process nucleolus organization and biogenesis nucleolus organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus. GOC:dph GOC:jid GOC:jl GOC:mah nucleolus organization and biogenesis GOC:mah 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. mitochondria organization mitochondrion organisation biological_process mitochondrion organization and biogenesis mitochondrion organization 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 mitochondria organization GOC:mah mitochondrion organisation GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrial membrane, either of the lipid bilayer surrounding a mitochondrion. mitochondrial membrane organisation biological_process mitochondrial membrane organization and biogenesis mitochondrial membrane organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrial membrane, either of the lipid bilayer surrounding a mitochondrion. GOC:ai GOC:dph GOC:jl GOC:mah mitochondrial membrane organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. plasma membrane organisation biological_process plasma membrane organization and biogenesis plasma membrane organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. GOC:dph GOC:jl GOC:mah plasma membrane organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. cytoskeleton organisation biological_process cytoskeletal organization and biogenesis cytoskeletal regulator activity cytoskeleton organization and biogenesis cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:dph GOC:jl GOC:mah cytoskeletal organization and biogenesis GOC:mah cytoskeleton organization and biogenesis GOC:mah Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. biological_process microtubule-based process Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. GOC:mah A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. biological_process microtubule-based movement A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. GOC:cjm ISBN:0815316194 The removal of tubulin heterodimers from one or both ends of a microtubule. microtubule disassembly microtubule shortening microtubule catastrophe microtubule depolymerization during nuclear congression biological_process microtubule depolymerization The removal of tubulin heterodimers from one or both ends of a microtubule. ISBN:0815316194 microtubule catastrophe GOC:dph GOC:tb The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation). Wikipedia:Microtubule_nucleation biological_process microtubule nucleation The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation). GOC:go_curators ISBN:0815316194 PMID:12517712 Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol. down regulation of microtubule depolymerization down-regulation of microtubule depolymerization downregulation of microtubule depolymerization microtubule stabilization negative regulation of microtubule disassembly inhibition of microtubule depolymerization microtubule rescue negative regulation of microtubule catastrophe biological_process negative regulation of microtubule depolymerization Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol. GOC:mah ISBN:0815316194 microtubule rescue GOC:dph GOC:tb negative regulation of microtubule catastrophe GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the depolymerization of the specialized microtubules of the axoneme. axonemal microtubule stabilization biological_process negative regulation of microtubule depolymerization in axoneme negative regulation of axonemal microtubule depolymerization Any process that stops, prevents, or reduces the frequency, rate or extent of the depolymerization of the specialized microtubules of the axoneme. GOC:dph GOC:mah negative regulation of microtubule depolymerization in axoneme GOC:dph 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. cytoplasm organisation biological_process cytoplasm organization and biogenesis cytoplasm organization 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 cytoplasm organization and biogenesis GOC:mah 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. ER organisation endoplasmic reticulum organisation biological_process ER organization and biogenesis endoplasmic reticulum morphology endoplasmic reticulum organization and biogenesis endoplasmic reticulum organization 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 ER organization and biogenesis GOC:mah endoplasmic reticulum organization and biogenesis GOC:mah 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. Golgi organisation biological_process Golgi organization and biogenesis Golgi organization 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 Golgi organization and biogenesis GOC:mah 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. peroxisome organisation biological_process peroxisome organization and biogenesis peroxisome-assembly ATPase activity peroxisome organization 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 peroxisome organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes. endosome organisation biological_process endosome organization and biogenesis endosome organization 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 endosome organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole. GO:0044086 vacuole organisation vacuolar assembly biological_process vacuole biogenesis vacuole organization and biogenesis vacuole organization 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 vacuolar assembly GOC:mah vacuole biogenesis GOC:mah vacuole organization and biogenesis GOC:mah The directed movement of substances into, out of or within a vacuole. biological_process vacuolar transport The directed movement of substances into, out of or within a vacuole. GOC:ai The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases. biological_process vacuolar protein breakdown vacuolar protein catabolic process vacuolar protein catabolism vacuolar protein degradation protein catabolic process in the vacuole The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases. GOC:mah GOC:vw A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lysosome. A lysosome is a cytoplasmic, membrane-bounded organelle that is found in most animal cells and that contains a variety of hydrolases. lysosome organisation biological_process lysosome organization and biogenesis lysosome organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lysosome. A lysosome is a cytoplasmic, membrane-bounded organelle that is found in most animal cells and that contains a variety of hydrolases. GOC:mah lysosome organization and biogenesis GOC:mah The directed movement of substances into, out of or within a lysosome. biological_process lysosomal transport The directed movement of substances into, out of or within a lysosome. GOC:ai 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. Wikipedia:Cell_cycle cell-division cycle biological_process cell cycle 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 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. Wikipedia:Chromosome_segregation chromosome division biological_process chromosome transmission chromosome segregation 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 The cell cycle process in which the controlled breakdown of the nuclear envelope during mitotic cell division occurs. mitotic nuclear envelope breakdown mitotic nuclear envelope catabolism mitotic nuclear envelope degradation biological_process mitotic nuclear envelope disassembly The cell cycle process in which the controlled breakdown of the nuclear envelope during mitotic cell division occurs. GOC:bf Any process that modulates the frequency, rate or extent of mitosis. regulation of mitosis biological_process regulation of mitotic nuclear division Any process that modulates the frequency, rate or extent of mitosis. GOC:go_curators The directed movement of the nucleus to a specific location within a cell. GO:0040023 establishment of position of nucleus nuclear movement nuclear positioning nucleus migration nucleus positioning positioning of nucleus biological_process establishment of cell nucleus localization establishment of localization of nucleus establishment of nucleus localisation establishment of nucleus localization nuclear migration The directed movement of the nucleus to a specific location within a cell. GOC:ai establishment of nucleus localisation GOC:mah 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. Wikipedia:Cell_signaling biological_process cell communication 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 The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. davidos 2014-04-15T15:59:10Z GO:0098602 Wikipedia:Cell_adhesion biological_process cell adhesion molecule activity single organism cell adhesion cell adhesion 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 Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion. down regulation of cell adhesion down-regulation of cell adhesion downregulation of cell adhesion inhibition of cell adhesion biological_process cell adhesion receptor inhibitor activity negative regulation of cell adhesion Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion. GOC:go_curators The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GO:0023033 Wikipedia:Signal_transduction signaling cascade signalling cascade biological_process signaling pathway signalling pathway Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. signal transduction The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GOC:go_curators GOC:mtg_signaling_feb11 signalling pathway GOC:mah Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. cell-cell signalling biological_process cell-cell signaling Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. GOC:dos GOC:mah The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). biological_process Note that this term was 'developmental process'. multicellular organism development The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:dph GOC:ems GOC:isa_complete GOC:tb Any process that modulates the rate or extent of progress through the mitotic cell cycle. mitotic cell cycle modulation mitotic cell cycle regulation modulation of mitotic cell cycle progression regulation of mitotic cell cycle progression regulation of progression through mitotic cell cycle biological_process mitotic cell cycle regulator regulation of mitotic cell cycle Any process that modulates the rate or extent of progress through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb regulation of progression through mitotic cell cycle GOC:dph GOC:tb The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. biological_process pan-neural process nervous system development The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. GOC:dgh A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700). GO:0016280 Wikipedia:Aging ageing biological_process aging A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700). GOC:PO_curators Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. molecular_function microtubule severing activity microtubule/chromatin interaction microtubule binding Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers. GOC:krc The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group. tRNA maturation biological_process tRNA processing The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group. GOC:jl PMID:12533506 tRNA maturation GOC:vw Merging of two or more mitochondria within a cell to form a single compartment. biological_process mitochondrial fusion Merging of two or more mitochondria within a cell to form a single compartment. PMID:11038192 Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton). molecular_function cytoskeletal protein binding Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton). GOC:mah Any process in which a protein is transported to, or maintained in, a specific location. GO:0008105 protein localisation biological_process asymmetric protein localisation asymmetric protein localization establishment and maintenance of asymmetric protein localization establishment and maintenance of protein localization protein localization Any process in which a protein is transported to, or maintained in, a specific location. GOC:ai protein localisation GOC:mah asymmetric protein localisation GOC:mah Interacting selectively and non-covalently with a transcription factor, a protein required to initiate or regulate transcription. TF binding molecular_function transcription factor binding Interacting selectively and non-covalently with a transcription factor, a protein required to initiate or regulate transcription. ISBN:0198506732 Functions during translation by interacting selectively and non-covalently with RNA during polypeptide synthesis at the ribosome. translation factor activity, nucleic acid binding molecular_function translation factor activity, RNA binding Functions during translation by interacting selectively and non-covalently with RNA during polypeptide synthesis at the ribosome. GOC:ai GOC:vw translation factor activity, nucleic acid binding GOC:mah 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. janelomax 2012-10-17T15:46:40Z GO:0044236 GO:0044710 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth multicellular organism metabolic process biological_process single-organism metabolic process Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process 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 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0004480 methylase EC:2.1.1 Reactome:R-HSA-379387 Reactome:R-HSA-379464 Reactome:R-HSA-6800149 Reactome:R-HSA-71286 molecular_function methyltransferase activity Catalysis of the transfer of a methyl group to an acceptor molecule. ISBN:0198506732 Reactome:R-HSA-379387 methylation of Dopamine to form 3-Methoxytyramine Reactome:R-HSA-379464 Methylation of 3,4-dihydroxyphenylacetic acid to homovanillic acid Reactome:R-HSA-6800149 N6AMT1:TRMT112 transfers CH3 group from AdoMet to MMAIII Reactome:R-HSA-71286 guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). biological_process accidental cell death necrosis This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term. cell death Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). GOC:mah GOC:mtg_apoptosis PMID:25236395 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. EC:3.4 Reactome:R-HSA-205112 Reactome:R-HSA-3000243 Reactome:R-HSA-3139027 Reactome:R-HSA-376149 Reactome:R-HSA-448678 Reactome:R-HSA-5655483 Reactome:R-HSA-5684864 Reactome:R-HSA-5685902 Reactome:R-HSA-5693319 hydrolase, acting on peptide bonds peptide hydrolase activity protease activity proteinase activity molecular_function peptidase activity 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 Reactome:R-HSA-205112 gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6 Reactome:R-HSA-3000243 Unknown protease degrades GIF:Cbl to release Cbl Reactome:R-HSA-3139027 Maturation of HIV Virion Reactome:R-HSA-376149 Proteolytic processing of SLIT Reactome:R-HSA-448678 CTSG cleaves CASP1(1-404) Reactome:R-HSA-5655483 USP1 autocleavage Reactome:R-HSA-5684864 NAPSA, CTSH, PGA3-5 cleave pro-SFTPB Reactome:R-HSA-5685902 NAPSA, CTSH, PGA3-5 cleave pro-SFTPC Reactome:R-HSA-5693319 CTRC hydrolyses PRSS1 The multiplication or reproduction of cells, resulting in the expansion of a cell population. biological_process cell proliferation 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. cell population proliferation The multiplication or reproduction of cells, resulting in the expansion of a cell population. GOC:mah GOC:mb Any process that activates or increases the rate or extent of cell proliferation. up regulation of cell proliferation up-regulation of cell proliferation upregulation of cell proliferation activation of cell proliferation stimulation of cell proliferation biological_process positive regulation of cell proliferation positive regulation of cell population proliferation Any process that activates or increases the rate or extent of cell proliferation. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of cell proliferation. down regulation of cell proliferation down-regulation of cell proliferation downregulation of cell proliferation inhibition of cell proliferation biological_process negative regulation of cell proliferation negative regulation of cell population proliferation Any process that stops, prevents or reduces the rate or extent of cell proliferation. GOC:go_curators Interacting selectively and non-covalently with a lipid. molecular_function lipid binding Interacting selectively and non-covalently with a lipid. GOC:ai Enables the transfer of a protein from one side of a membrane to the other. GO:0015266 GO:0015463 Reactome:R-HSA-1268022 Reactome:R-HSA-1299475 Reactome:R-HSA-5205661 Reactome:R-HSA-5210943 Reactome:R-HSA-5210947 Reactome:R-HSA-5228406 Reactome:R-HSA-5244404 Reactome:R-HSA-5244428 Reactome:R-HSA-5244506 Reactome:R-HSA-5246514 Reactome:R-HSA-5250616 Reactome:R-HSA-5250884 Reactome:R-HSA-5250972 Reactome:R-HSA-5336420 molecular_function protein channel activity protein transmembrane transporter activity GO_REF:0000090 Enables the transfer of a protein from one side of a membrane to the other. GOC:jl Reactome:R-HSA-1268022 TOMM40 complex translocates proteins from the cytosol to the mitochondrial intermembrane space Reactome:R-HSA-1299475 TIMM23 PAM translocates proteins from the mitochndrial intermebrane space to the mitochondrial matrix Reactome:R-HSA-5205661 Pink1 is recruited from the cytoplasm to the mitochondria Reactome:R-HSA-5210943 PA63:ANTRX2 oligomer transports EF and LF (target cell endosome to cytosol) Reactome:R-HSA-5210947 PA63:ANTRX1 oligomer transports EF and LF (target cell endosome to cytosol) Reactome:R-HSA-5228406 TeNT HC transports TeNT LC from target cell endosome membrane into cytosol Reactome:R-HSA-5244404 BoNT/B HC transports BoNT/B LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5244428 BoNT/A HC transports BoNT/A LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5244506 BoNT/E HC transports BoNT/E LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5246514 BoNT/C HC transports BoNT/C LC from target cell synaptic vesicle membrane to cytosol Reactome:R-HSA-5250616 BoNT/D HC transports BoNT/D LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5250884 BoNT/F HC transports BoNT/F LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5250972 BoNT/G HC transports BoNT/G LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5336420 DT fragment B transports DT fragment A from target cell endosome membrane The directed movement of substances from endosomes to lysosomes. biological_process endosome to lysosome transport The directed movement of substances from endosomes to lysosomes. GOC:ai ISBN:0716731363 The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. lipid anabolism lipid biosynthesis lipid formation lipid synthesis lipogenesis biological_process lipid biosynthetic process The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. GOC:go_curators lipogenesis GOC:sl 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. GO:0006861 GO:0008644 sugar transport biological_process carbohydrate transport 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 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents. Wikipedia:Amino_acid_synthesis amino acid biosynthetic process cellular amino acid anabolism cellular amino acid biosynthesis cellular amino acid formation cellular amino acid synthesis biological_process cellular amino acid biosynthetic process The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. janelomax 2012-10-17T15:52:35Z GO:0044243 GO:0044712 Wikipedia:Catabolism breakdown catabolism degradation multicellular organismal catabolic process biological_process single-organism catabolic process catabolic process The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. ISBN:0198547684 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. GO:0043285 GO:0044266 biopolymer catabolic process macromolecule breakdown macromolecule catabolism macromolecule degradation multicellular organismal macromolecule catabolic process biological_process macromolecule catabolic process 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. GOC:mah biopolymer catabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. janelomax 2012-10-17T15:52:18Z GO:0044274 GO:0044711 formation Wikipedia:Anabolism anabolism biosynthesis synthesis multicellular organismal biosynthetic process biological_process single-organism biosynthetic process biosynthetic process The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 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. GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis macromolecule formation macromolecule synthesis biological_process macromolecule biosynthetic process 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. GOC:mah biopolymer biosynthetic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents. amino acid catabolic process cellular amino acid breakdown cellular amino acid catabolism cellular amino acid degradation biological_process cellular amino acid catabolic process The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents. GOC:ai The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined. Wikipedia:Nucleoid cellular_component nucleoid The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined. GOC:bm GOC:ma ISBN:3540076689 The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template. rRNA biosynthesis rRNA biosynthetic process rRNA synthesis biological_process rRNA transcription The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template. GOC:jl ISBN:0198506732 The synthesis of transfer RNA (tRNA) from a DNA template. tRNA biosynthesis tRNA biosynthetic process tRNA synthesis biological_process tRNA transcription The synthesis of transfer RNA (tRNA) from a DNA template. GOC:jl The controlled release of proteins from a cell. GO:0045166 GO:0045731 glycoprotein secretion protein secretion during cell fate commitment protein secretion resulting in cell fate commitment biological_process protein secretion The controlled release of proteins from a cell. GOC:ai 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. amine metabolism biological_process amine metabolic process 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 The chemical reactions and pathways resulting in the formation of 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. amine anabolism amine biosynthesis amine formation amine synthesis biological_process amine biosynthetic process The chemical reactions and pathways resulting in the formation of 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 The chemical reactions and pathways resulting in the breakdown of 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. amine breakdown amine catabolism amine degradation biological_process amine catabolic process The chemical reactions and pathways resulting in the breakdown of 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 A circular DNA molecule containing plastid encoded genes. cellular_component plastid chromosome A circular DNA molecule containing plastid encoded genes. ISBN:0943088399 The proteinaceous ground substance of plastids. cellular_component plastid stroma The proteinaceous ground substance of plastids. ISBN:0943088399 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. Wikipedia:Plastid cellular_component plastid 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 A ribosome contained within a plastid. cellular_component plastid ribosome A ribosome contained within a plastid. GOC:tair_curators 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. Wikipedia:Thylakoid cellular_component photosynthetic membrane A thylakoid is not considered an organelle, but some thylakoids are part of organelles. thylakoid 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 The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. embryogenesis and morphogenesis Wikipedia:Morphogenesis anatomical structure organization morphogenesis biological_process anatomical structure morphogenesis The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. GOC:go_curators ISBN:0521436125 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plastid. plastid organisation biological_process plastid organization and biogenesis plastid organization 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 plastid organization and biogenesis GOC:mah The partitioning of plastids between daughter cells at cell division. biological_process plastid inheritance The partitioning of plastids between daughter cells at cell division. GOC:mah 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 carbohydrate stimulus. response to carbohydrate stimulus biological_process response to carbohydrate 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 carbohydrate stimulus. GOC:jl response to carbohydrate stimulus GOC:dos The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis embryonal development biological_process embryo development The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GOC:go_curators GOC:isa_complete GOC:mtg_sensu Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. regulation of anabolism regulation of biosynthesis regulation of formation regulation of synthesis biological_process regulation of biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. down regulation of biosynthetic process down-regulation of biosynthetic process downregulation of biosynthetic process negative regulation of anabolism negative regulation of biosynthesis negative regulation of formation negative regulation of synthesis inhibition of biosynthetic process biological_process negative regulation of biosynthetic process Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. positive regulation of anabolism positive regulation of biosynthesis positive regulation of formation positive regulation of synthesis up regulation of biosynthetic process up-regulation of biosynthetic process upregulation of biosynthetic process activation of biosynthetic process stimulation of biosynthetic process biological_process positive regulation of biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044252 down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism negative regulation of organismal metabolism inhibition of metabolic process inhibition of organismal metabolic process negative regulation of multicellular organismal metabolic process biological_process negative regulation of metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044253 positive regulation of metabolism up regulation of metabolic process up-regulation of metabolic process upregulation of metabolic process activation of metabolic process positive regulation of multicellular organismal metabolic process positive regulation of organismal metabolism stimulation of metabolic process stimulation of organismal metabolic process up-regulation of organismal metabolic process biological_process positive regulation of metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. regulation of breakdown regulation of catabolism regulation of degradation biological_process regulation of catabolic process Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. down regulation of catabolic process down-regulation of catabolic process downregulation of catabolic process negative regulation of breakdown negative regulation of catabolism negative regulation of degradation inhibition of catabolic process biological_process negative regulation of catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. positive regulation of breakdown positive regulation of catabolism positive regulation of degradation up regulation of catabolic process up-regulation of catabolic process upregulation of catabolic process activation of catabolic process stimulation of catabolic process biological_process positive regulation of catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators Any process that modulates the frequency, rate or extent of signal transduction. GO:0035466 biological_process regulation of signaling pathway regulation of signalling pathway regulation of signal transduction Any process that modulates the frequency, rate or extent of signal transduction. GOC:sm regulation of signalling pathway GOC:mah Any process that activates or increases the frequency, rate or extent of signal transduction. GO:0035468 up regulation of signal transduction up-regulation of signal transduction upregulation of signal transduction activation of signal transduction stimulation of signal transduction biological_process positive regulation of signaling pathway positive regulation of signalling pathway positive regulation of signal transduction Any process that activates or increases the frequency, rate or extent of signal transduction. GOC:sm positive regulation of signalling pathway GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GO:0035467 down regulation of signal transduction down-regulation of signal transduction downregulation of signal transduction inhibition of signal transduction biological_process negative regulation of signaling pathway negative regulation of signalling pathway negative regulation of signal transduction Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GOC:sm negative regulation of signalling pathway GOC:mah Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. janelomax 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. GO:1990367 process resulting in tolerance to organic substance biological_process response to organic substance Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. GOC:sm PMID:23356676 Any process that modulates the frequency, rate or extent of photosynthesis. biological_process regulation of photosynthesis Any process that modulates the frequency, rate or extent of photosynthesis. GOC:sm The process in which the anatomical structures of the soma are generated and organized. biological_process body morphogenesis The process in which the anatomical structures of the soma are generated and organized. GOC:ems ISBN:0140512888 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond. response to organic nitrogen biological_process response to organonitrogen compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond. PMID:9869419 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. endomembrane organization endomembrane system organisation biological_process endomembrane system organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. GOC:mah GOC:sm endomembrane system organisation GOC:mah Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins. biological_process negative regulation of peptidase activity Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins. GOC:dph GOC:tb The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Wikipedia:Gene_expression biological_process gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Wikipedia:Regulation_of_gene_expression regulation of protein expression biological_process regulation of gene product expression This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation. regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb The movement of substances between cells. jl 2013-12-19T13:24:56Z GO:1902585 biological_process single organism intercellular transport single-organism intercellular transport intercellular transport The movement of substances between cells. GOC:dhl single organism intercellular transport GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome. proteasome-mediated protein catabolic process proteasome-mediated protein catabolism biological_process proteasomal protein catabolic process The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome. GOC:tb Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm. biological_process regulation of autophagy Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm. GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm. biological_process negative regulation of autophagy Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm. GOC:dph GOC:tb Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm. biological_process positive regulation of autophagy Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites. biological_process regulation of transposition Any process that modulates the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites. biological_process negative regulation of transposition Any process that decreases the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites. biological_process positive regulation of transposition Any process that increases the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of membrane disassembly. biological_process regulation of membrane disassembly Any process that modulates the frequency, rate or extent of membrane disassembly. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of 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. biological_process regulation of macromolecule biosynthetic process Any process that modulates the rate, frequency or extent of 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. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of 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. biological_process positive regulation of macromolecule biosynthetic process Any process that increases the rate, frequency or extent of 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. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of 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. biological_process negative regulation of macromolecule biosynthetic process Any process that decreases the rate, frequency or extent of 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. GOC:dph GOC:tb Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. biological_process regulation of cell cycle process Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any process that modulates 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. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. biological_process regulation of cellular ketone metabolic process Any process that modulates 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. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a ketone, carried out by individual cells. biological_process regulation of ketone biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a ketone, carried out by individual cells. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells. biological_process regulation of ketone catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of 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. biological_process positive regulation of macromolecule metabolic process Any process that increases the frequency, rate or extent of 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. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of 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. biological_process negative regulation of macromolecule metabolic process Any process that decreases the frequency, rate or extent of 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. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. biological_process posttranscriptional regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. GOC:dph GOC:tb The activation of endogenous cellular processes that result in the death of a cell as part of its development. developmental programmed cell death programmed cell death involved in development biological_process This process is part of the natural developmental program of some cell types, but it does not always happen as part of the development or shaping of a gross anatomical structure. programmed cell death involved in cell development The activation of endogenous cellular processes that result in the death of a cell as part of its development. GOC:dph GOC:mtg_apoptosis GOC:tb Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. biological_process positive regulation of gene expression Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. biological_process This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation. negative regulation of gene expression Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of merging of two or more mitochondria within a cell to form a single compartment. biological_process regulation of mitochondrial fusion Any process that modulates the frequency, rate or extent of merging of two or more mitochondria within a cell to form a single compartment. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of merging of two or more mitochondria within a cell to form a single compartment. biological_process positive regulation of mitochondrial fusion Any process that increases the frequency, rate or extent of merging of two or more mitochondria within a cell to form a single compartment. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of merging of two or more mitochondria within a cell to form a single compartment. biological_process negative regulation of mitochondrial fusion Any process that decreases the frequency, rate or extent of merging of two or more mitochondria within a cell to form a single compartment. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. positive regulation of organelle organisation biological_process positive regulation of organelle organization and biogenesis positive regulation of organelle organization Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb positive regulation of organelle organisation GOC:mah positive regulation of organelle organization and biogenesis GOC:mah Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. negative regulation of organelle organisation biological_process negative regulation of organelle organization and biogenesis negative regulation of organelle organization Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb negative regulation of organelle organisation GOC:mah negative regulation of organelle organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the 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. biological_process regulation of cell communication Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the 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:dph GOC:tb Any process that increases the frequency, rate or extent of cell communication. Cell communication is the 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. biological_process positive regulation of cell communication Any process that increases the frequency, rate or extent of cell communication. Cell communication is the 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:dph GOC:tb Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the 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. biological_process negative regulation of cell communication Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the 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:dph GOC:tb Any process that modulates the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix. regulation of extracellular matrix breakdown regulation of extracellular matrix degradation biological_process regulation of extracellular matrix disassembly Any process that modulates the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix. GOC:BHF GOC:dph GOC:tb regulation of extracellular matrix breakdown GOC:dph GOC:tb regulation of extracellular matrix degradation GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix. down regulation of extracellular matrix disassembly down-regulation of extracellular matrix disassembly downregulation of extracellular matrix disassembly negative regulation of extracellular matrix breakdown negative regulation of extracellular matrix degradation inhibition of extracellular matrix disassembly biological_process negative regulation of extracellular matrix disassembly Any process that decreases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix. GOC:BHF GOC:dph GOC:tb down regulation of extracellular matrix disassembly GOC:dph GOC:tb down-regulation of extracellular matrix disassembly GOC:dph GOC:tb downregulation of extracellular matrix disassembly GOC:dph GOC:tb negative regulation of extracellular matrix breakdown GOC:dph GOC:tb negative regulation of extracellular matrix degradation GOC:dph GOC:tb inhibition of extracellular matrix disassembly GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process positive regulation of cell development Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process negative regulation of cell development Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. biological_process regulation of cell morphogenesis involved in differentiation Any process that modulates the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. biological_process positive regulation of cell morphogenesis involved in differentiation Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. biological_process negative regulation of cell morphogenesis involved in differentiation Any process that decreases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. regulation of mitochondrion organisation biological_process regulation of mitochondrion organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. GOC:dph GOC:tb regulation of mitochondrion organisation GOC:mah Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. positive regulation of mitochondrion organisation biological_process positive regulation of mitochondrion organization Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. GOC:dph GOC:tb positive regulation of mitochondrion organisation GOC:mah Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. negative regulation of mitochondrion organisation biological_process negative regulation of mitochondrion organization Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. GOC:dph GOC:tb negative regulation of mitochondrion organisation GOC:mah Any process in which a lipid is transported to, or maintained in, a specific location. lipid localisation biological_process lipid localization Any process in which a lipid is transported to, or maintained in, a specific location. GOC:BHF GOC:dph GOC:tb lipid localisation GOC:mah Any process that modulates the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. biological_process regulation of isomerase activity Any process that modulates the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. GOC:dph GOC:tb Any process that increases the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. biological_process positive regulation of isomerase activity Any process that increases the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. GOC:dph GOC:tb Any process that modulates the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. biological_process regulation of phosphatase activity Any process that modulates the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. GOC:BHF GOC:dph GOC:tb Any process that increases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. biological_process positive regulation of phosphatase activity Any process that increases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. GOC:BHF GOC:dph GOC:tb Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. biological_process negative regulation of phosphatase activity Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. GOC:BHF GOC:dph GOC:tb The cellular component assembly that is part of the initial shaping of the component during its developmental progression. biological_process cellular component assembly involved in morphogenesis The cellular component assembly that is part of the initial shaping of the component during its developmental progression. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of cytoplasmic microtubule depolymerization. biological_process regulation of cytoplasmic microtubule depolymerization Any process that modulates the frequency, rate or extent of cytoplasmic microtubule depolymerization. GOC:dph GOC:tb The removal of tubulin heterodimers from one or both ends of a cytoplasmic microtubule. biological_process cytoplasmic microtubule depolymerization The removal of tubulin heterodimers from one or both ends of a cytoplasmic microtubule. GOC:dph GOC:tb Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. biological_process regulation of cell death Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. GOC:dph GOC:tb Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. biological_process positive regulation of cell death Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. tanyaberardini 2009-04-27T09:53:22Z biological_process negative regulation of cell cycle process Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. tanyaberardini 2009-04-27T11:45:39Z biological_process positive regulation of endopeptidase activity Any process that increases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. tanyaberardini 2009-04-27T11:47:01Z biological_process negative regulation of endopeptidase activity Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins. tanyaberardini 2009-04-27T11:54:32Z biological_process positive regulation of peptidase activity Any process that increases the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell. tanyaberardini 2009-05-20T11:51:21Z biological_process regulation of microtubule nucleation Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell. GOC:dph GOC:tb The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. tanyaberardini 2009-05-27T10:56:08Z microtubule-based transport establishment of localization by movement along microtubule movement along microtubule biological_process transport along microtubule The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. GOC:dph GOC:mah GOC:tb establishment of localization by movement along microtubule GOC:dph Any process that modulates the rate, frequency or extent of cell wall macromolecule metabolism. Cell wall macromolecule metabolic processes are the chemical reactions and pathways involving macromolecules forming, or destined to form, part of the cell wall. A cell wall is a 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. tanyaberardini 2009-06-01T11:55:35Z biological_process regulation of cell wall macromolecule metabolic process Any process that modulates the rate, frequency or extent of cell wall macromolecule metabolism. Cell wall macromolecule metabolic processes are the chemical reactions and pathways involving macromolecules forming, or destined to form, part of the cell wall. A cell wall is a 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:dph GOC:tb A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. GO:0016244 regulated cell death Wikipedia:Programmed_cell_death caspase-independent cell death non-apoptotic programmed cell death nonapoptotic programmed cell death biological_process PCD RCD caspase-independent apoptosis Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children. programmed cell death A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. GOC:lr GOC:mtg_apoptosis A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. Wikipedia:Endomembrane_system cellular_component endomembrane system A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. GOC:lh The lipid bilayer surrounding any membrane-bounded vesicle in the cell. NIF_Subcellular:sao1153182838 cellular_component vesicle membrane The lipid bilayer surrounding any membrane-bounded vesicle in the cell. GOC:mah GOC:vesicle Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups. response to amine stimulus biological_process response to amine Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups. GOC:ef response to amine stimulus GOC:dos 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. GO:0015831 enzyme transport biological_process protein transport 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 Enables the transfer of an ion from one side of a membrane to the other. ion transporter activity molecular_function ion transmembrane transporter activity GO_REF:0000090 Enables the transfer of an ion from one side of a membrane to the other. GOC:dgf GOC:mtg_transport ISBN:0815340729 Enables the transfer of carbohydrate from one side of a membrane to the other. GO:1901476 sugar transporter molecular_function carbohydrate transporter activity carbohydrate transmembrane transporter activity GO_REF:0000090 Enables the transfer of carbohydrate from one side of a membrane to the other. GOC:jl GOC:mtg_transport ISBN:0815340729 Enables the transfer of a solute from one side of a membrane to the other, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is powered by a primary energy source, directly using ATP. Primary energy sources known to be coupled to transport are chemical, electrical and solar sources. TC:3 molecular_function primary active transporter primary active transmembrane transporter activity Enables the transfer of a solute from one side of a membrane to the other, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is powered by a primary energy source, directly using ATP. Primary energy sources known to be coupled to transport are chemical, electrical and solar sources. GOC:mtg_transport ISBN:0815340729 TC:3.-.-.-.- The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. cellular_component microtubule cytoskeleton The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. GOC:jl ISBN:0395825172 Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules. molecular_function tubulin binding Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules. GOC:clt 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. biological_process amine/polyamine transport amine transport 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 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. biological_process organic acid transport 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 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. biological_process nucleobase, nucleoside, nucleotide and nucleic acid transport nucleobase-containing compound transport 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 nucleobase, nucleoside, nucleotide and nucleic acid transport GOC:dph GOC:tb Enables the transfer of nucleobases, nucleosides, nucleotides and nucleic acids from one side of a membrane to the other. molecular_function nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity nucleobase-containing compound transmembrane transporter activity Enables the transfer of nucleobases, nucleosides, nucleotides and nucleic acids from one side of a membrane to the other. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity GOC:dph GOC:tb 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. Wikipedia:Photosynthesis biological_process photosynthesis 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 A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. Wikipedia:Biological_membrane cellular_component membrane A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. GOC:dos GOC:mah ISBN:0815316194 The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. Wikipedia:Transmembrane_protein integral to membrane cellular_component transmembrane integral component of membrane The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. GOC:dos GOC:go_curators transmembrane GOC:mah The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. GO:0006724 GO:0044240 Wikipedia:Lipid_catabolism lipid breakdown lipid catabolism lipid degradation lipolysis multicellular organism lipid catabolic process multicellular organismal lipid catabolic process biological_process lipid catabolic process The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. GOC:go_curators A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:ai GOC:jl GOC:mah cellular component organisation at cellular level GOC:mah cellular component organisation in other organism GOC:mah cell organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle. vesicle organisation biological_process vesicle organization and biogenesis vesicle organization 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 vesicle organization and biogenesis GOC:mah The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0006093 anabolic carbohydrate metabolic process anabolic carbohydrate metabolism carbohydrate anabolism carbohydrate biosynthesis carbohydrate formation carbohydrate synthesis biological_process carbohydrate biosynthetic process The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. janelomax 2012-10-23T16:34:39Z GO:0006095 GO:0044276 GO:0044724 carbohydrate breakdown carbohydrate catabolism carbohydrate degradation catabolic carbohydrate metabolic process catabolic carbohydrate metabolism multicellular organismal carbohydrate catabolic process biological_process single-organism carbohydrate catabolic process carbohydrate catabolic process The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage. organic acid anabolism organic acid biosynthesis organic acid formation organic acid synthesis biological_process organic acid biosynthetic process The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage. organic acid breakdown organic acid catabolism organic acid degradation biological_process organic acid catabolic process The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage. ISBN:0198506732 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. RNA metabolism biological_process RNA metabolic process 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 The chemical reactions and pathways involving mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes. mRNA metabolism biological_process mRNA metabolic process The chemical reactions and pathways involving mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes. ISBN:0198506732 The chemical reactions and pathways involving rRNA, ribosomal RNA, a structural constituent of ribosomes. rRNA metabolism biological_process rRNA metabolic process The chemical reactions and pathways involving rRNA, ribosomal RNA, a structural constituent of ribosomes. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes. rRNA breakdown rRNA catabolism rRNA degradation biological_process rRNA catabolic process The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes. GOC:ai The chemical reactions and pathways resulting in the breakdown of tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. tRNA breakdown tRNA catabolism tRNA degradation biological_process tRNA catabolic process The chemical reactions and pathways resulting in the breakdown of tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. GOC:ai 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. GO:0006899 vesicle transport vesicular transport nonselective vesicle transport biological_process protein sorting along secretory pathway vesicle trafficking vesicle-mediated transport 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 vesicular transport GOC:mah The directed movement of substances mediated by an endosome, a membrane-bounded organelle that carries materials enclosed in the lumen or located in the endosomal membrane. GO:0032439 endosome localisation biological_process endosome localization endosome transport endosomal transport The directed movement of substances mediated by an endosome, a membrane-bounded organelle that carries materials enclosed in the lumen or located in the endosomal membrane. ISBN:0198506732 endosome localisation GOC:mah endosome transport GOC:bf Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity molecular_function Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. Wikipedia:Phosphorylation biological_process phosphorylation The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. ISBN:0198506732 The process of removing one or more phosphoric (ester or anhydride) residues from a molecule. Wikipedia:Dephosphorylation biological_process dephosphorylation The process of removing one or more phosphoric (ester or anhydride) residues from a molecule. ISBN:0198506732 Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments. Reactome:R-HSA-6810472 molecular_function pyrophosphatase activity Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments. EC:3.6.1.- GOC:curators Reactome:R-HSA-6810472 NUDT13 hydrolyses AP6A to AP4 and ADP The directed movement of substances or organelles within the cytosol. biological_process cytosolic transport The directed movement of substances or organelles within the cytosol. GOC:ai 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. EC:1 Reactome:R-HSA-1614362 Reactome:R-HSA-209921 Reactome:R-HSA-209960 Reactome:R-HSA-3095889 Reactome:R-HSA-390425 Reactome:R-HSA-390438 Reactome:R-HSA-5662660 Reactome:R-HSA-8878581 Reactome:R-HSA-8936442 Reactome:R-HSA-9020249 Reactome:R-HSA-9020260 Reactome:R-HSA-9024624 Reactome:R-HSA-9024630 Reactome:R-HSA-9025007 Reactome:R-HSA-9026001 Reactome:R-HSA-9026917 Reactome:R-HSA-9027033 redox activity oxidoreductase activity, acting on other substrates molecular_function oxidoreductase activity 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 Reactome:R-HSA-1614362 SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases Reactome:R-HSA-209921 Monoiodinated tyrosine can be deiodinated Reactome:R-HSA-209960 Diiodinated tyrosine can be deiodinated Reactome:R-HSA-3095889 MMACHC reduces Cbl Reactome:R-HSA-390425 FAR1 reduces PalmCoA to HXOL Reactome:R-HSA-390438 FAR2 reduces PalmCoA to HXOL Reactome:R-HSA-5662660 Dopachrome is transformed to DHICA by DCT Reactome:R-HSA-8878581 TYRP1 oxidises DHICA to IQCA Reactome:R-HSA-8936442 MARC1,MARC2 reduce N-hydroxylated compounds Reactome:R-HSA-9020249 Hydroperoxy reductase reduces 4(S)-Hp-17(S)-HDHA to RvD6 Reactome:R-HSA-9020260 Hydroperoxy reducatse reduces 7(S)-Hp-17(S)-HDHA to RvD5 Reactome:R-HSA-9024624 Hydroperoxy reductase reduces 4(S)-Hp-17(R)-HDHA to AT-RvD6 Reactome:R-HSA-9024630 Hydroperoxy reductase reduces 7(S)-Hp-17(R)-HDHA to AT-RvD5 Reactome:R-HSA-9025007 Hydroperoxy reductase reduces 7(S),14(S)-diHp-DHA to 7-epi-MaR1 Reactome:R-HSA-9026001 Hydroperoxy reductase reduces 7,17-diHp-DPAn-3 to RvD5n-3DPA Reactome:R-HSA-9026917 Lipoxygenase dehydrogenates 7(S),17(S)-diHp-DHA to 7S(8)-epoxy-17(S)-HDHA Reactome:R-HSA-9027033 Hydroperoxy reducatase reduces 14(S)-Hp-DHA to 14(S)-HDHA The division of a mature peroxisome within a cell to form two or more separate peroxisome compartments. peroxisome division peroxisome proliferation biological_process peroxisome fission The division of a mature peroxisome within a cell to form two or more separate peroxisome compartments. GOC:mah PMID:11687502 PMID:14754507 Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents. molecular_function amino acid binding Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents. GOC:ai 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. EC:2 Reactome:R-HSA-1483089 Reactome:R-HSA-1483186 Reactome:R-HSA-5668414 Reactome:R-HSA-6787403 Reactome:R-HSA-8868783 molecular_function transferase activity 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 Reactome:R-HSA-1483089 PE is converted to PS by PTDSS2 Reactome:R-HSA-1483186 PC is converted to PS by PTDSS1 Reactome:R-HSA-5668414 TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK Reactome:R-HSA-6787403 GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA Reactome:R-HSA-8868783 TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 Catalysis of the transfer of a one-carbon group from one compound (donor) to another (acceptor). EC:2.1 molecular_function transferase activity, transferring one-carbon groups Catalysis of the transfer of a one-carbon group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor). GO:0008415 EC:2.3 Reactome:R-HSA-159431 Reactome:R-HSA-192312 Reactome:R-HSA-193491 Reactome:R-HSA-6792572 Reactome:R-HSA-8858298 acyltransferase activity molecular_function transferase activity, transferring acyl groups Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Reactome:R-HSA-159431 Cytosolic chenodeoxycholoyl-CoA or choloyl-CoA are conjugated with glycine or taurine Reactome:R-HSA-192312 Choloyl CoA reacts with glycine or taurine to form glycocholate or taurocholate Reactome:R-HSA-193491 Chenodeoxycholoyl CoA reacts with glycine or taurine to form glycochenodeoxycholate or taurochenodeoxycholate Reactome:R-HSA-6792572 LIPT1 transfers lipoyl group from lipoyl-GCSH to DHs Reactome:R-HSA-8858298 HRASLS transfer acyl group from PC to PE to form NAPE Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor). GO:0016932 EC:2.4 Reactome:R-HSA-5173005 Reactome:R-HSA-6785565 glycosyltransferase activity transglycosidase activity transglycosylase activity transferase activity, transferring other glycosyl groups molecular_function transferase activity, transferring glycosyl groups Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Reactome:R-HSA-5173005 B3GALTL transfers glucose to O-fucosyl-proteins Reactome:R-HSA-6785565 Defective B3GALTL does not transfer glucose to O-fucosyl-proteins Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor). GO:0016766 EC:2.5 EC:2.5.1 Reactome:R-HSA-4419978 Reactome:R-HSA-4755545 Reactome:R-HSA-6782893 transferase activity, transferring alkyl or aryl groups, other than methyl groups molecular_function transferase activity, transferring alkyl or aryl (other than methyl) groups Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Reactome:R-HSA-4419978 DHDDS:NUS1 elongates E,E-FPP with (n)IPPP to form pPPP Reactome:R-HSA-4755545 Defective DHDDS does not elongate E,E-FPP Reactome:R-HSA-6782893 TRMT12 transforms yW-187 yielding yW-86 at nucleotide 37 of tRNA(Phe) Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). EC:2.7 molecular_function Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. transferase activity, transferring phosphorus-containing groups Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Catalysis of the transfer of a nucleotidyl group to a reactant. EC:2.7.7 Reactome:R-HSA-6782434 molecular_function nucleotidyltransferase activity Catalysis of the transfer of a nucleotidyl group to a reactant. ISBN:0198506732 Reactome:R-HSA-6782434 THG1L transfers GMP to 5' end of tRNA(His) 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. EC:3 Reactome:R-HSA-1236938 Reactome:R-HSA-2029475 Reactome:R-HSA-5694583 Reactome:R-HSA-5695964 Reactome:R-HSA-6786190 Reactome:R-HSA-6788295 Reactome:R-HSA-8938314 Reactome:R-HSA-8952137 molecular_function hydrolase activity 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 Reactome:R-HSA-1236938 Partial proteolysis of antigen in phagolysosomes Reactome:R-HSA-2029475 Production of AA by iPLA2 upon FCGR activation Reactome:R-HSA-5694583 ABHD4 hydrolyses NAPE Reactome:R-HSA-5695964 ABHD14B hydrolyses PNPB Reactome:R-HSA-6786190 CMBL hydrolyses OM to OLMS Reactome:R-HSA-6788295 HDHD1:Mg2+ dephosphorylates PURIDP Reactome:R-HSA-8938314 ENPPs hydrolyse CoA-SH to PPANT, PAP Reactome:R-HSA-8952137 Phospholipid phosphatase 6 hydrolyses Presqualene diphosphate to presqualene monophosphate Catalysis of the hydrolysis of any ester bond. EC:3.1 Reactome:R-HSA-162729 Reactome:R-HSA-9023617 Reactome:R-HSA-9023619 esterase activity molecular_function hydrolase activity, acting on ester bonds Catalysis of the hydrolysis of any ester bond. GOC:jl Reactome:R-HSA-162729 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid Reactome:R-HSA-9023617 Butyrylcholinesterase hydrolyzes acyl Ghrelin Reactome:R-HSA-9023619 Platelet-activating factor acetylhydrolase (PLA2G7) hydrolyzes acyl Ghrelin Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. GO:0003869 GO:0016302 EC:3.1.3 MetaCyc:4-NITROPHENYLPHOSPHATASE-RXN RHEA:21664 Reactome:R-HSA-4419986 phosphoric monoester hydrolase activity 4-nitrophenylphosphatase activity 4-nitrophenylphosphate phosphohydrolase activity K-pNPPase activity NPPase activity PNPPase activity ecto-p-nitrophenyl phosphatase activity nitrophenyl phosphatase activity p-nitrophenylphosphatase activity p-nitrophenylphosphate phosphohydrolase activity para-nitrophenyl phosphatase activity molecular_function phosphatase phosphatase activity Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. EC:3.1.3 GOC:curators GOC:pg Reactome:R-HSA-4419986 Unknown pPPP phosphatase dephosphorylates pPPP to pPNOL 4-nitrophenylphosphate phosphohydrolase activity EC:3.1.3.41 K-pNPPase activity EC:3.1.3.41 NPPase activity EC:3.1.3.41 PNPPase activity EC:3.1.3.41 ecto-p-nitrophenyl phosphatase activity EC:3.1.3.41 nitrophenyl phosphatase activity EC:3.1.3.41 p-nitrophenylphosphatase activity EC:3.1.3.41 p-nitrophenylphosphate phosphohydrolase activity EC:3.1.3.41 para-nitrophenyl phosphatase activity EC:3.1.3.41 Catalysis of the hydrolysis of any glycosyl bond. EC:3.2 Reactome:R-HSA-1793176 Reactome:R-HSA-2065233 glycosidase activity N-glycosylase glycosylase molecular_function hydrolase activity, acting on glycosyl bonds Catalysis of the hydrolysis of any glycosyl bond. GOC:jl Reactome:R-HSA-1793176 DS is cleaved from its proteoglycan Reactome:R-HSA-2065233 CS is cleaved from its proteoglycan Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds. EC:3.5 Reactome:R-HSA-6803753 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in other compounds molecular_function hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds. GOC:jl Reactome:R-HSA-6803753 NAAA hydrolyses NAEs to FAs and ethanolamine Catalysis of the hydrolysis of any acid anhydride. EC:3.6 hydrolase activity, acting on acid anhydrides, involved in cellular and subcellular movement molecular_function hydrolase activity, acting on acid anhydrides Catalysis of the hydrolysis of any acid anhydride. GOC:jl Catalysis of the hydrolysis of any acid anhydride which contains phosphorus. EC:3.6.1 molecular_function hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides Catalysis of the hydrolysis of any acid anhydride which contains phosphorus. GOC:jl 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 Reactome:R-HSA-5696408 Reactome:R-HSA-6782895 other lyase activity molecular_function lyase activity 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. ISBN:0198547684 Reactome:R-HSA-5696408 PHYKPL tetramer hydrolyses 5PHL Reactome:R-HSA-6782895 TYW1:FMN:4Fe-4S transforms 1-methylguanosine yielding yW-187 (4-demethylwyosine) at nucleotide 37 of tRNA(Phe) Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. EC:5 Reactome:R-HSA-6787623 other isomerase activity molecular_function isomerase activity Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. ISBN:0198506732 Reactome:R-HSA-6787623 TSTA3 dimer epimerises GDP-DHDMan to GDP-KDGal 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 synthetase activity molecular_function ligase activity 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 synthetase activity GOC:jh2 Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction. https://github.com/geneontology/go-ontology/issues/19078 GO:0004002 GO:0042623 EC:3.6.1.3 MetaCyc:ADENOSINETRIPHOSPHATASE-RXN RHEA:13065 Reactome:R-HSA-159101 Reactome:R-HSA-3371422 Reactome:R-HSA-416985 Reactome:R-HSA-5618093 Reactome:R-HSA-5654989 Reactome:R-HSA-5694425 Reactome:R-HSA-6809015 Reactome:R-HSA-6811422 Reactome:R-HSA-6814670 Reactome:R-HSA-6814678 Reactome:R-HSA-6814683 Reactome:R-HSA-72139 Reactome:R-HSA-8847638 Reactome:R-HSA-8868658 Reactome:R-HSA-8939203 Reactome:R-HSA-9038161 Reactome:R-HSA-917693 Reactome:R-HSA-9609860 ATP hydrolase activity ATP monophosphatase activity ATP phosphohydrolase activity adenosine 5'-triphosphatase activity adenosine triphosphatase activity adenosinetriphosphatase activity (Ca2+ + Mg2+)-ATPase ATP phosphohydrolase (polypeptide-unfolding) HCO3--ATPase complex V (mitochondrial electron transport) molecular_function ATPase activity, coupled SV40 T-antigen chaperonin chaperonin ATPase activity non-chaperonin molecular chaperone ATPase activity nucleoplasmin ATPase activity peroxisome-assembly ATPase activity vesicle-fusing ATPase activity ATPase activity Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction. EC:3.6.1.3 GOC:jl Reactome:R-HSA-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B) Reactome:R-HSA-3371422 ATP hydrolysis by HSP70 Reactome:R-HSA-416985 Trafficking of GluR2-containing AMPA receptors to synapse Reactome:R-HSA-5618093 ATP hydrolysis by HSP90 Reactome:R-HSA-5654989 SPRTN:VCP-mediated release of POLH from monoUb:K164-PCNA Reactome:R-HSA-5694425 NSF ATPase activity dissociates cis-SNARE Reactome:R-HSA-6809015 NSF ATPase activity dissociates cis-SNARE at cis-Golgi Reactome:R-HSA-6811422 NSF ATPase activity dissociates cis-SNARE at the ER Reactome:R-HSA-6814670 ATP hydrolysis by RHOBTB3 promotes PLIN3 dissociation Reactome:R-HSA-6814678 ATP hydrolysis by NSF disassembles the cis-SNARE at the TGN Reactome:R-HSA-6814683 NSF-dependent ATP hydrolysis disassembles the cis-SNARE at the TGN Reactome:R-HSA-72139 Formation of the active Spliceosomal C (B*) complex Reactome:R-HSA-8847638 ATP hydrolysis by NSF disassembles the cis-SNARE at the Golgi membrane Reactome:R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating Reactome:R-HSA-8939203 HSP90-dependent ATP hydrolysis promotes release of ESR:ESTG from chaperone complex Reactome:R-HSA-9038161 Progesterone stimulation promotes PGR:P4 binding to ESR1:ESTG Reactome:R-HSA-917693 ESCRT Disassembly Reactome:R-HSA-9609860 Tail-anchored protein:SGTA:BAG6:GET4:UBL4A:ASNA1:ATP dissociates and ASNA1 hydrolyzes ATP yielding Tail-anchored protein:ASNA1:ADP ATP hydrolase activity EC:3.6.1.3 ATP monophosphatase activity EC:3.6.1.3 adenosine 5'-triphosphatase activity EC:3.6.1.3 adenosine triphosphatase activity EC:3.6.1.3 (Ca2+ + Mg2+)-ATPase EC:3.6.1.3 ATP phosphohydrolase (polypeptide-unfolding) EC:3.6.4.9 HCO3--ATPase EC:3.6.1.3 complex V (mitochondrial electron transport) EC:3.6.1.3 SV40 T-antigen EC:3.6.1.3 chaperonin EC:3.6.4.9 vesicle-fusing ATPase activity EC:3.6.4.6 The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall. GO:0044039 cellular cell wall macromolecule breakdown cellular cell wall macromolecule catabolic process cellular cell wall macromolecule catabolism cellular cell wall macromolecule degradation biological_process cell wall breakdown cell wall catabolism cell wall degradation cell wall macromolecule catabolic process The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall. GOC:go_curators cellular cell wall macromolecule breakdown GOC:mah cellular cell wall macromolecule catabolism GOC:mah cellular cell wall macromolecule degradation GOC:mah cell wall breakdown GOC:mah cell wall catabolism GOC:mah cell wall degradation GOC:mah Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate. apyrase activity EC:3.6.1.15 MetaCyc:NUCLEOSIDE-TRIPHOSPHATASE-RXN RHEA:23680 Reactome:R-HSA-8850846 Reactome:R-HSA-8851089 Reactome:R-HSA-8851110 Reactome:R-HSA-8851234 Reactome:R-HSA-8851494 Reactome:R-HSA-8851538 NTPase activity nucleoside 5-triphosphatase activity nucleoside triphosphatase activity nucleoside triphosphate hydrolase activity nucleoside triphosphate phosphohydrolase activity nucleoside-5-triphosphate phosphohydrolase activity unspecific diphosphate phosphohydrolase activity molecular_function nucleoside-triphosphatase activity Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate. EC:3.6.1.15 Reactome:R-HSA-8850846 NTPDase1 hydrolyzes nucleoside triphosphates Reactome:R-HSA-8851089 NTPDase2 hydrolyzes nucleoside triphosphates Reactome:R-HSA-8851110 NTPDase3 hydrolyzes nucleoside triphosphates Reactome:R-HSA-8851234 NTPDase4 hydrolyzes nucleoside triphosphates Reactome:R-HSA-8851494 NTPDase7 hydrolyzes nucleoside triphosphates Reactome:R-HSA-8851538 NTPDase8 hydrolyzes nucleoside triphosphates NTPase activity EC:3.6.1.15 nucleoside 5-triphosphatase activity EC:3.6.1.15 nucleoside triphosphate hydrolase activity EC:3.6.1.15 nucleoside triphosphate phosphohydrolase activity EC:3.6.1.15 nucleoside-5-triphosphate phosphohydrolase activity EC:3.6.1.15 unspecific diphosphate phosphohydrolase activity EC:3.6.1.15 A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells. nucleolus biogenesis nucleolus assembly biological_process nucleologenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells. GOC:jl ISBN:0198506732 nucleolus assembly GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GO:0016478 down regulation of protein biosynthetic process down-regulation of protein biosynthetic process downregulation of protein biosynthetic process negative regulation of protein anabolism negative regulation of protein biosynthesis negative regulation of protein biosynthetic process negative regulation of protein formation negative regulation of protein synthesis inhibition of protein biosynthetic process biological_process protein biosynthesis inhibitor activity protein biosynthetic process inhibitor activity negative regulation of translation Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GOC:isa_complete Any process that modulates the frequency, rate or extent of exocytosis. biological_process regulation of exocytosis Any process that modulates the frequency, rate or extent of exocytosis. GOC:go_curators Any process in which mitochondrial RNA is transported to, or maintained in, a specific location. establishment and maintenance of mitochondrial RNA localization mitochondrial RNA localisation mtRNA localization biological_process mitochondrial RNA localization Any process in which mitochondrial RNA is transported to, or maintained in, a specific location. GOC:ai mitochondrial RNA localisation GOC:mah Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule. molecular_function kinase regulator activity Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:ai Modulates the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule. molecular_function phosphatase regulator activity Modulates the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. regulation of lipid metabolism biological_process regulation of lipid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process regulation of nucleobase-containing compound metabolic process Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. regulation of phosphate metabolism biological_process regulation of phosphate metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044246 regulation of metabolism regulation of multicellular organismal metabolic process regulation of organismal metabolic process biological_process regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators regulation of organismal metabolic process GOC:tb The chemical reactions and pathways involving a protein. Includes protein modification. GO:0006411 GO:0044268 Wikipedia:Protein_metabolism protein metabolic process and modification protein metabolism protein metabolism and modification multicellular organismal protein metabolic process biological_process protein metabolic process The chemical reactions and pathways involving a protein. Includes protein modification. GOC:ma Any process involved in the maintenance of an internal steady state at the level of the cell. biological_process cellular homeostasis Any process involved in the maintenance of an internal steady state at the level of the cell. GOC:isa_complete GOC:jl ISBN:0395825172 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. Wikipedia:Secondary_metabolism secondary metabolism secondary metabolite metabolic process secondary metabolite metabolism biological_process secondary metabolic process 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 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). carboxylic acid metabolism biological_process carboxylic acid metabolic process The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). ISBN:0198506732 The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the peroxisome. biological_process vesicle fusion with peroxisome The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the peroxisome. GOC:jid Interacting selectively and non-covalently with ribosomal RNA. GO:0000944 base pairing with rRNA molecular_function rRNA binding Interacting selectively and non-covalently with ribosomal RNA. GOC:jl Interacting selectively and non-covalently with any enzyme. molecular_function enzyme binding Interacting selectively and non-covalently with any enzyme. GOC:jl Interacting selectively and non-covalently with any phosphatase. molecular_function phosphatase binding Interacting selectively and non-covalently with any phosphatase. GOC:jl A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state. biological_process developmental maturation A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process cell cycle process The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. GOC:isa_complete GOC:mtg_cell_cycle 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. membrane docking biological_process membrane docking 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 A cellular process that results in the breakdown of a cellular component. GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process cellular component disassembly A cellular process that results in the breakdown of a cellular component. GOC:isa_complete A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. janelomax 2012-09-19T15:56:06Z GO:0044702 biological_process single organism reproductive process reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:dph GOC:isa_complete Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. regulation of morphogenesis biological_process regulation of anatomical structure morphogenesis Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. GOC:mah Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized. biological_process negative regulation of cell shape and cell size positive regulation of cell shape and cell size regulation of cell shape and cell size regulation of cell morphogenesis Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized. GOC:isa_complete negative regulation of cell shape and cell size GOC:dph GOC:tb positive regulation of cell shape and cell size GOC:dph GOC:tb regulation of cell shape and cell size GOC:dph GOC:tb The aggregation, arrangement and bonding together of a cellular component. GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process cellular component assembly The aggregation, arrangement and bonding together of a cellular component. GOC:isa_complete The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions. biological_process biological adhesion 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 A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. RNA-protein complex biogenesis ribonucleoprotein complex biogenesis and assembly biological_process ribonucleoprotein complex biogenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. GOC:isa_complete GOC:mah RNA-protein complex biogenesis GOC:mah ribonucleoprotein complex biogenesis and assembly GOC:mah A process that results in the breakdown of the extracellular matrix. biological_process extracellular matrix disassembly A process that results in the breakdown of the extracellular matrix. GOC:jid The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. RNA-protein complex assembly RNP complex assembly protein-RNA complex assembly biological_process ribonucleoprotein complex assembly The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. GOC:jl A ribosome located in the cytosol. GO:0005830 GO:0009281 GO:0030871 70S ribosome 80S ribosome cellular_component cytosolic ribosome A ribosome located in the cytosol. GOC:mtg_sensu Enables the transfer of a specific substance or related group of substances from one side of a membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction. active carrier activity carrier activity permease activity pump activity molecular_function active transmembrane transporter activity Enables the transfer of a specific substance or related group of substances from one side of a membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction. GOC:mtg_transport ISBN:0815340729 Enables the transfer of an ion from one side of a membrane to the other up the solute's concentration gradient. This is carried out by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction. molecular_function active ion transmembrane transporter activity Enables the transfer of an ion from one side of a membrane to the other up the solute's concentration gradient. This is carried out by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction. GOC:mtg_transport ISBN:0815340729 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. GO:0005386 GO:0015563 GO:0015646 GO:0022891 GO:0022892 Reactome:R-HSA-1236947 Reactome:R-HSA-429036 Reactome:R-HSA-5638209 Reactome:R-HSA-5671707 Reactome:R-HSA-6784434 Reactome:R-HSA-6784436 molecular_function substrate-specific transmembrane transporter activity substrate-specific transporter activity uptake permease activity uptake transmembrane transporter activity transmembrane transporter activity Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. GOC:jid GOC:mtg_transport ISBN:0815340729 Reactome:R-HSA-1236947 Egress of internalized antigen to the cytosol via sec61 Reactome:R-HSA-429036 SLC2A9 transports Fru, Glc, urate Reactome:R-HSA-5638209 Defective SLC2A9 does not transport Fru, Glc, urate Reactome:R-HSA-5671707 Fe3+ dissociates from SLC22A17:LCN2:2,5DHBA Reactome:R-HSA-6784434 An unknown carrier transports cytosolic glyoxylate to the peroxisome Reactome:R-HSA-6784436 An unknown carrier transports mitochondrial glyoxylate to the cytosol Enables the transfer of a macromolecule from one side of a membrane to the other. molecular_function macromolecule transmembrane transporter activity Enables the transfer of a macromolecule from one side of a membrane to the other. GOC:mtg_transport ISBN:0815340729 Any process that modulates the frequency, rate or extent of transmembrane transporter activity. biological_process regulation of transmembrane transporter activity Any process that modulates the frequency, rate or extent of transmembrane transporter activity. GOC:dph GOC:mtg_cardio GOC:mtg_transport Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another. 2010-02-16T09:30:50Z biological_process regulation of gene expression as a consequence of signal transmission signal transduction involved in regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another. GOC:mtg_signal regulation of gene expression as a consequence of signal transmission GOC:bf Any process that modulates the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process regulation of signaling process regulation of signalling process regulation of signaling Any process that modulates the frequency, rate or extent of a signaling process. GOC:mtg_signal regulation of signaling process GOC:bf regulation of signalling process GOC:mah The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. janelomax 2010-02-16T09:30:50Z GO:0023046 GO:0044700 biological signaling signaling process signalling biological_process signalling process single organism signaling Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. signaling The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. GOC:mtg_signal GOC:mtg_signaling_feb11 GOC:signaling signalling process GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z positive regulation of signalling process biological_process positive regulation of signaling process positive regulation of signaling Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. GOC:mtg_signal positive regulation of signalling process GOC:mah positive regulation of signaling process GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process negative regulation of signaling process negative regulation of signalling process negative regulation of signaling Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. GOC:mtg_signal negative regulation of signaling process GOC:bf negative regulation of signalling process GOC:mah The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. 2010-02-16T09:30:50Z signal secretion biological_process signal release The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. GOC:mtg_signal signal secretion GOC:bf A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. cell projection organisation biological_process cell projection organization and biogenesis cell surface structure organization and biogenesis cell projection organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection organization and biogenesis GOC:mah cell surface structure organization and biogenesis GOC:mah Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. formation of a cell surface projection biological_process cell projection biogenesis cell projection assembly Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection biogenesis GOC:mah A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella. Wikipedia:Cell_junction cellular_component cell junction A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella. GOC:aruk GOC:bc GOC:mah ISBN:0198506732 PMID:26820516 PMID:28096264 http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. Wikipedia:Cellular_differentiation biological_process cell differentiation The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. ISBN:0198506732 Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix. biological_process cell adhesion receptor regulator activity regulation of cell adhesion Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix. GOC:mah Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. regulation of peptidolysis biological_process regulation of proteolysis Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. GOC:mah The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. GO:0044254 Wikipedia:Protein_catabolism protein breakdown protein catabolism protein degradation multicellular organismal protein catabolic process biological_process pheromone catabolic process pheromone catabolism This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children. protein catabolic process The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. extracellular matrix organisation biological_process extracellular matrix organization and biogenesis extracellular matrix organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. GOC:mah extracellular matrix organization and biogenesis GOC:mah Binds to and modulates the activity of an enzyme. GO:0010576 catalytic regulator activity enzyme modulator metalloenzyme regulator activity molecular_function 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'. enzyme regulator activity Binds to and modulates the activity of an enzyme. GOC:dph GOC:mah GOC:tb catalytic regulator activity GOC:dph The process in which peroxisomes are delivered to a type of vacuole and degraded in response to changing nutrient conditions. peroxisome degradation biological_process pexophagy autophagy of peroxisome The process in which peroxisomes are delivered to a type of vacuole and degraded in response to changing nutrient conditions. GOC:autophagy PMID:10547367 PMID:20083110 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. GO:0005529 sugar binding molecular_function selectin carbohydrate binding 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. GOC:mah A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space. cellular_component 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'. external encapsulating structure 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 The controlled breakdown of any cell membrane in the context of a normal process such as autophagy. membrane breakdown membrane catabolism membrane degradation biological_process membrane disassembly The controlled breakdown of any cell membrane in the context of a normal process such as autophagy. GOC:mah The directed movement of the nucleus along microtubules within the cell, mediated by motor proteins. GO:0000065 nuclear movement, microtubule-mediated nucleus migration microtubule cytoskeleton-dependent nuclear positioning microtubule cytoskeleton-dependent nucleus positioning microtubule-dependent nuclear positioning microtubule-dependent nucleus positioning microtubule-mediated nuclear migration nuclear migration, microtubule-mediated transport of nucleus by microtubules transport of nucleus, microtubule-mediated biological_process nuclear migration along microtubule The directed movement of the nucleus along microtubules within the cell, mediated by motor proteins. GOC:mah GOC:sgd_curators The codon binding activity of a tRNA that positions an activated amino acid, mediating its insertion at the correct point in the sequence of a nascent polypeptide chain during protein synthesis. molecular_function tRNA transfer RNA Note that this term can be used in place of the obsolete term 'transfer RNA ; GO:0005563'. triplet codon-amino acid adaptor activity The codon binding activity of a tRNA that positions an activated amino acid, mediating its insertion at the correct point in the sequence of a nascent polypeptide chain during protein synthesis. GOC:hjd GOC:mtg_MIT_16mar07 ISBN:0198506732 Specifies the site of a posttranscriptional modification in an RNA molecule by base pairing with a short sequence around the target residue. molecular_function Note that this term describes the activity of a nucleic acid, usually RNA, gene product that interacts with other RNA molecules via base pairing; it should not be used to annotate proteins. RNA modification guide activity Specifies the site of a posttranscriptional modification in an RNA molecule by base pairing with a short sequence around the target residue. GOC:mah PMID:12457565 The binding activity of a protein that brings together another macromolecule in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid. https://github.com/geneontology/go-ontology/issues/18655 protein binding, bridging protein-protein adaptor molecular_function protein-macromolecule adaptor activity The binding activity of a protein that brings together another macromolecule in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid. GOC:bf GOC:mah GOC:vw The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. biological_process cytoskeleton-dependent intracellular transport The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. GOC:mah 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. cellular_component retromer complex 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 The directed movement of unfolded or misfolded proteins from the endoplasmic reticulum to the cytosol through the translocon. protein dislocation from ER protein retrotranslocation, ER to cytosol retrograde protein transport, endoplasmic reticulum to cytosol biological_process retrograde protein transport, ER to cytosol The directed movement of unfolded or misfolded proteins from the endoplasmic reticulum to the cytosol through the translocon. PMID:11994744 protein dislocation from ER GOC:dph GOC:krc protein retrotranslocation, ER to cytosol GOC:bf A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. intraflagellar transport complex intraflagellar transport particle cellular_component IFT complex Note that we deem cilia and microtubule-based flagella to be equivalent. intraciliary transport particle 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 A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. GO:0005578 NIF_Subcellular:nlx_subcell_20090513 Wikipedia:Extracellular_matrix proteinaceous extracellular matrix matrisome cellular_component extracellular matrix 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 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. microtubule organising center organisation biological_process microtubule organizing center organization and biogenesis microtubule organizing center organization 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 microtubule organizing center organization and biogenesis GOC:mah A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. NIF_Subcellular:sao830981606 cellular_component intracellular membrane organelle membrane A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GOC:dos GOC:mah intracellular membrane NIF_Subcellular:sao830981606 Assembly or disassembly of microtubules by the addition or removal of tubulin heterodimers from a microtubule. biological_process microtubule polymerization or depolymerization Assembly or disassembly of microtubules by the addition or removal of tubulin heterodimers from a microtubule. GOC:mah Any process that modulates the frequency, rate or extent of microtubule polymerization or depolymerization by the addition or removal of tubulin heterodimers from a microtubule. biological_process regulation of microtubule polymerization or depolymerization Any process that modulates the frequency, rate or extent of microtubule polymerization or depolymerization by the addition or removal of tubulin heterodimers from a microtubule. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization or depolymerization. down regulation of microtubule polymerization or depolymerization down-regulation of microtubule polymerization or depolymerization downregulation of microtubule polymerization or depolymerization inhibition of microtubule polymerization or depolymerization biological_process negative regulation of microtubule polymerization or depolymerization Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization or depolymerization. GOC:mah Any process that activates or increases the frequency, rate or extent of microtubule polymerization or depolymerization. up regulation of microtubule polymerization or depolymerization up-regulation of microtubule polymerization or depolymerization upregulation of microtubule polymerization or depolymerization activation of microtubule polymerization or depolymerization stimulation of microtubule polymerization or depolymerization biological_process positive regulation of microtubule polymerization or depolymerization Any process that activates or increases the frequency, rate or extent of microtubule polymerization or depolymerization. GOC:mah Any process that modulates the frequency, rate or extent of microtubule polymerization. biological_process regulation of microtubule polymerization Any process that modulates the frequency, rate or extent of microtubule polymerization. GOC:mah Any process that modulates the frequency, rate or extent of microtubule depolymerization. regulation of microtubule disassembly biological_process regulation of microtubule depolymerization Any process that modulates the frequency, rate or extent of microtubule depolymerization. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization. down regulation of microtubule polymerization down-regulation of microtubule polymerization downregulation of microtubule polymerization inhibition of microtubule polymerization biological_process negative regulation of microtubule polymerization Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization. GOC:mah Any process that activates or increases the frequency, rate or extent of microtubule polymerization. up regulation of microtubule polymerization up-regulation of microtubule polymerization upregulation of microtubule polymerization activation of microtubule polymerization stimulation of microtubule polymerization biological_process positive regulation of microtubule polymerization Any process that activates or increases the frequency, rate or extent of microtubule polymerization. GOC:mah Any process that activates or increases the frequency, rate or extent of microtubule depolymerization. microtubule destabilization positive regulation of microtubule disassembly up regulation of microtubule depolymerization up-regulation of microtubule depolymerization upregulation of microtubule depolymerization activation of microtubule depolymerization positive regulation of microtubule catastrophe stimulation of microtubule depolymerization biological_process positive regulation of microtubule depolymerization Any process that activates or increases the frequency, rate or extent of microtubule depolymerization. GOC:mah positive regulation of microtubule catastrophe GOC:dph GOC:tb A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell. cytoplasmic microtubule organisation biological_process cytoplasmic microtubule organization and biogenesis cytoplasmic microtubule organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell. GOC:mah cytoplasmic microtubule organization and biogenesis GOC:mah Any process in which the proteasome is transported to, or maintained in, a specific location. establishment and maintenance of proteasome localization proteasome localisation biological_process proteasome localization Any process in which the proteasome is transported to, or maintained in, a specific location. GOC:mah proteasome localisation GOC:mah The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane. intrinsic to membrane cellular_component Note that proteins intrinsic to membranes cannot be removed without disrupting the membrane, e.g. by detergent. intrinsic component of membrane The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane. GOC:mah The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. intrinsic to plasma membrane cellular_component intrinsic component of plasma membrane The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. GOC:dos GOC:mah Catalysis of the reaction: ATP + H2O + amine(out) = ADP + phosphate + amine(in). ATP-dependent amine transporter activity amine-transporting ATPase activity amine ABC transporter molecular_function ATPase-coupled amine transporter activity Catalysis of the reaction: ATP + H2O + amine(out) = ADP + phosphate + amine(in). GOC:mlg The component of the organelle membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. intrinsic to organelle membrane cellular_component intrinsic component of organelle membrane The component of the organelle membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane. GOC:dos GOC:mah The component of the organelle membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. integral to organelle membrane cellular_component integral component of organelle membrane The component of the organelle membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. GOC:dos GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. regulation of cellular metabolism biological_process regulation of cellular metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. down regulation of cellular metabolic process down-regulation of cellular metabolic process downregulation of cellular metabolic process negative regulation of cellular metabolism inhibition of cellular metabolic process biological_process negative regulation of cellular metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. positive regulation of cellular metabolism up regulation of cellular metabolic process up-regulation of cellular metabolic process upregulation of cellular metabolic process activation of cellular metabolic process stimulation of cellular metabolic process biological_process positive regulation of cellular metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. regulation of cellular anabolism regulation of cellular biosynthesis regulation of cellular formation regulation of cellular synthesis biological_process regulation of cellular biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. down regulation of cellular biosynthetic process down-regulation of cellular biosynthetic process downregulation of cellular biosynthetic process negative regulation of cellular anabolism negative regulation of cellular biosynthesis negative regulation of cellular formation negative regulation of cellular synthesis inhibition of cellular biosynthetic process biological_process negative regulation of cellular biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. positive regulation of cellular anabolism positive regulation of cellular biosynthesis positive regulation of cellular formation positive regulation of cellular synthesis up regulation of cellular biosynthetic process up-regulation of cellular biosynthetic process upregulation of cellular biosynthetic process activation of cellular biosynthetic process stimulation of cellular biosynthetic process biological_process positive regulation of cellular biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. regulation of cellular breakdown regulation of cellular catabolism regulation of cellular degradation biological_process regulation of cellular catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. down regulation of cellular catabolic process down-regulation of cellular catabolic process downregulation of cellular catabolic process negative regulation of cellular breakdown negative regulation of cellular catabolism negative regulation of cellular degradation inhibition of cellular catabolic process biological_process negative regulation of cellular catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. positive regulation of cellular breakdown positive regulation of cellular catabolism positive regulation of cellular degradation up regulation of cellular catabolic process up-regulation of cellular catabolic process upregulation of cellular catabolic process activation of cellular catabolic process stimulation of cellular catabolic process biological_process positive regulation of cellular catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly. down regulation of protein complex assembly down-regulation of protein complex assembly downregulation of protein complex assembly inhibition of protein complex assembly biological_process negative regulation of protein complex assembly negative regulation of protein-containing complex assembly Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly. GOC:mah Any process that activates or increases the frequency, rate or extent of protein complex assembly. up regulation of protein complex assembly up-regulation of protein complex assembly upregulation of protein complex assembly activation of protein complex assembly stimulation of protein complex assembly biological_process positive regulation of protein complex assembly positive regulation of protein-containing complex assembly Any process that activates or increases the frequency, rate or extent of protein complex assembly. GOC:mah Any process that modulates the frequency, rate or extent of vesicle fusion. biological_process regulation of vesicle fusion Any process that modulates the frequency, rate or extent of vesicle fusion. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion. down regulation of vesicle fusion down-regulation of vesicle fusion downregulation of vesicle fusion inhibition of vesicle fusion biological_process negative regulation of vesicle fusion Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion. GOC:mah Any process that activates or increases the frequency, rate or extent of vesicle fusion. up regulation of vesicle fusion up-regulation of vesicle fusion upregulation of vesicle fusion activation of vesicle fusion stimulation of vesicle fusion biological_process positive regulation of vesicle fusion Any process that activates or increases the frequency, rate or extent of vesicle fusion. GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. regulation of cell projection organisation biological_process regulation of cell projection organization and biogenesis regulation of cell projection organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah regulation of cell projection organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. down regulation of cell projection organization down-regulation of cell projection organization downregulation of cell projection organization negative regulation of cell projection organisation inhibition of cell projection organization biological_process negative regulation of cell projection organization and biogenesis negative regulation of cell projection organization Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah down regulation of cell projection organization GOC:mah negative regulation of cell projection organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. positive regulation of cell projection organisation up regulation of cell projection organization up-regulation of cell projection organization upregulation of cell projection organization activation of cell projection organization stimulation of cell projection organization biological_process positive regulation of cell projection organization and biogenesis positive regulation of cell projection organization Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah positive regulation of cell projection organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. biological_process regulation of protein modification process Any process that modulates the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. GOC:mah GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. down regulation of protein modification down-regulation of protein modification downregulation of protein modification inhibition of protein modification biological_process negative regulation of protein modification process Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. GOC:mah GOC:tb Any process that activates or increases the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. up regulation of protein modification up-regulation of protein modification upregulation of protein modification activation of protein modification stimulation of protein modification biological_process positive regulation of protein modification process Any process that activates or increases the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. GOC:mah GOC:tb Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). molecular_function carboxylic acid binding 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 A vesicle found in the cytoplasm of a cell. GO:0016023 NIF_Subcellular:sao180601769 cellular_component cytoplasmic membrane bounded vesicle cytoplasmic membrane-enclosed vesicle cytoplasmic, membrane-bounded vesicle cytoplasmic vesicle A vesicle found in the cytoplasm of a cell. GOC:ai GOC:mah GOC:vesicles Any process that modulates the frequency, rate or extent of mRNA cleavage, any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. biological_process regulation of mRNA cleavage Any process that modulates the frequency, rate or extent of mRNA cleavage, any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of mRNA cleavage. down regulation of mRNA cleavage down-regulation of mRNA cleavage downregulation of mRNA cleavage inhibition of mRNA cleavage biological_process negative regulation of mRNA cleavage Any process that stops, prevents, or reduces the frequency, rate or extent of mRNA cleavage. GOC:mah Any process that activates or increases the frequency, rate or extent of mRNA cleavage. up regulation of mRNA cleavage up-regulation of mRNA cleavage upregulation of mRNA cleavage activation of mRNA cleavage stimulation of mRNA cleavage biological_process positive regulation of mRNA cleavage Any process that activates or increases the frequency, rate or extent of mRNA cleavage. GOC:mah A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. establishment and maintenance of protein complex localization protein complex localisation biological_process protein complex localization protein-containing complex localization A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. GOC:mah protein complex localisation GOC:mah A proteasome found in the nucleus of a cell. cellular_component nuclear proteasome complex A proteasome found in the nucleus of a cell. GOC:mah Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system. regulation of neurological process regulation of neurological system process regulation of neurophysiological process biological_process regulation of nervous system process Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system. GOC:dph GOC:mah GOC:tb regulation of neurological process GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process. down regulation of neurological process down-regulation of neurological process downregulation of neurological process negative regulation of neurological process negative regulation of neurological system process negative regulation of neurophysiological process inhibition of neurological process biological_process negative regulation of nervous system process Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process. GOC:dph GOC:mah GOC:tb negative regulation of neurological process GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of a neurophysiological process. positive regulation of neurological process positive regulation of neurological system process positive regulation of neurophysiological process up regulation of neurological process up-regulation of neurological process upregulation of neurological process activation of neurological process stimulation of neurological process biological_process positive regulation of nervous system process Any process that activates or increases the frequency, rate or extent of a neurophysiological process. GOC:dph GOC:mah GOC:tb positive regulation of neurological process GOC:dph GOC:tb The directed movement of a lipid droplet along a microtubule, mediated by motor proteins. adiposome transport along microtubule lipid body transport along microtubule lipid particle transport along microtubule biological_process lipid droplet transport along microtubule The directed movement of a lipid droplet along a microtubule, mediated by motor proteins. PMID:9491895 A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. cellular_component organelle envelope A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. GOC:mah GOC:pz The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. cellular_component membrane-enclosed lumen The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. GOC:add GOC:mah A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. cellular_component envelope A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. GOC:mah GOC:pz Any thylakoid within a plastid. cellular_component plastid thylakoid Any thylakoid within a plastid. GOC:pz The volume enclosed by the nuclear inner membrane. cellular_component nuclear lumen The volume enclosed by the nuclear inner membrane. GOC:mah GOC:pz Any small, fluid-filled, spherical organelle enclosed by membrane. GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component membrane-bounded vesicle membrane-enclosed vesicle vesicle Any small, fluid-filled, spherical organelle enclosed by membrane. GOC:mah GOC:pz GOC:vesicles A compartment that consists of a lumen and an enclosing membrane, and is part of an organelle. suborganelle compartment cellular_component Note that this term refers to membrane-bounded compartments that are not considered organelles in their own right, but form parts of larger organelles. organelle subcompartment A compartment that consists of a lumen and an enclosing membrane, and is part of an organelle. GOC:mah GOC:pz The chemical reactions and pathways involving mitochondrial DNA. mitochondrial DNA metabolism mtDNA metabolic process mtDNA metabolism biological_process mitochondrial DNA metabolic process The chemical reactions and pathways involving mitochondrial DNA. GOC:mah The chemical reactions and pathways resulting in the breakdown of mitochondrial DNA. mitochondrial DNA breakdown mitochondrial DNA catabolism mitochondrial DNA degradation mtDNA breakdown mtDNA catabolic process mtDNA catabolism mtDNA degradation biological_process mitochondrial DNA catabolic process The chemical reactions and pathways resulting in the breakdown of mitochondrial DNA. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ciliary basal body, a short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum). microtubule basal body organisation microtubule basal body organization biological_process microtubule basal body organization and biogenesis ciliary basal body organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ciliary basal body, a short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum). GOC:cilia GOC:dph GOC:jl GOC:krc GOC:mah PMID:9889124 microtubule basal body organisation GOC:mah microtubule basal body organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids. biological_process nuclease regulator activity regulation of nuclease activity Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids. GOC:mah Any process that modulates the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. biological_process DNase regulator deoxyribonuclease regulator regulation of deoxyribonuclease activity Any process that modulates the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids. down regulation of nuclease activity down-regulation of nuclease activity downregulation of nuclease activity inhibition of nuclease activity biological_process nuclease inhibitor negative regulation of nuclease activity Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids. GOC:mah Any process that activates or increases the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids. up regulation of nuclease activity up-regulation of nuclease activity upregulation of nuclease activity activation of nuclease activity stimulation of nuclease activity biological_process nuclease activator positive regulation of nuclease activity Any process that activates or increases the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids. GOC:mah Any process that stops or reduces the rate of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. down regulation of deoxyribonuclease activity down-regulation of deoxyribonuclease activity downregulation of deoxyribonuclease activity inhibition of deoxyribonuclease activity biological_process DNase inhibitor deoxyribonuclease inhibitor negative regulation of deoxyribonuclease activity Any process that stops or reduces the rate of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah Any process that activates or increases the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. up regulation of deoxyribonuclease activity up-regulation of deoxyribonuclease activity upregulation of deoxyribonuclease activity activation of deoxyribonuclease activity stimulation of deoxyribonuclease activity biological_process DNase activator deoxyribonuclease activator positive regulation of deoxyribonuclease activity Any process that activates or increases the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. down regulation of protein binding down-regulation of protein binding downregulation of protein binding inhibition of protein binding biological_process negative regulation of protein binding Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. GOC:mah Any process that activates or increases the frequency, rate or extent of protein binding. up regulation of protein binding up-regulation of protein binding upregulation of protein binding activation of protein binding stimulation of protein binding biological_process positive regulation of protein binding Any process that activates or increases the frequency, rate or extent of protein binding. GOC:mah Interacting selectively and non-covalently with a small conjugating protein such as ubiquitin or a ubiquitin-like protein. small conjugating protein binding molecular_function ubiquitin-like protein binding Interacting selectively and non-covalently with a small conjugating protein such as ubiquitin or a ubiquitin-like protein. GOC:mah small conjugating protein binding GOC:dph Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites. Wikipedia:Transposon biological_process transposition Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites. GOC:jp ISBN:1555812090 Any process that modulates the frequency, rate or extent of 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. biological_process regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport regulation of nucleobase-containing compound transport Any process that modulates the frequency, rate or extent of 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:mah regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of 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. down regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport downregulation of nucleobase, nucleoside, nucleotide and nucleic acid transport inhibition of nucleobase, nucleoside, nucleotide and nucleic acid transport biological_process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport negative regulation of nucleobase-containing compound transport Any process that stops, prevents, or reduces the frequency, rate or extent of 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:mah negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of 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. up regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport upregulation of nucleobase, nucleoside, nucleotide and nucleic acid transport activation of nucleobase, nucleoside, nucleotide and nucleic acid transport stimulation of nucleobase, nucleoside, nucleotide and nucleic acid transport biological_process positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport positive regulation of nucleobase-containing compound transport Any process that activates or increases the frequency, rate or extent of 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:mah positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. regulation of cellular protein metabolism biological_process regulation of cellular protein metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. down regulation of cellular protein metabolic process down-regulation of cellular protein metabolic process downregulation of cellular protein metabolic process negative regulation of cellular protein metabolism inhibition of cellular protein metabolic process biological_process negative regulation of cellular protein metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. positive regulation of cellular protein metabolism up regulation of cellular protein metabolic process up-regulation of cellular protein metabolic process upregulation of cellular protein metabolic process activation of cellular protein metabolic process stimulation of cellular protein metabolic process biological_process positive regulation of cellular protein metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. GOC:mah Any process that modulates the frequency, rate or extent of the process of creating protein polymers. regulation of protein polymerisation biological_process regulation of protein polymerization Any process that modulates the frequency, rate or extent of the process of creating protein polymers. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the process of creating protein polymers. down regulation of protein polymerization down-regulation of protein polymerization downregulation of protein polymerization inhibition of protein polymerization biological_process negative regulation of protein polymerization Any process that stops, prevents, or reduces the frequency, rate or extent of the process of creating protein polymers. GOC:mah Any process that activates or increases the frequency, rate or extent of the process of creating protein polymers. up regulation of protein polymerization up-regulation of protein polymerization upregulation of protein polymerization activation of protein polymerization stimulation of protein polymerization biological_process positive regulation of protein polymerization Any process that activates or increases the frequency, rate or extent of the process of creating protein polymers. GOC:mah The directed movement of lipids within cells. biological_process intracellular lipid transport The directed movement of lipids within cells. GOC:mah Any process that modulates the frequency, rate or extent of 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. biological_process regulation of lipid transport Any process that modulates the frequency, rate or extent of 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. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of 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. down regulation of lipid transport down-regulation of lipid transport downregulation of lipid transport inhibition of lipid transport biological_process negative regulation of lipid transport Any process that stops, prevents, or reduces the frequency, rate or extent of 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. GOC:mah Any process that activates or increases the frequency, rate or extent of 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. up regulation of lipid transport up-regulation of lipid transport upregulation of lipid transport activation of lipid transport stimulation of lipid transport biological_process positive regulation of lipid transport Any process that activates or increases the frequency, rate or extent of 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. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells. biological_process regulation of intracellular lipid transport Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells. down regulation of intracellular lipid transport down-regulation of intracellular lipid transport downregulation of intracellular lipid transport inhibition of intracellular lipid transport biological_process negative regulation of intracellular lipid transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells. up regulation of intracellular lipid transport up-regulation of intracellular lipid transport upregulation of intracellular lipid transport activation of intracellular lipid transport stimulation of intracellular lipid transport biological_process positive regulation of intracellular lipid transport Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. biological_process regulation of intracellular transport Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. down regulation of intracellular transport down-regulation of intracellular transport downregulation of intracellular transport inhibition of intracellular transport biological_process negative regulation of intracellular transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. up regulation of intracellular transport up-regulation of intracellular transport upregulation of intracellular transport activation of intracellular transport stimulation of intracellular transport biological_process positive regulation of intracellular transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that modulates the activity of a transporter. biological_process regulation of transporter activity Any process that modulates the activity of a transporter. GOC:mah Any process that stops or reduces the activity of a transporter. down regulation of transporter activity down-regulation of transporter activity downregulation of transporter activity inhibition of transporter activity biological_process negative regulation of transporter activity Any process that stops or reduces the activity of a transporter. GOC:mah Any process that activates or increases the activity of a transporter. up regulation of transporter activity up-regulation of transporter activity upregulation of transporter activity activation of transporter activity stimulation of transporter activity biological_process positive regulation of transporter activity Any process that activates or increases the activity of a transporter. GOC:mah Any process that modulates the activity of an ion transporter. regulation of ion transporter activity biological_process regulation of ion transmembrane transporter activity Any process that modulates the activity of an ion transporter. GOC:mah GOC:tb regulation of ion transporter activity GOC:tb Any process that stops or reduces the activity of an ion transporter. down regulation of ion transporter activity down-regulation of ion transporter activity downregulation of ion transporter activity negative regulation of ion transporter activity inhibition of ion transporter activity biological_process negative regulation of ion transmembrane transporter activity Any process that stops or reduces the activity of an ion transporter. GOC:mah GOC:tb negative regulation of ion transporter activity GOC:tb Any process that activates or increases the activity of an ion transporter. positive regulation of ion transporter activity up regulation of ion transporter activity up-regulation of ion transporter activity upregulation of ion transporter activity activation of ion transporter activity stimulation of ion transporter activity biological_process positive regulation of ion transmembrane transporter activity Any process that activates or increases the activity of an ion transporter. GOC:mah GOC:tb positive regulation of ion transporter activity GOC:tb Any process in which a lysosome is transported to, and/or maintained in, a specific location. lysosome localisation biological_process lysosome localization Any process in which a lysosome is transported to, and/or maintained in, a specific location. GOC:mah lysosome localisation GOC:mah Any biological process, occurring at the level of a multicellular organism, pertinent to its function. janelomax 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GOC:curators GOC:dph GOC:isa_complete GOC:tb 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. janelomax 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process developmental process 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 The directed movement of proteins from the endoplasmic reticulum. protein exit from ER protein export from ER protein export from endoplasmic reticulum biological_process protein exit from endoplasmic reticulum The directed movement of proteins from the endoplasmic reticulum. GOC:rb protein export from ER GOC:mah protein export from endoplasmic reticulum GOC:mah The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code. mitochondrial protein anabolism mitochondrial protein biosynthesis mitochondrial protein formation mitochondrial protein synthesis mitochondrial protein translation biological_process mitochondrial translation The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code. GOC:go_curators The chemical reactions and pathways resulting in the formation of a protein in a plastid. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the plastid has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code. plastid protein anabolism plastid protein biosynthesis plastid protein formation plastid protein synthesis plastid protein translation biological_process plastid translation The chemical reactions and pathways resulting in the formation of a protein in a plastid. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the plastid has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code. GOC:go_curators The directed movement of a protein from one location to another within a lipid bilayer. protein translocation within membrane receptor translocation within membrane receptor transport within lipid bilayer biological_process protein transport within lipid bilayer The directed movement of a protein from one location to another within a lipid bilayer. GOC:mah The chemical reactions and pathways resulting in the formation of 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. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication. RNA anabolism RNA biosynthesis RNA formation RNA synthesis biological_process Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study. RNA biosynthetic process The chemical reactions and pathways resulting in the formation of 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. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication. GOC:mah GOC:txnOH Any process that stops or reduces the rate of ATP hydrolysis by an ATPase. down regulation of ATPase activity down-regulation of ATPase activity downregulation of ATPase activity negative regulation of adenosinetriphosphatase activity inhibition of ATPase activity biological_process negative regulation of ATPase activity Any process that stops or reduces the rate of ATP hydrolysis by an ATPase. GOC:mah Any process that activates or increases the rate of ATP hydrolysis by an ATPase. positive regulation of adenosinetriphosphatase activity up regulation of ATPase activity up-regulation of ATPase activity upregulation of ATPase activity activation of ATPase activity stimulation of ATPase activity biological_process positive regulation of ATPase activity Any process that activates or increases the rate of ATP hydrolysis by an ATPase. GOC:mah The disaggregation of a ribosome into its constituent components; includes the dissociation of ribosomal subunits. ribosome recycling biological_process ribosome dissociation factor ribosome disassembly The disaggregation of a ribosome into its constituent components; includes the dissociation of ribosomal subunits. GOC:mah GOC:vk ribosome recycling GOC:db PMID:9463391 All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. cellular_component plasma membrane bounded cell projection cytoplasm All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. GOC:krc GOC:mah Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion. biological_process regulation of karyogamy Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion. GOC:mah Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. regulation of localisation biological_process regulation of localization Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. GOC:mah regulation of localisation GOC:mah Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. regulation of protein localisation biological_process regulation of protein localization Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. GOC:dph GOC:mah GOC:tb regulation of protein localisation GOC:mah Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton. biological_process regulation of microtubule-based process Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process regulation of organic acid transport Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of organic acid transport down-regulation of organic acid transport downregulation of organic acid transport inhibition of organic acid transport biological_process negative regulation of organic acid transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of organic acid transport up-regulation of organic acid transport upregulation of organic acid transport activation of organic acid transport stimulation of organic acid transport biological_process positive regulation of organic acid transport Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah The controlled release of a substance by a cell. Wikipedia:Secretion cellular secretion biological_process secretion by cell The controlled release of a substance by a cell. GOC:mah The disaggregation of a protein-containing macromolecular complex into its constituent components. GO:0034623 GO:0043241 protein complex disassembly biological_process cellular macromolecule complex disassembly macromolecule complex disassembly protein-containing complex disassembly The disaggregation of a protein-containing macromolecular complex into its constituent components. GOC:mah The disaggregation of a protein-RNA complex into its constituent components. RNA-protein complex disassembly RNP complex disassembly protein-RNA complex disassembly biological_process ribonucleoprotein complex disassembly The disaggregation of a protein-RNA complex into its constituent components. GOC:mah The process in which cellular structures, including whole cells or cell parts, are generated and organized. cellular structure morphogenesis biological_process cellular component morphogenesis The process in which cellular structures, including whole cells or cell parts, are generated and organized. GOC:dph GOC:mah GOC:tb cellular structure morphogenesis GOC:dph GOC:tb The process in which the anatomical structures of a cell part are generated and organized. biological_process cell part morphogenesis The process in which the anatomical structures of a cell part are generated and organized. GOC:mah Any process in which a macromolecule is transported to, or maintained in, a specific location. macromolecule localisation biological_process macromolecule localization Any process in which a macromolecule is transported to, or maintained in, a specific location. GOC:mah macromolecule localisation GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. regulation of organelle organisation biological_process regulation of organelle organization and biogenesis regulation of organelle organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:mah regulation of organelle organisation GOC:mah regulation of organelle organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome. regulation of chromosome organisation biological_process regulation of chromosome organization and biogenesis regulation of chromosome organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome. GOC:mah regulation of chromosome organisation GOC:mah regulation of chromosome organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. biological_process regulation of intracellular protein transport Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines. regulation of amine metabolism biological_process regulation of cellular amine metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines. negative regulation of amine metabolism biological_process negative regulation of cellular amine metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines. positive regulation of amine metabolism biological_process positive regulation of cellular amine metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. regulation of amine breakdown regulation of amine catabolism regulation of amine degradation biological_process regulation of cellular amine catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. negative regulation of amine breakdown negative regulation of amine catabolism negative regulation of amine degradation biological_process negative regulation of cellular amine catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. positive regulation of amine breakdown positive regulation of amine catabolism positive regulation of amine degradation biological_process positive regulation of cellular amine catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. GOC:mah Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + organic acid(out/in) = ADP + phosphate + organic acid(in/out). ATP-dependent organic acid transmembrane transporter activity organic acid-transporting ATPase activity molecular_function ATPase-coupled organic acid transmembrane transporter activity Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + organic acid(out/in) = ADP + phosphate + organic acid(in/out). GOC:mlg A process in which a protein is transported to, or maintained in, a location within an organelle. protein localisation to organelle protein localization in organelle biological_process protein localization to organelle A process in which a protein is transported to, or maintained in, a location within an organelle. GOC:mah protein localisation to organelle GOC:mah protein localization in organelle GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). biological_process 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. cellular response to stress Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. down regulation of kinase activity down-regulation of kinase activity downregulation of kinase activity inhibition of kinase activity kinase inhibitor biological_process negative regulation of kinase activity Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. up regulation of kinase activity up-regulation of kinase activity upregulation of kinase activity kinase activator stimulation of kinase activity biological_process positive regulation of kinase activity Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah A process in which a ribosome is transported to, and/or maintained in, a specific location. GO:0033753 biological_process establishment of ribosome localisation establishment of ribosome localization ribosome localisation ribosome localization A process in which a ribosome is transported to, and/or maintained in, a specific location. GOC:mah 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 lipid stimulus. biological_process response to lipid 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 lipid stimulus. GOC:sl Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + lipid(in) = ADP + phosphate + lipid(out). lipid-transporting ATPase activity ATP-dependent lipid transmembrane transporter activity molecular_function ATPase-coupled lipid transmembrane transporter activity Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + lipid(in) = ADP + phosphate + lipid(out). GOC:BHF GOC:rl A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus. midori 2011-02-14T02:26:36Z GO:0000042 GO:0072600 protein localisation in Golgi apparatus protein localization in Golgi apparatus establishment of protein localisation to Golgi establishment of protein localization in Golgi establishment of protein localization to Golgi establishment of protein localization to Golgi apparatus biological_process protein targeting to Golgi protein-Golgi targeting protein localization to Golgi apparatus A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus. GOC:mah protein localisation in Golgi apparatus GOC:mah establishment of protein localisation to Golgi GOC:mah establishment of protein localization to Golgi apparatus GOC:mah The process in which a carbohydrate is transported across a membrane. carbohydrate membrane transport transmembrane carbohydrate transport biological_process Note that this term is not intended for use in annotating lateral movement within membranes. carbohydrate transmembrane transport The process in which a carbohydrate is transported across a membrane. GOC:mah transmembrane carbohydrate transport GOC:dph GOC:tb A process in which an ion is transported across a membrane. GO:0099131 ion membrane transport transmembrane ion transport ATP hydrolysis coupled ion transmembrane transport biological_process Note that this term is not intended for use in annotating lateral movement within membranes. ion transmembrane transport A process in which an ion is transported across a membrane. GOC:mah transmembrane ion transport GOC:dph GOC:tb Any process that stops or reduces the rate of GTP hydrolysis by a GTPase. GO:0034259 GO:0034261 GO:1902264 GO:1902881 down regulation of GTPase activity down-regulation of GTPase activity downregulation of GTPase activity negative regulation of guanosinetriphosphatase activity down regulation of Rab GTPase activity down regulation of Ras GTPase activity down regulation of Rho GTPase activity down regulation of regulation of Ran GTPase activity down-regulation of Rab GTPase activity down-regulation of Ras GTPase activity down-regulation of Rho GTPase activity down-regulation of regulation of Ran GTPase activity downregulation of Rab GTPase activity downregulation of Ras GTPase activity downregulation of Rho GTPase activity downregulation of regulation of Ran GTPase activity inhibition of GTPase activity inhibition of Rab GTPase activity inhibition of Ras GTPase activity inhibition of Rho GTPase activity inhibition of regulation of Ran GTPase activity negative regulation of Rab GTPase activity negative regulation of Ran GTPase activity negative regulation of Ras GTPase activity negative regulation of Rho GTPase activity biological_process An example of this is P2xA in Dictyostelium (UniProt symbol Q86JM7) in PMID:24335649. negative regulation of GTPase activity Any process that stops or reduces the rate of GTP hydrolysis by a GTPase. GOC:TermGenie GOC:mah GOC:rb GO_REF:0000058 PMID:16143306 PMID:24335649 down regulation of Rab GTPase activity GOC:pf down regulation of regulation of Ran GTPase activity GOC:TermGenie down-regulation of Rab GTPase activity GOC:pf down-regulation of regulation of Ran GTPase activity GOC:TermGenie downregulation of Rab GTPase activity GOC:pf downregulation of regulation of Ran GTPase activity GOC:TermGenie inhibition of Rab GTPase activity GOC:pf inhibition of regulation of Ran GTPase activity GOC:TermGenie A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction. biological_process cell junction assembly A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix. cell junction assembly and maintenance cell junction organisation biological_process cell junction biogenesis cell junction organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix. GOC:dph GOC:jl GOC:mah cell junction organisation GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lipid particle. https://github.com/geneontology/go-ontology/issues/13534 https://github.com/geneontology/go-ontology/issues/15963 lipid particle organization and biogenesis adiposome organization lipid body organization lipid particle organisation lipid particle organization biological_process lipid droplet organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lipid particle. GOC:dph GOC:jl GOC:mah PMID:18093937 PMID:18250201 lipid particle organization and biogenesis GOC:mah Any process that results in the conversion of one or more primary non-coding RNA (ncRNA) transcripts into one or more mature ncRNA molecules. biological_process ncRNA processing Any process that results in the conversion of one or more primary non-coding RNA (ncRNA) transcripts into one or more mature ncRNA molecules. GOC:mah The process in which a solute is transported from one side of the vacuolar membrane to the other. vacuolar membrane transport biological_process Note that this term is not intended for use in annotating lateral movement within membranes. vacuolar transmembrane transport The process in which a solute is transported from one side of the vacuolar membrane to the other. GOC:mah Any process in which a protein is transported to, or maintained at, a specific location on a chromosome. protein localisation to chromosome condensin localization to chromosome biological_process protein localization to chromosome Any process in which a protein is transported to, or maintained at, a specific location on a chromosome. GOC:mah protein localisation to chromosome GOC:mah A process in which a protein transports or maintains the localization of another protein to the nucleus. 2012-11-07T15:45:54Z GO:0044744 protein localisation to nucleus protein localization in cell nucleus protein localization in nucleus biological_process protein targeting to nucleus protein localization to nucleus A process in which a protein transports or maintains the localization of another protein to the nucleus. GOC:ecd protein localisation to nucleus GOC:mah protein localization in nucleus GOC:mah Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GO:0016249 cellular protein localisation channel localizer activity biological_process cellular protein localization Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:mah cellular protein localisation GOC:mah channel localizer activity GOC:mah The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell. GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly cellular protein-containing complex assembly The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell. GOC:jl A protein complex localization process that takes place at the cellular level; as a result, a protein complex is transported to, or maintained in, a specific location within a cell. cellular protein complex localisation establishment and maintenance of cellular protein complex localization biological_process cellular protein complex localization cellular protein-containing complex localization A protein complex localization process that takes place at the cellular level; as a result, a protein complex is transported to, or maintained in, a specific location within a cell. GOC:mah cellular protein complex localisation GOC:mah The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. cellular nitrogen compound metabolism biological_process cellular nitrogen compound metabolic process The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. GOC:mah The directed movement of the mitochondrion to a specific location, by a process involving microtubules. establishment of mitochondrion localisation, microtubule-mediated microtubule-mediated mitochondrion localization mitochondrial localization, microtubule-mediated biological_process establishment of mitochondrion localization, microtubule-mediated The directed movement of the mitochondrion to a specific location, by a process involving microtubules. GOC:mah PMID:12972644 PMID:15979253 PMID:16306220 establishment of mitochondrion localisation, microtubule-mediated GOC:mah 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, carried out by individual cells. GO:0034961 cellular biopolymer biosynthetic process cellular macromolecule anabolism cellular macromolecule biosynthesis cellular macromolecule formation cellular macromolecule synthesis biological_process cellular macromolecule biosynthetic process 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, carried out by individual cells. GOC:mah cellular biopolymer biosynthetic process GOC:mtg_chebi_dec09 cellular macromolecule anabolism GOC:mah cellular macromolecule biosynthesis GOC:mah cellular macromolecule formation GOC:mah cellular macromolecule synthesis GOC:mah The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid anabolism nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis nucleobase, nucleoside, nucleotide and nucleic acid formation nucleobase, nucleoside, nucleotide and nucleic acid synthesis biological_process nucleobase-containing compound biosynthetic process The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids. GOC:mah The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid breakdown nucleobase, nucleoside, nucleotide and nucleic acid catabolism nucleobase, nucleoside, nucleotide and nucleic acid degradation biological_process nucleobase, nucleoside, nucleotide and nucleic acid catabolic process nucleobase-containing compound catabolic process The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. GOC:mah nucleobase, nucleoside, nucleotide and nucleic acid catabolic process GOC:dph GOC:tb The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs). ncRNA metabolism biological_process ncRNA metabolic process The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs). GOC:mah The chemical reactions and pathways resulting in the breakdown of non-coding RNA transcripts (ncRNAs). Includes the breakdown of cryptic unstable transcripts (CUTs). ncRNA breakdown ncRNA catabolism ncRNA degradation biological_process ncRNA catabolic process The chemical reactions and pathways resulting in the breakdown of non-coding RNA transcripts (ncRNAs). Includes the breakdown of cryptic unstable transcripts (CUTs). GOC:rb PMID:18591258 A protein complex that possesses methyltransferase activity. cellular_component methyltransferase complex A protein complex that possesses methyltransferase activity. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. regulation of membrane transport biological_process regulation of transmembrane transport Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. down regulation of transmembrane transport down-regulation of transmembrane transport downregulation of transmembrane transport negative regulation of membrane transport inhibition of transmembrane transport biological_process negative regulation of transmembrane transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. positive regulation of membrane transport up regulation of transmembrane transport up-regulation of transmembrane transport upregulation of transmembrane transport activation of transmembrane transport stimulation of transmembrane transport biological_process positive regulation of transmembrane transport Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. regulation of ion membrane transport regulation of transmembrane ion transport biological_process regulation of ion transmembrane transport Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah regulation of transmembrane ion transport GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. down regulation of transmembrane ion transport down-regulation of transmembrane ion transport downregulation of transmembrane ion transport negative regulation of ion membrane transport negative regulation of transmembrane ion transport inhibition of transmembrane ion transport biological_process negative regulation of ion transmembrane transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah negative regulation of transmembrane ion transport GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. positive regulation of ion membrane transport positive regulation of transmembrane ion transport up regulation of transmembrane ion transport up-regulation of transmembrane ion transport upregulation of transmembrane ion transport activation of transmembrane ion transport stimulation of transmembrane ion transport biological_process positive regulation of ion transmembrane transport Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen. ER stress response cellular response to endoplasmic reticulum stress response to ER stress biological_process response to endoplasmic reticulum stress Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen. GOC:cjm GOC:mah The assembly and organization of an axoneme, 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. GO:0035083 GO:0035084 ciliary axoneme assembly cilium axoneme assembly flagellar axoneme assembly flagellum axoneme assembly biological_process axoneme biogenesis cilium axoneme biogenesis Note that cilia and eukaryotic flagella are deemed to be equivalent. axoneme assembly The assembly and organization of an axoneme, 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 GOC:jl ISBN:0815316194 axoneme biogenesis GOC:mah cilium axoneme biogenesis GOC:mah Any process that modulates the frequency, rate or extent of removal of phosphate groups from a molecule. biological_process regulation of dephosphorylation Any process that modulates the frequency, rate or extent of removal of phosphate groups from a molecule. GOC:bf Any process the stops, prevents, or reduces the frequency, rate or extent of removal of phosphate groups from a molecule. down regulation of dephosphorylation down-regulation of dephosphorylation downregulation of dephosphorylation inhibition of dephosphorylation biological_process negative regulation of dephosphorylation Any process the stops, prevents, or reduces the frequency, rate or extent of removal of phosphate groups from a molecule. GOC:bf Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a molecule. up regulation of dephosphorylation up-regulation of dephosphorylation upregulation of dephosphorylation activation of dephosphorylation stimulation of dephosphorylation biological_process positive regulation of dephosphorylation Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a molecule. GOC:bf A process in which a protein is transported to, or maintained at, a microtubule. rfoulger 2010-03-11T11:00:56Z protein localisation to microtubule biological_process protein localization to microtubule A process in which a protein is transported to, or maintained at, a microtubule. GOC:bf GOC:lb protein localisation to microtubule GOC:mah The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. rfoulger 2010-05-14T01:14:37Z GO:0007242 GO:0007243 GO:0023013 GO:0023034 intracellular signaling chain intracellular protein kinase cascade intracellular signal transduction pathway protein kinase cascade signal transmission via intracellular cascade biological_process intracellular signaling cascade intracellular signaling pathway signal transduction via intracellular signaling cascade intracellular signal transduction The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. GOC:bf GOC:jl GOC:signaling ISBN:3527303782 intracellular signaling chain ISBN:3527303782 intracellular protein kinase cascade GOC:signaling protein kinase cascade GOC:signaling intracellular signaling cascade GOC:signaling The directed movement of a protein to a specific location within the extracellular region. rfoulger 2010-11-09T10:25:08Z establishment of protein localisation in extracellular region establishment of protein localization in extracellular region biological_process establishment of protein localization to extracellular region The directed movement of a protein to a specific location within the extracellular region. GOC:BHF GOC:bf establishment of protein localisation in extracellular region GOC:mah The chemical reactions and pathways resulting in the breakdown of a mitochondrial protein. This process is necessary to maintain the healthy state of mitochondria and is thought to occur via the induction of an intramitochondrial lysosome-like organelle that acts to eliminate the damaged oxidised mitochondrial proteins without destroying the mitochondrial structure. rfoulger 2011-02-28T11:06:40Z catabolism of mitochondrial protein degradation of damaged mitochondrial protein biological_process mitochondrial protein catabolic process The chemical reactions and pathways resulting in the breakdown of a mitochondrial protein. This process is necessary to maintain the healthy state of mitochondria and is thought to occur via the induction of an intramitochondrial lysosome-like organelle that acts to eliminate the damaged oxidised mitochondrial proteins without destroying the mitochondrial structure. GOC:sp PMID:21264221 PMID:21264228 catabolism of mitochondrial protein GOC:bf degradation of damaged mitochondrial protein GOC:bf The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. rfoulger 2011-03-17T10:55:42Z intraflagellar transport Reactome:R-HSA-5620924.2 biological_process intraciliary transport involved in cilium morphogenesis intraflagellar transport involved in cilium morphogenesis intraciliary transport involved in cilium assembly The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. GOC:bf GOC:cilia Reactome:R-HSA-5620924.2 A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm. rfoulger 2011-05-25T03:09:58Z cilial transition zone cilium transition zone cellular_component connecting cilium Depending on the species, this region may have a distinct geometrically shaped electron-dense structure within the axonemal lumen visible in electron microscopy images; most animals don't display this inner structure. The axoneme extends through the ciliary transition zone, but only consists of the outer doublets. The central pair, axonemal spokes, and dynein complexes are not found in this part of the ciliary shaft. Note that the connecting cilium of the photoreceptor cells is thought to be equivalent to the transition zone. ciliary transition zone A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm. GOC:cilia GOC:kmv PMID:21422230 A process in which a protein is transported to, or maintained in, a location within an endosome. rfoulger 2011-10-06T02:42:18Z protein localisation in endosome protein localization in endosome biological_process protein localization to endosome A process in which a protein is transported to, or maintained in, a location within an endosome. GOC:yaf protein localisation in endosome GOC:bf A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport. rfoulger 2011-12-15T10:40:20Z GO:0005932 basal body NIF_Subcellular:sao11978067 cilial basal body cilium basal body microtubule basal body cellular_component In most eukaryotic cells, 'ciliary basal body' (GO:0036064) and 'centriole' (GO:0005814) represent a common entity that cycles through its function in cell division, then ciliogenesis, then cell division again. However, these structures are modified extensively as they transition into each other, and may contain different proteins, specific to each component. ciliary basal body A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport. GOC:cilia GOC:clt PMID:21750193 cilium basal body GOC:bf Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule. rfoulger 2012-01-17T04:20:34Z molecular_function Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule binding Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:pde GOC:pm The chemical reactions and pathways resulting in the breakdown of a histone protein by individual cells. rfoulger 2012-04-24T04:48:48Z histone protein catabolic process biological_process This term was created even though it describes a process relating to a group of gene products, because histones are highly conserved proteins that are essential components of cellular chromatin in eukaryotic cells. histone catabolic process The chemical reactions and pathways resulting in the breakdown of a histone protein by individual cells. GOC:krc histone protein catabolic process GOC:bf GOC:jl The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). rfoulger 2012-04-26T01:47:12Z protein modification biological_process protein modification process The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). GOC:bf GOC:jl protein modification GOC:bf Catalysis of the reaction: ATP + H2O = ADP + phosphate, which promotes unfolding of protein substrates, and channel opening of the core proteasome. rfoulger 2013-08-12T11:38:20Z ATPase involved in positive regulation of proteasomal protein catabolic process proteasomal ATPase activity proteasome channel gating activity proteasome channel opening activity molecular_function proteasome-activating ATPase activity Catalysis of the reaction: ATP + H2O = ADP + phosphate, which promotes unfolding of protein substrates, and channel opening of the core proteasome. GOC:rb PMID:11430818 ATPase involved in positive regulation of proteasomal protein catabolic process GOC:bf proteasomal ATPase activity GOC:bf proteasome channel gating activity GOC:rb proteasome channel opening activity GOC:rb The protein catabolic pathway which targets endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. It begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein modifications necessary for correct substrate transfer (e.g. ubiquitination), transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome. rebeccafoulger 2015-05-14T11:43:06Z endoplasmic reticulum-associated degradation protein degradation by ERAD biological_process ER-associated degradation pathway endoplasmic reticulum-associated protein degradation pathway ER-associated protein degradation (ERAD) pathways target misfolded ER lumenal proteins (ERAD-L), ER membrane proteins (ERAD-M), and ER proteins with misfolded cytosolic domains (ERAD-C) by recognizing aberrant proteins, retrotranslocating these substrates to the cytosol, followed by substrate ubiquitination and proteosomal-mediated degradation. In contrast the stress-induced homeostatically regulated protein degradation (SHRED) pathway (GO:0120174), although inducible by stress, targets diverse ER membrane, and cytosolic proteins as well as numerous other native proteins in the absence of stress. Stress results in the protease-mediated (Nma111p) generation of a Roq1p cleavage product that then binds to the type-1 active site of Ubr1p, altering its substrate specificity, and leading to the proteasome-mediated degradation of both misfolded and native proteins. Although the SHRED pathway may contain some components in common with ERAD pathways (GO:0036503), such as UBR1, RAD6 and CDC48, other ERAD components, such as HRD1 and DOA10, do not appear to be involved, and as such these pathways are currently considered to be distinct. ERAD pathway The protein catabolic pathway which targets endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. It begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein modifications necessary for correct substrate transfer (e.g. ubiquitination), transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome. GOC:PARL GOC:bf PMID:20940304 PMID:21969857 endoplasmic reticulum-associated degradation PMID:22535891 protein degradation by ERAD GOC:bf ER-associated degradation pathway PMID:24699081 endoplasmic reticulum-associated protein degradation pathway GOC:bf The increase in size or mass of an entire organism, a part of an organism or a cell. GO:0048590 biological_process growth pattern non-developmental growth See also the biological process term 'cell growth ; GO:0016049'. growth The increase in size or mass of an entire organism, a part of an organism or a cell. GOC:bf GOC:ma non-developmental growth GOC:mah Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. biological_process regulation of growth Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. GOC:ems GOC:mah Self-propelled movement of a cell or organism from one location to another. biological_process locomotion Self-propelled movement of a cell or organism from one location to another. GOC:dgh Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. biological_process regulation of locomotion Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. GOC:ems Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. down regulation of locomotion down-regulation of locomotion downregulation of locomotion inhibition of locomotion biological_process negative regulation of locomotion Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. up regulation of locomotion up-regulation of locomotion upregulation of locomotion activation of locomotion stimulation of locomotion biological_process positive regulation of locomotion Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of embryonic development. up regulation of embryonic development up-regulation of embryonic development upregulation of embryonic development activation of embryonic development stimulation of embryonic development biological_process positive regulation of embryonic development Any process that activates or increases the frequency, rate or extent of embryonic development. GOC:go_curators Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein. down regulation of mRNA translation, ncRNA-mediated down-regulation of mRNA translation, ncRNA-mediated downregulation of mRNA translation, ncRNA-mediated inhibition of mRNA translation, ncRNA-mediated biological_process negative regulation of translation, ncRNA-mediated Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein. GOC:dph GOC:ems GOC:tb The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. GO:0035734 Wikipedia:Intraflagellar_transport intraflagellar transport intraflagellar transport involved in cilium organization intraflagellar transport involved in microtubule-based flagellum organisation biological_process IFT Note that we deem cilium and microtubule-based flagellum to be equivalent. intraciliary transport The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. GOC:cilia GOC:kmv PMID:17981739 PMID:18180368 PMID:22869374 Reactome:R-HSA-5620924.2 Any process that modulates the frequency, rate or extent of cell proliferation. biological_process regulation of cell proliferation regulation of cell population proliferation Any process that modulates the frequency, rate or extent of cell proliferation. GOC:jl The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport. retrograde (endosome to Golgi) transport biological_process retrograde transport, endosome to Golgi The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport. GOC:jl PMID:10873832 PMID:16936697 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. regulation of protein breakdown regulation of protein catabolism regulation of protein degradation biological_process regulation of protein catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. GOC:go_curators GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. down regulation of protein catabolic process down-regulation of protein catabolic process downregulation of protein catabolic process negative regulation of protein breakdown negative regulation of protein catabolism negative regulation of protein degradation inhibition of protein catabolic process biological_process negative regulation of protein catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. GOC:go_curators GOC:jl PMID:10207076 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. ketone metabolism biological_process cellular ketone metabolic process 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 The chemical reactions and pathways resulting in the formation of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. ketone anabolism ketone biosynthesis ketone formation ketone synthesis biological_process ketone biosynthetic process The chemical reactions and pathways resulting in the formation of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. ketone breakdown ketone catabolism ketone degradation biological_process ketone catabolic process The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. GOC:go_curators Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. response to chemical stimulus response to chemical substance biological_process 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. response to chemical Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. GOC:jl response to chemical stimulus GOC:dos 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. GO:0007046 ribosome biogenesis and assembly biological_process ribosome biogenesis 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 The aggregation, arrangement and bonding together of the mature ribosome and of its subunits. GO:0042257 ribosomal subunit assembly biological_process ribosome assembly The aggregation, arrangement and bonding together of the mature ribosome and of its subunits. GOC:ma ribosomal subunit assembly GOC:mah GOC:vw Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. biological_process regulation of phosphorylation Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. GOC:jl Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. down regulation of phosphorylation down-regulation of phosphorylation downregulation of phosphorylation inhibition of phosphorylation biological_process negative regulation of phosphorylation Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. GOC:jl Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. up regulation of phosphorylation up-regulation of phosphorylation upregulation of phosphorylation activation of phosphorylation stimulation of phosphorylation biological_process positive regulation of phosphorylation Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. GOC:jl Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity. molecular_function histone-specific chaperone activity histone binding Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity. GOC:jl A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall. Includes biosynthesis of constituent macromolecules, such as proteins and polysaccharides, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. A cell wall is 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. cell wall assembly biological_process cell wall biogenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall. Includes biosynthesis of constituent macromolecules, such as proteins and polysaccharides, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. A cell wall is 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:jl GOC:mah GOC:mtg_sensu ISBN:0198506732 Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3. molecular_function phosphoric ester hydrolase activity Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3. GOC:jl Cytoplasmic organelles, spherical or oval in shape, that are bounded by a single membrane and contain oxidative enzymes, especially those utilizing hydrogen peroxide (H2O2). Wikipedia:Microbody cellular_component microbody 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 Any biological process involved in the maintenance of an internal steady state. GO:0032844 GO:0032845 GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process biological_process negative regulation of homeostatic process positive regulation of homeostatic process regulation of homeostatic process homeostatic process Any biological process involved in the maintenance of an internal steady state. GOC:jl ISBN:0395825172 Enables the transfer of an ion from one side of a membrane to the other, driven by the reaction: ATP + H2O = ADP + phosphate. ATP-dependent ion transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions ATPase coupled ion transmembrane transporter activity molecular_function ATPase-coupled ion transmembrane transporter activity Enables the transfer of an ion from one side of a membrane to the other, driven by the reaction: ATP + H2O = ADP + phosphate. GOC:jl GOC:mtg_transport ISBN:0815340729 Primary active transporter of a solute across a membrane, via the reaction: ATP + H2O = ADP + phosphate, to directly drive the transport of a substance across a membrane. The transport protein may be transiently phosphorylated (P-type transporters), or not (ABC-type transporters and other families of transporters). Primary active transport occurs up the solute's concentration gradient and is driven by a primary energy source. https://github.com/geneontology/go-ontology/issues/14642 https://github.com/geneontology/go-ontology/issues/17373 GO:0015405 GO:0016820 P-P-bond-hydrolysis-driven transmembrane transporter activity P-P-bond-hydrolysis-driven transporter EC:7.2.2 Reactome:R-HSA-266070 Reactome:R-HSA-5223313 Reactome:R-HSA-5362459 Reactome:R-HSA-5387389 Reactome:R-HSA-5683325 ATP-coupled transmembrane transporter activity ATP-dependent transmembrane transporter activity ATPase activity, coupled to transmembrane movement of substances hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances molecular_function ATPase-coupled transmembrane transporter activity Primary active transporter of a solute across a membrane, via the reaction: ATP + H2O = ADP + phosphate, to directly drive the transport of a substance across a membrane. The transport protein may be transiently phosphorylated (P-type transporters), or not (ABC-type transporters and other families of transporters). Primary active transport occurs up the solute's concentration gradient and is driven by a primary energy source. GOC:mtg_transport ISBN:0815340729 Reactome:R-HSA-266070 LTC4 is exported from the cytosol by ABCC1 Reactome:R-HSA-5223313 ABCD4 may transport Cbl from lysosomal lumen to cytosol Reactome:R-HSA-5362459 VCP-catalyzed ATP hydrolysis promotes the translocation of Hh-C into the cytosol Reactome:R-HSA-5387389 Hh processing variants are translocated to the cytosol in a VCP-dependent manner Reactome:R-HSA-5683325 Defective ABCD4 does not transport Cbl from lysosomal lumen to cytosol The region of a mitochondrion to which the DNA is confined. cellular_component mitochondrial nucleoid The region of a mitochondrion to which the DNA is confined. GOC:jl The region of a plastid to which the DNA is confined. cellular_component plastid nucleoid The region of a plastid to which the DNA is confined. GOC:jl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur. regulation of sulfur metabolism regulation of sulphur metabolic process regulation of sulphur metabolism biological_process regulation of sulfur metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur. GOC:go_curators A prolongation or process extending from a cell, e.g. a flagellum or axon. cell process cellular process cellular projection cellular_component cell projection A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl http://www.cogsci.princeton.edu/~wn/ Any process that modulates the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. biological_process regulation of Golgi to plasma membrane protein transport Any process that modulates the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. down regulation of Golgi to plasma membrane protein transport down-regulation of Golgi to plasma membrane protein transport downregulation of Golgi to plasma membrane protein transport inhibition of Golgi to plasma membrane protein transport biological_process negative regulation of Golgi to plasma membrane protein transport Any process that stops, prevents, or reduces the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. GOC:jl Any process that activates or increases the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. up regulation of Golgi to plasma membrane protein transport up-regulation of Golgi to plasma membrane protein transport upregulation of Golgi to plasma membrane protein transport activation of Golgi to plasma membrane protein transport stimulation of Golgi to plasma membrane protein transport biological_process positive regulation of Golgi to plasma membrane protein transport Any process that activates or increases the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. GOC:jl The directed movement of proteins from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane. biological_process Golgi to plasma membrane protein transport The directed movement of proteins from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane. ISBN:0716731363 Interacting selectively and non-covalently with any complex of RNA and protein. RNP binding protein-RNA complex binding ribonucleoprotein binding molecular_function ribonucleoprotein complex binding Interacting selectively and non-covalently with any complex of RNA and protein. GOC:bf GOC:go_curators GOC:vk protein-RNA complex binding GOC:bf GOC:vk ribonucleoprotein binding GOC:bf GOC:vk Interacting selectively and non-covalently with any part of a ribosome. GO:0030376 ribosome receptor activity molecular_function ribosome binding Interacting selectively and non-covalently with any part of a ribosome. GOC:go_curators 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. extracellular structure organisation extracellular structure organization and biogenesis biological_process extracellular structure organization 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 extracellular structure organization and biogenesis GOC:dph GOC:jl GOC:mah Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043070 regulation of non-apoptotic programmed cell death biological_process regulation of programmed cell death Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043071 up regulation of programmed cell death up-regulation of programmed cell death upregulation of programmed cell death activation of programmed cell death positive regulation of non-apoptotic programmed cell death stimulation of programmed cell death biological_process positive regulation of programmed cell death Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043072 down regulation of programmed cell death down-regulation of programmed cell death downregulation of programmed cell death inhibition of programmed cell death negative regulation of non-apoptotic programmed cell death biological_process negative regulation of programmed cell death Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process that activates or increases the activity of an enzyme. GO:0048554 positive regulation of enzyme activity up regulation of enzyme activity up-regulation of enzyme activity upregulation of enzyme activity activation of enzyme activity activation of metalloenzyme activity positive regulation of metalloenzyme activity stimulation of enzyme activity stimulation of metalloenzyme activity up regulation of metalloenzyme activity up-regulation of metalloenzyme activity upregulation of metalloenzyme activity biological_process positive regulation of catalytic activity Any process that activates or increases the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw positive regulation of enzyme activity GOC:tb Any process that stops or reduces the activity of an enzyme. GO:0048553 down regulation of enzyme activity down-regulation of enzyme activity down-regulation of metalloenzyme activity downregulation of enzyme activity negative regulation of enzyme activity down regulation of metalloenzyme activity downregulation of metalloenzyme activity inhibition of enzyme activity inhibition of metalloenzyme activity negative regulation of metalloenzyme activity biological_process negative regulation of catalytic activity Any process that stops or reduces the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw negative regulation of enzyme activity GOC:tb Any process that modulates the rate of GTP hydrolysis by a GTPase. GO:0032312 GO:0032313 GO:0032314 GO:0032315 GO:0032316 GO:0032317 GO:0032318 GO:0032319 GO:0043088 regulation of ARF GTPase activity regulation of Cdc42 GTPase activity regulation of Rab GTPase activity regulation of Rac GTPase activity regulation of Ral GTPase activity regulation of Ran GTPase activity regulation of Rap GTPase activity regulation of Ras GTPase activity regulation of Rho GTPase activity biological_process regulation of GTPase activity Any process that modulates the rate of GTP hydrolysis by a GTPase. GOC:jl GOC:mah Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location. establishment and maintenance of translational machinery localization establishment and maintenance of translational protein localization regulation of translation by machinery localisation translational machinery localization translational protein localization biological_process regulation of translation by machinery localization Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location. GOC:jl regulation of translation by machinery localisation GOC:mah translational machinery localization GOC:dph GOC:tb Interacting selectively and non-covalently with ions, charged atoms or groups of atoms. molecular_function atom binding ion binding Interacting selectively and non-covalently with ions, charged atoms or groups of atoms. GOC:jl 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. GO:0043283 GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism multicellular organismal macromolecule metabolic process biological_process macromolecule metabolic process 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. GOC:mah biopolymer metabolic process GOC:mtg_chebi_dec09 Interacting selectively and non-covalently with any organic compound that is weakly basic in character and contains an amino or a substituted amino group. molecular_function amine binding 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 Interacting selectively and non-covalently with an organic acid, any acidic compound containing carbon in covalent linkage. molecular_function organic acid binding Interacting selectively and non-covalently with an organic acid, any acidic compound containing carbon in covalent linkage. GOC:jl ISBN:0198506732 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O = ADP + phosphate, to directly drive the transport of carbohydrates across a membrane. ATP-dependent carbohydrate transmembrane transporter activity carbohydrate-transporting ATPase activity carbohydrate ABC transporter molecular_function ATPase-coupled carbohydrate transmembrane transporter activity Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O = ADP + phosphate, to directly drive the transport of carbohydrates across a membrane. GOC:mlg 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. NIF_Subcellular:sao1539965131 Wikipedia:Organelle cellular_component organelle 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 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. GOC:go_curators 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. cellular_component intracellular organelle 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 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. cellular_component extracellular organelle 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 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. intracellular membrane-enclosed organelle cellular_component intracellular membrane-bounded organelle 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 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. intracellular non-membrane-enclosed organelle cellular_component intracellular non-membrane-bounded organelle 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 The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. cellular_component organelle lumen The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. GOC:jl GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. down regulation of protein complex disassembly down-regulation of protein complex disassembly downregulation of protein complex disassembly inhibition of protein complex disassembly biological_process negative regulation of protein complex disassembly negative regulation of protein-containing complex disassembly Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. GOC:jl Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. up regulation of protein complex disassembly up-regulation of protein complex disassembly upregulation of protein complex disassembly activation of protein complex disassembly stimulation of protein complex disassembly biological_process positive regulation of protein complex disassembly positive regulation of protein-containing complex disassembly Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. GOC:jl Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. biological_process regulation of protein complex disassembly regulation of protein-containing complex disassembly Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. GOC:jl The aggregation, arrangement and bonding together of a mature, active proteasome complex. proteasome complex assembly proteasome maturation 26S proteasome assembly biological_process proteasome assembly The aggregation, arrangement and bonding together of a mature, active proteasome complex. GOC:go_curators PMID:10872471 Any process that modulates the frequency, rate or extent of protein complex assembly. biological_process regulation of protein complex assembly regulation of protein-containing complex assembly Any process that modulates the frequency, rate or extent of protein complex assembly. GOC:jl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates. regulation of carbohydrate anabolism regulation of carbohydrate biosynthesis regulation of carbohydrate formation regulation of carbohydrate synthesis biological_process regulation of carbohydrate biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates. GOC:jl Any process that modulates the frequency, rate or extent of 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. biological_process regulation of ion transport Any process that modulates the frequency, rate or extent of 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:jl Any process that activates or increases the frequency, rate or extent of 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. up regulation of ion transport up-regulation of ion transport upregulation of ion transport activation of ion transport stimulation of ion transport biological_process positive regulation of ion transport Any process that activates or increases the frequency, rate or extent of 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:jl Any process that stops, prevents, or reduces the frequency, rate or extent of 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. down regulation of ion transport down-regulation of ion transport downregulation of ion transport inhibition of ion transport biological_process negative regulation of ion transport Any process that stops, prevents, or reduces the frequency, rate or extent of 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:jl Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). up regulation of DNA binding up-regulation of DNA binding upregulation of DNA binding activation of DNA binding stimulation of DNA binding biological_process positive regulation of DNA binding Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). GOC:dph GOC:jl GOC:tb Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). down regulation of DNA binding down-regulation of DNA binding downregulation of DNA binding inhibition of DNA binding biological_process negative regulation of DNA binding Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). GOC:dph GOC:jl GOC:tb Any process that modulates the frequency, rate or extent of protein binding. biological_process regulation of protein binding Any process that modulates the frequency, rate or extent of protein binding. GOC:go_curators 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. biological_process macromolecule modification 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 Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription. 2011-07-15T10:56:12Z GO:1904168 GO:2000824 negative regulation of transcription factor activity down regulation of transcription factor activity down-regulation of transcription factor activity downregulation of transcription factor activity negative regulation of DNA binding transcription factor activity negative regulation of sequence-specific DNA binding transcription factor activity inhibition of transcription factor activity negative regulation of androgen receptor activity negative regulation of thyroid hormone receptor activity biological_process negative regulation of DNA-binding transcription factor activity Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription. GOC:jl negative regulation of transcription factor activity GOC:dph GOC:tb The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). keto acid metabolic process keto acid metabolism ketoacid metabolic process ketoacid metabolism oxo acid metabolic process oxo acid metabolism oxoacid metabolism biological_process oxoacid metabolic process The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). Wikipedia:Oxyacid Any process that modulates the frequency, rate or extent of secondary metabolism, the chemical reactions and pathways involving compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. regulation of secondary metabolism biological_process regulation of secondary metabolic process Any process that modulates the frequency, rate or extent of secondary metabolism, the chemical reactions and pathways involving compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. GOC:jl Any process that modulates the rate of ATP hydrolysis by an ATPase. regulation of adenosinetriphosphatase activity biological_process regulation of ATPase activity Any process that modulates the rate of ATP hydrolysis by an ATPase. GOC:jl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances. biological_process regulation of generation of precursor metabolites and energy Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances. GOC:jl Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates. biological_process regulation of carbohydrate catabolic process Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates. GOC:mlg The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. biological_process pigmentation The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. GOC:jl Any process that activates or increases the activity of a GTPase. GO:0032320 GO:0032321 GO:0032850 GO:0032851 GO:0032852 GO:0032853 GO:0032854 GO:0032855 GO:0043089 up regulation of GTPase activity up-regulation of GTPase activity upregulation of GTPase activity activation of GTPase activity positive regulation of ARF GTPase activity positive regulation of Cdc42 GTPase activity positive regulation of Rab GTPase activity positive regulation of Rac GTPase activity positive regulation of Ral GTPase activity positive regulation of Ran GTPase activity positive regulation of Rap GTPase activity positive regulation of Ras GTPase activity positive regulation of Rho GTPase activity stimulation of ARF GTPase activity stimulation of Cdc42 GTPase activity stimulation of GTPase activity stimulation of Rab GTPase activity stimulation of Rac GTPase activity stimulation of Ral GTPase activity stimulation of Ran GTPase activity stimulation of Rap GTPase activity stimulation of Ras GTPase activity stimulation of Rho GTPase activity up regulation of ARF GTPase activity up regulation of Cdc42 GTPase activity up regulation of Rab GTPase activity up regulation of Rac GTPase activity up regulation of Ral GTPase activity up regulation of Ran GTPase activity up regulation of Rap GTPase activity up regulation of Ras GTPase activity up regulation of Rho GTPase activity up-regulation of ARF GTPase activity up-regulation of Cdc42 GTPase activity up-regulation of Rab GTPase activity up-regulation of Rac GTPase activity up-regulation of Ral GTPase activity up-regulation of Ran GTPase activity up-regulation of Rap GTPase activity up-regulation of Ras GTPase activity up-regulation of Rho GTPase activity upregulation of ARF GTPase activity upregulation of Cdc42 GTPase activity upregulation of Rab GTPase activity upregulation of Rac GTPase activity upregulation of Ral GTPase activity upregulation of Ran GTPase activity upregulation of Rap GTPase activity upregulation of Ras GTPase activity upregulation of Rho GTPase activity biological_process positive regulation of GTPase activity Any process that activates or increases the activity of a GTPase. GOC:jl GOC:mah Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. biological_process regulation of kinase activity Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:bf Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. sequence specific DNA binding molecular_function sequence-specific DNA binding Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. GOC:jl The creation of two or more plastids by division of one plastid. A plastid is any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. biological_process plastid fission The creation of two or more plastids by division of one plastid. A plastid is any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. GOC:jl Transport of substances into, out of or within a peroxisome, a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules. biological_process peroxisomal transport Transport of substances into, out of or within a peroxisome, a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules. GOC:jl The disaggregation of a protein complex into its constituent components, occurring at the level of an individual cell. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups. biological_process cellular protein complex disassembly The disaggregation of a protein complex into its constituent components, occurring at the level of an individual cell. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups. GOC:jl Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. biological_process regulation of multi-organism process Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. biological_process negative regulation of multi-organism process Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. GOC:jl Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. biological_process positive regulation of multi-organism process Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species. GOC:jl Any process that modulates the frequency, rate or extent of symbiosis, an interaction between two organisms living together in more or less intimate association. https://github.com/geneontology/go-ontology/issues/19222 biological_process regulation of symbiosis, encompassing mutualism through parasitism regulation of interspecies interactions between organisms Any process that modulates the frequency, rate or extent of symbiosis, an interaction between two organisms living together in more or less intimate association. GOC:jl Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. midori 2010-09-08T10:01:42Z GO:0034600 GO:0034621 GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process cellular macromolecular complex organization cellular macromolecular complex subunit organisation cellular macromolecular complex subunit organization macromolecular complex organization macromolecular complex subunit organisation macromolecular complex subunit organization protein-containing complex subunit organization Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. GOC:mah protein complex subunit organisation GOC:mah A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves more than one organism. multi-organism metabolism multi-organismal metabolic process multi-organismal metabolism biological_process multi-organism metabolic process A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves more than one organism. GOC:jl A catabolic process - chemical reactions and pathways resulting in the breakdown of substances - which involves more than one organism. multi-organism catabolism multi-organismal catabolic process multi-organismal catabolism biological_process multi-organism catabolic process A catabolic process - chemical reactions and pathways resulting in the breakdown of substances - which involves more than one organism. GOC:jl The chemical reactions and pathways involving macromolecules forming, or destined to form, part of the cell wall. A cell wall is a 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. GO:0010382 cellular cell wall macromolecule metabolic process cellular cell wall macromolecule metabolism biological_process cell wall macromolecule metabolic process The chemical reactions and pathways involving macromolecules forming, or destined to form, part of the cell wall. A cell wall is a 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:jl GOC:mah The chemical reactions and pathways involving macromolecules forming, or destined to form, part of a cell wall, involving more than one organism. A cell wall is a 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. multi-organism cell wall macromolecule metabolism biological_process multi-organism cell wall macromolecule metabolic process The chemical reactions and pathways involving macromolecules forming, or destined to form, part of a cell wall, involving more than one organism. A cell wall is a 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 GOC:tair_curators multi-organism cell wall macromolecule metabolism GOC:mah The chemical reactions and pathways resulting in the formation of a macromolecule destined to form part of a cell wall. cell wall macromolecule anabolism cell wall macromolecule biosynthesis cell wall macromolecule biosynthetic process at cellular level cell wall macromolecule synthesis cellular cell wall macromolecule biosynthetic process biological_process cell wall macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule destined to form part of a cell wall. GOC:go_curators cell wall macromolecule anabolism GOC:mah cell wall macromolecule biosynthesis GOC:mah cell wall macromolecule biosynthetic process at cellular level GOC:mah cell wall macromolecule synthesis GOC:mah cellular cell wall macromolecule biosynthetic process GOC:mah The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, that involve more than one organism. multi-organism carbohydrate metabolism main pathways of carbohydrate metabolic process main pathways of carbohydrate metabolism biological_process multi-organism carbohydrate metabolic process The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, that involve more than one organism. GOC:jl The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, involving more than one organism. multi-organism carbohydrate breakdown multi-organism carbohydrate catabolism multi-organism carbohydrate degradation biological_process multi-organism carbohydrate catabolic process The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, involving more than one organism. GOC:jl Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system. biological_process regulation of system process Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system. GOC:jl 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. GO:0071843 cellular component biogenesis at cellular level biological_process cellular component biogenesis 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 Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process regulation of cellular component biogenesis Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. GOC:jl Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole. regulation of vacuole organisation biological_process regulation of vacuole biogenesis regulation of vacuole organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole. GOC:jl GOC:mah regulation of vacuole organisation GOC:mah regulation of vacuole biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process positive regulation of cellular component biogenesis Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. GOC:jl Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole. positive regulation of vacuole organisation biological_process positive regulation of vacuole biogenesis positive regulation of vacuole organization Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole. GOC:jl GOC:mah positive regulation of vacuole organisation GOC:mah positive regulation of vacuole biogenesis GOC:mah A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane. biological_process membrane biogenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane. GOC:jl Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jane 2009-04-21T04:07:27Z biological_process negative regulation of molecular function Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jane 2009-04-21T04:11:06Z biological_process positive regulation of molecular function Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group, as carried out by individual cells. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. jane 2009-07-15T11:55:44Z biological_process cellular amine metabolic process The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group, as carried out by individual cells. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. GOC:jl The progression of an organism from an initial condition to a later condition, occurring when the organism is in a symbiotic interaction. jane 2009-07-30T02:26:46Z GO:0044152 development on or near surface of other organism involved in symbiotic interaction biological_process development during symbiotic interaction development on or near surface of other organism during symbiotic interaction This term partially replaces the obsolete term 'growth or development during symbiotic interaction ; GO:0052171'. See also 'growth during symbiotic interaction ; GO:0044110'. development involved in symbiotic interaction The progression of an organism from an initial condition to a later condition, occurring when the organism is in a symbiotic interaction. GO:jl GOC:pamgo_curators development during symbiotic interaction gOC:dph development on or near surface of other organism during symbiotic interaction GOC:dph Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) that contributes to the process of protein folding. jane 2009-09-25T11:33:48Z chaperone activity protein binding involved in protein folding molecular_function protein folding chaperone Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) that contributes to the process of protein folding. GOC:mtg_cambridge_2009 A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). jane 2009-10-22T02:38:55Z translation initiation (ternary) complex Met-tRNA/eIF2.GTP ternary complex cellular_component translation initiation ternary complex A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). GOC:jl Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. kchris 2009-11-04T12:58:25Z GO:0000975 regulatory region DNA binding molecular_function To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA-binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". transcription regulatory region DNA binding Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. GOC:jl GOC:txnOH SO:0005836 The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. GOC:go_curators intermediary metabolism GOC:mah 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. primary metabolism biological_process primary metabolic process 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 The chemical reactions and pathways resulting in the breakdown of lipids, as carried out by individual cells. cellular lipid breakdown cellular lipid catabolism cellular lipid degradation biological_process cellular lipid catabolic process The chemical reactions and pathways resulting in the breakdown of lipids, as carried out by individual cells. GOC:jl The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. cellular breakdown cellular catabolism cellular degradation biological_process cellular catabolic process The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:jl The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. cellular anabolism cellular biosynthesis cellular formation cellular synthesis biological_process cellular biosynthetic process The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:jl The chemical reactions and pathways involving lipids, as carried out by individual cells. cellular lipid metabolism biological_process cellular lipid metabolic process The chemical reactions and pathways involving lipids, as carried out by individual cells. GOC:jl The chemical reactions and pathways resulting in the breakdown of a protein by individual cells. cellular protein breakdown cellular protein catabolism cellular protein degradation biological_process cellular protein catabolic process The chemical reactions and pathways resulting in the breakdown of a protein by individual cells. GOC:jl 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, as carried out by individual cells. GO:0034960 cellular biopolymer metabolic process cellular macromolecule metabolism biological_process cellular macromolecule metabolic process 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, as carried out by individual cells. GOC:mah cellular biopolymer metabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells. GO:0034962 cellular biopolymer catabolic process cellular macromolecule breakdown cellular macromolecule catabolism cellular macromolecule degradation biological_process cellular macromolecule catabolic process The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells. GOC:jl cellular biopolymer catabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification. cellular protein metabolism biological_process cellular protein metabolic process The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification. GOC:jl The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. nitrogen compound breakdown nitrogen compound catabolism nitrogen compound degradation biological_process cellular nitrogen compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. nitrogen compound anabolism nitrogen compound biosynthesis nitrogen compound formation nitrogen compound synthesis biological_process cellular nitrogen compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. sulfur compound anabolism sulfur compound biosynthesis sulfur compound formation sulfur compound synthesis sulfur biosynthesis sulfur biosynthetic process biological_process sulfur compound biosynthetic process The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. GOC:jl The chemical reactions and pathways resulting in the breakdown of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. sulfur compound breakdown sulfur compound catabolism sulfur compound degradation sulfur catabolic process sulfur catabolism biological_process sulfur compound catabolic process The chemical reactions and pathways resulting in the breakdown of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. GOC:jl A process that results in the breakdown of the cell wall. jane 2010-01-14T02:00:34Z GO:0060871 cellular cell wall disassembly biological_process cell wall disassembly A process that results in the breakdown of the cell wall. GOC:jl The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule. jane 2010-01-26T12:05:20Z small molecule metabolism biological_process Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule metabolic process The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:pde GOC:vw The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule. jane 2010-01-26T12:06:10Z small molecule catabolism biological_process Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule catabolic process The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:vw The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule. jane 2010-01-26T12:06:49Z small molecule biosynthesis biological_process Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule biosynthetic process The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:pde GOC:vw A process in which a protein is transported to, or maintained in, a location within the cytoskeleton. janelomax 2011-12-13T11:43:24Z protein localisation to cytoskeleton biological_process protein localization to cytoskeleton A process in which a protein is transported to, or maintained in, a location within the cytoskeleton. GOC:jl protein localisation to cytoskeleton GOC:mah A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts. https://github.com/geneontology/go-ontology/issues/14807 GO:0043298 GO:0044404 GO:0072519 GO:0085031 commensalism host-pathogen interaction parasitism biological_process symbiosis symbiosis, encompassing mutualism through parasitism symbiotic interaction symbiotic interaction between host and organism symbiotic interaction between organisms symbiotic interaction between species symbiotic process A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts. GOC:cc https://study.com/academy/lesson/symbiont-definition-lesson-quiz.html Any process in which an organism has an effect on an organism of a different species. interaction with another species interspecies interaction interspecies interaction with other organisms biological_process interspecies interaction between organisms Any process in which an organism has an effect on an organism of a different species. GOC:cc A biological process that directly contributes to the process of producing new individuals, involving another organism. janelomax 2012-09-19T15:56:30Z biological_process multi-organism reproductive process A biological process that directly contributes to the process of producing new individuals, involving another organism. GOC:jl A multicellular organism process which involves another multicellular organism of the same or different species. janelomax 2012-09-19T16:06:16Z biological_process multi-multicellular organism process A multicellular organism process which involves another multicellular organism of the same or different species. GOC:jl Any process that is carried out at the cellular level which involves another organism of the same or different species. janelomax 2012-12-11T17:00:50Z biological_process multi-organism cellular process Any process that is carried out at the cellular level which involves another organism of the same or different species. GOC:jl The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving more than one organism. janelomax 2012-12-13T16:25:50Z biological_process multi-organism transport The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving more than one organism. GOC:jl A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. janelomax 2013-03-27T15:09:58Z microtubule-based flagellum organization biological_process Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GOC:cilia GOC:jl The membrane organization process that joins two lipid bilayers to form a single membrane, involving more than one organism. janelomax 2013-09-10T15:06:11Z biological_process multi-organism membrane fusion The membrane organization process that joins two lipid bilayers to form a single membrane, involving more than one organism. GOC:jl A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane, involving more than one organism. janelomax 2013-09-10T15:11:41Z biological_process multi-organism membrane organization A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane, involving more than one organism. GOC:jl A form of autophagy, by which damaged or non-essential parts of the nucleus, or even an entire nucleus is degraded. janelomax 2013-09-10T15:50:25Z nucleus degradation biological_process nucleophagy autophagy of nucleus A form of autophagy, by which damaged or non-essential parts of the nucleus, or even an entire nucleus is degraded. GOC:autophagy GOC:jl PMID:24013549 Interacting selectively and non-covalently with a macromolecular complex. janelomax 2014-12-16T11:38:58Z GO:0032403 protein complex binding molecular_function macromolecular complex binding protein-containing complex binding Interacting selectively and non-covalently with a macromolecular complex. GOC:jl The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. GO:0006947 cell fusion cell-cell fusion biological_process plasma membrane fusion The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. GOC:elh GOC:mtg_muscle The acquisition of peroxisomes by daughter cells from the mother cell after replication. In Saccharomyces cerevisiae, the number of peroxisomes cells is fairly constant; a subset of the organelles are targeted and segregated to the bud in a highly ordered, vectorial process. Efficient segregation of peroxisomes from mother to bud is dependent on the actin cytoskeleton, and active movement of peroxisomes along actin filaments is driven by the class V myosin motor protein, Myo2p. biological_process Note that 'vectorial' is used in the definition in the mathematical and physical sense of pertaining to 'a quantity having direction as well as magnitude, especially as determining the position of one point in space relative to another. peroxisome inheritance The acquisition of peroxisomes by daughter cells from the mother cell after replication. In Saccharomyces cerevisiae, the number of peroxisomes cells is fairly constant; a subset of the organelles are targeted and segregated to the bud in a highly ordered, vectorial process. Efficient segregation of peroxisomes from mother to bud is dependent on the actin cytoskeleton, and active movement of peroxisomes along actin filaments is driven by the class V myosin motor protein, Myo2p. PMID:11733545 The process of directing proteins towards the endoplasmic reticulum (ER) using signals contained within the protein. One common mechanism uses a 16- to 30-residue signal sequence, typically located at the N-terminus of the protein and containing positively charged amino acids followed by a continuous stretch of hydrophobic residues, which directs the ribosome to the ER membrane and initiates transport of the growing polypeptide across the ER membrane. protein targeting to endoplasmic reticulum protein-ER targeting protein-endoplasmic reticulum targeting biological_process protein targeting to ER The process of directing proteins towards the endoplasmic reticulum (ER) using signals contained within the protein. One common mechanism uses a 16- to 30-residue signal sequence, typically located at the N-terminus of the protein and containing positively charged amino acids followed by a continuous stretch of hydrophobic residues, which directs the ribosome to the ER membrane and initiates transport of the growing polypeptide across the ER membrane. ISBN:0716731363 Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome. translation factor activity molecular_function translation regulator activity Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome. GOC:ai The directed movement of a protein to a specific location. establishment of protein localisation protein positioning protein recruitment biological_process establishment of protein localization The directed movement of a protein to a specific location. GOC:bf establishment of protein localisation GOC:mah 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. external encapsulating structure organisation external encapsulating structure organization and biogenesis biological_process external encapsulating structure organization 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 external encapsulating structure organization and biogenesis GOC:dph GOC:jl GOC:mah Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. biological_process regulation of cell differentiation Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. down regulation of cell differentiation down-regulation of cell differentiation downregulation of cell differentiation inhibition of cell differentiation biological_process negative regulation of cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell differentiation. up regulation of cell differentiation up-regulation of cell differentiation upregulation of cell differentiation activation of cell differentiation stimulation of cell differentiation biological_process positive regulation of cell differentiation Any process that activates or increases the frequency, rate or extent of cell differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the formation of a cilium. positive regulation of flagellum assembly up regulation of cilium assembly up-regulation of cilium assembly upregulation of cilium assembly activation of cilium assembly stimulation of cilium assembly biological_process positive regulation of flagellum biogenesis positive regulation of cilium assembly Any process that activates or increases the frequency, rate or extent of the formation of a cilium. GOC:cilia GOC:go_curators positive regulation of flagellum biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GO:0045946 positive regulation of protein anabolism positive regulation of protein biosynthesis positive regulation of protein biosynthetic process positive regulation of protein formation positive regulation of protein synthesis up regulation of protein biosynthetic process up-regulation of protein biosynthetic process upregulation of protein biosynthetic process activation of protein biosynthetic process stimulation of protein biosynthetic process biological_process positive regulation of translation Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GOC:dph GOC:go_curators GOC:tb positive regulation of protein biosynthetic process GOC:tb Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. positive regulation of protein breakdown positive regulation of protein catabolism positive regulation of protein degradation up regulation of protein catabolic process up-regulation of protein catabolic process upregulation of protein catabolic process activation of protein catabolic process stimulation of protein catabolic process biological_process positive regulation of protein catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid. down regulation of amino acid metabolic process down-regulation of amino acid metabolic process downregulation of amino acid metabolic process negative regulation of amino acid metabolism inhibition of amino acid metabolic process biological_process negative regulation of cellular amino acid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid. positive regulation of amino acid metabolism up regulation of amino acid metabolic process up-regulation of amino acid metabolic process upregulation of amino acid metabolic process activation of amino acid metabolic process stimulation of amino acid metabolic process biological_process positive regulation of cellular amino acid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell adhesion. up regulation of cell adhesion up-regulation of cell adhesion upregulation of cell adhesion activation of cell adhesion stimulation of cell adhesion biological_process positive regulation of cell adhesion Any process that activates or increases the frequency, rate or extent of cell adhesion. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle. down regulation of progression through cell cycle down-regulation of progression through cell cycle downregulation of progression through cell cycle negative regulation of cell cycle progression negative regulation of progression through cell cycle inhibition of progression through cell cycle biological_process negative regulation of cell cycle Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle. GOC:dph GOC:go_curators GOC:tb Any process that activates or increases the rate or extent of progression through the cell cycle. positive regulation of cell cycle progression positive regulation of progression through cell cycle up regulation of progression through cell cycle up-regulation of progression through cell cycle upregulation of progression through cell cycle activation of progression through cell cycle stimulation of progression through cell cycle biological_process positive regulation of cell cycle Any process that activates or increases the rate or extent of progression through the cell cycle. GOC:go_curators positive regulation of progression through cell cycle GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. down regulation of lipid metabolic process down-regulation of lipid metabolic process downregulation of lipid metabolic process negative regulation of lipid metabolism inhibition of lipid metabolic process biological_process negative regulation of lipid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. positive regulation of lipid metabolism up regulation of lipid metabolic process up-regulation of lipid metabolic process upregulation of lipid metabolic process activation of lipid metabolic process stimulation of lipid metabolic process biological_process positive regulation of lipid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother. down regulation of mitosis down-regulation of mitosis downregulation of mitosis negative regulation of mitosis inhibition of mitosis biological_process negative regulation of mitotic nuclear division Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother. GOC:dph GOC:go_curators GOC:tb Any process that activates or increases the frequency, rate or extent of mitosis. positive regulation of mitosis up regulation of mitosis up-regulation of mitosis upregulation of mitosis activation of mitosis mitogenic activity stimulation of mitosis biological_process positive regulation of mitotic nuclear division Any process that activates or increases the frequency, rate or extent of mitosis. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. down regulation of proteolysis down-regulation of proteolysis downregulation of proteolysis negative regulation of peptidolysis inhibition of proteolysis biological_process negative regulation of proteolysis Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. positive regulation of peptidolysis up regulation of proteolysis up-regulation of proteolysis upregulation of proteolysis activation of proteolysis stimulation of proteolysis biological_process positive regulation of proteolysis Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. GO:0016481 GO:0032582 GO:0061021 down regulation of transcription, DNA-dependent down-regulation of transcription, DNA-dependent downregulation of transcription, DNA-dependent negative regulation of cellular transcription, DNA-dependent negative regulation of transcription, DNA-dependent inhibition of transcription, DNA-dependent biological_process down regulation of gene-specific transcription down-regulation of gene-specific transcription downregulation of gene-specific transcription inhibition of gene-specific transcription negative regulation of gene-specific transcription transcription repressor activity negative regulation of transcription, DNA-templated Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. GOC:go_curators GOC:txnOH negative regulation of transcription, DNA-dependent GOC:txnOH Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. GO:0043193 GO:0045941 GO:0061020 positive regulation of cellular transcription, DNA-dependent positive regulation of transcription, DNA-dependent up regulation of transcription, DNA-dependent up-regulation of transcription, DNA-dependent upregulation of transcription, DNA-dependent activation of transcription, DNA-dependent stimulation of gene-specific transcription stimulation of transcription, DNA-dependent biological_process activation of gene-specific transcription positive regulation of gene-specific transcription transcription activator activity up regulation of gene-specific transcription up-regulation of gene-specific transcription upregulation of gene-specific transcription positive regulation of transcription, DNA-templated Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. GOC:go_curators GOC:txnOH positive regulation of transcription, DNA-dependent GOC:txnOH Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation. down regulation of translational elongation down-regulation of translational elongation downregulation of translational elongation inhibition of translational elongation biological_process negative regulation of translational elongation Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of translational elongation. up regulation of translational elongation up-regulation of translational elongation upregulation of translational elongation activation of translational elongation stimulation of translational elongation biological_process positive regulation of translational elongation Any process that activates or increases the frequency, rate or extent of translational elongation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination. down regulation of translational termination down-regulation of translational termination downregulation of translational termination inhibition of translational termination biological_process negative regulation of translational termination Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination. GOC:go_curators Any process that activates or increases the frequency, rate or extent of translational termination. up regulation of translational termination up-regulation of translational termination upregulation of translational termination activation of translational termination stimulation of translational termination biological_process positive regulation of translational termination Any process that activates or increases the frequency, rate or extent of translational termination. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. down regulation of carbohydrate metabolic process down-regulation of carbohydrate metabolic process downregulation of carbohydrate metabolic process negative regulation of carbohydrate metabolism inhibition of carbohydrate metabolic process biological_process negative regulation of carbohydrate metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. positive regulation of carbohydrate metabolism up regulation of carbohydrate metabolic process up-regulation of carbohydrate metabolic process upregulation of carbohydrate metabolic process activation of carbohydrate metabolic process stimulation of carbohydrate metabolic process biological_process positive regulation of carbohydrate metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis. down regulation of exocytosis down-regulation of exocytosis downregulation of exocytosis inhibition of exocytosis biological_process negative regulation of exocytosis Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis. GOC:go_curators Any process that activates or increases the frequency, rate or extent of exocytosis. up regulation of exocytosis up-regulation of exocytosis upregulation of exocytosis activation of exocytosis stimulation of exocytosis biological_process positive regulation of exocytosis Any process that activates or increases the frequency, rate or extent of exocytosis. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. down regulation of growth down-regulation of growth downregulation of growth inhibition of growth biological_process negative regulation of growth Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. GOC:go_curators Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism. up regulation of growth up-regulation of growth upregulation of growth activation of growth stimulation of growth biological_process positive regulation of growth Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle. down regulation of progression through mitotic cell cycle down-regulation of progression through mitotic cell cycle downregulation of progression through mitotic cell cycle negative regulation of mitotic cell cycle progression negative regulation of progression through mitotic cell cycle inhibition of progression through mitotic cell cycle biological_process negative regulation of mitotic cell cycle Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb negative regulation of progression through mitotic cell cycle GOC:dph GOC:tb Any process that activates or increases the rate or extent of progression through the mitotic cell cycle. positive regulation of mitotic cell cycle progression positive regulation of progression through mitotic cell cycle up regulation of progression through mitotic cell cycle up-regulation of progression through mitotic cell cycle upregulation of progression through mitotic cell cycle activation of progression through mitotic cell cycle stimulation of progression through mitotic cell cycle biological_process positive regulation of mitotic cell cycle Any process that activates or increases the rate or extent of progression through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb positive regulation of progression through mitotic cell cycle GOC:dph GOC:tb Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process negative regulation of nucleobase-containing compound metabolic process Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process positive regulation of nucleobase-containing compound metabolic process Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. down regulation of phosphate metabolic process down-regulation of phosphate metabolic process downregulation of phosphate metabolic process negative regulation of phosphate metabolism inhibition of phosphate metabolic process biological_process negative regulation of phosphate metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. positive regulation of phosphate metabolism up regulation of phosphate metabolic process up-regulation of phosphate metabolic process upregulation of phosphate metabolic process activation of phosphate metabolic process stimulation of phosphate metabolic process biological_process positive regulation of phosphate metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation. down regulation of translational initiation down-regulation of translational initiation downregulation of translational initiation inhibition of translational initiation biological_process negative regulation of translational initiation Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of translational initiation. up regulation of translational initiation up-regulation of translational initiation upregulation of translational initiation activation of translational initiation stimulation of translational initiation biological_process positive regulation of translational initiation Any process that activates or increases the frequency, rate or extent of translational initiation. GOC:go_curators Any process, mediated by small non-coding RNAs, that modulates the frequency, rate or extent that mRNAs are effectively translated into protein. biological_process regulation of translation, ncRNA-mediated Any process, mediated by small non-coding RNAs, that modulates the frequency, rate or extent that mRNAs are effectively translated into protein. GOC:dph GOC:go_curators GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development. down regulation of embryonic development down-regulation of embryonic development downregulation of embryonic development inhibition of embryonic development biological_process negative regulation of embryonic development Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development. GOC:go_curators Any process that modulates the frequency, rate or extent of embryonic development. biological_process regulation of embryonic development Any process that modulates the frequency, rate or extent of embryonic development. GOC:go_curators The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. carboxylic acid anabolism carboxylic acid biosynthesis carboxylic acid formation carboxylic acid synthesis biological_process carboxylic acid biosynthetic process The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. carboxylic acid breakdown carboxylic acid catabolism carboxylic acid degradation biological_process carboxylic acid catabolic process The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. ISBN:0198506732 The addition of tubulin heterodimers to one or both ends of a microtubule. microtubule assembly biological_process microtubule formation microtubule polymerization The addition of tubulin heterodimers to one or both ends of a microtubule. GOC:ai GOC:go_curators Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. biological_process regulation of nucleocytoplasmic transport Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances between the cytoplasm and the nucleus. down regulation of nucleocytoplasmic transport down-regulation of nucleocytoplasmic transport downregulation of nucleocytoplasmic transport inhibition of nucleocytoplasmic transport biological_process negative regulation of nucleocytoplasmic transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances between the cytoplasm and the nucleus. GOC:bf Any process that activates or increases the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. up regulation of nucleocytoplasmic transport up-regulation of nucleocytoplasmic transport upregulation of nucleocytoplasmic transport activation of nucleocytoplasmic transport stimulation of nucleocytoplasmic transport biological_process positive regulation of nucleocytoplasmic transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. GOC:bf Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. positive regulation of lipid anabolism positive regulation of lipid biosynthesis positive regulation of lipid formation positive regulation of lipid synthesis positive regulation of lipogenesis up regulation of lipid biosynthetic process up-regulation of lipid biosynthetic process upregulation of lipid biosynthetic process activation of lipid biosynthetic process stimulation of lipid biosynthetic process biological_process positive regulation of lipid biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GOC:ai positive regulation of lipogenesis GOC:sl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. regulation of lipid anabolism regulation of lipid biosynthesis regulation of lipid formation regulation of lipid synthesis regulation of lipogenesis biological_process regulation of lipid biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GOC:ai regulation of lipogenesis GOC:sl The controlled release of a substance by a cell or a tissue. biological_process secretion The controlled release of a substance by a cell or a tissue. GOC:ai The directed movement of substances within a cell. jl 2013-12-18T14:04:50Z GO:1902582 biological_process single organism intracellular transport single-organism intracellular transport intracellular transport The directed movement of substances within a cell. GOC:ai single organism intracellular transport GOC:TermGenie The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). biological_process carboxylic acid transport The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). GOC:ai The directed movement of substances from the cytosol to the endoplasmic reticulum of a cell. cytosol to ER transport cytosol to endoplasmic reticulum transport biological_process cytosol to endoplasmic reticulum transport The directed movement of substances from the cytosol to the endoplasmic reticulum of a cell. GOC:ai The directed movement of a vesicle along a microtubule, mediated by motor proteins. This process begins with the attachment of a vesicle to a microtubule, and ends when the vesicle reaches its final destination. microtubule-based vesicle localization biological_process vesicle transport along microtubule The directed movement of a vesicle along a microtubule, mediated by motor proteins. This process begins with the attachment of a vesicle to a microtubule, and ends when the vesicle reaches its final destination. GOC:ecd GOC:rl microtubule-based vesicle localization GOC:rl The directed movement of a mitochondrion along a microtubule, mediated by motor proteins. mitochondrial migration along microtubule mitochondrial transport along microtubule biological_process mitochondrion transport along microtubule The directed movement of a mitochondrion along a microtubule, mediated by motor proteins. GOC:ecd 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. molecular_function cofactor binding 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 The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. biological_process Golgi-derived vesicle transport Golgi vesicle transport The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. GOC:jid ISBN:0716731363 PMID:10219233 The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. Golgi vesicle targeting dictyosome vesicle targeting vesicle targeting, to, from or within dictyosome biological_process vesicle targeting, to, from or within Golgi The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. GOC:jid GOC:mah ISBN:0716731363 PMID:10219233 Any process that modulates the frequency, rate, or destination of vesicle-mediated transport to, from or within the Golgi apparatus. regulation of Golgi vesicle targeting biological_process regulation of vesicle targeting, to, from or within Golgi Any process that modulates the frequency, rate, or destination of vesicle-mediated transport to, from or within the Golgi apparatus. GOC:jid GOC:mah ISBN:0716731363 PMID:10219233 Transport of a vesicle from the plasma membrane to the endosome. biological_process plasma membrane to endosome transport Transport of a vesicle from the plasma membrane to the endosome. GOC:jid The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the endoplasmic reticulum. vesicle fusion with ER biological_process vesicle fusion with endoplasmic reticulum The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the endoplasmic reticulum. GOC:jid The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi. biological_process vesicle fusion with Golgi apparatus The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi. GOC:jid The creation of a single organelle from two or more organelles. biological_process organelle fusion The creation of a single organelle from two or more organelles. GOC:jid The creation of two or more organelles by division of one organelle. biological_process organelle fission The creation of two or more organelles by division of one organelle. GOC:jid The partitioning of organelles between daughter cells at cell division. biological_process organelle inheritance The partitioning of organelles between daughter cells at cell division. GOC:jid The partitioning of endoplasmic reticulum between daughter cells at cell division. ER inheritance biological_process endoplasmic reticulum inheritance The partitioning of endoplasmic reticulum between daughter cells at cell division. GOC:jid The partitioning of nuclei between daughter cells at cell division. cell nucleus inheritance biological_process nucleus inheritance The partitioning of nuclei between daughter cells at cell division. GOC:jid Any process that establishes the spatial arrangement of mitochondria between and within cells. distribution of mitochondria mitochondrial distribution biological_process positioning of mitochondria mitochondrion distribution Any process that establishes the spatial arrangement of mitochondria between and within cells. GOC:jid The partitioning of Golgi apparatus between daughter cells at cell division. Golgi division Golgi partitioning biological_process Golgi inheritance The partitioning of Golgi apparatus between daughter cells at cell division. GOC:jid PMID:12851069 Golgi division GOC:ascb_2009 GOC:dph GOC:tb The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process terminal differentiation cell development The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:go_curators terminal differentiation GOC:dph GOC:tb Any process that activates or increases 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. GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process upregulation of biological process activation of biological process stimulation of biological process biological_process positive regulation of biological process Any process that activates or increases 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:jid Any process that stops, prevents, or reduces 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. GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process negative regulation of physiological process inhibition of biological process biological_process negative regulation of biological process Any process that stops, prevents, or reduces 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:jid Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051242 positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process upregulation of cellular process activation of cellular process stimulation of cellular process biological_process positive regulation of cellular process Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051243 down regulation of cellular process down-regulation of cellular process downregulation of cellular process negative regulation of cellular physiological process inhibition of cellular process biological_process negative regulation of cellular process Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is 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. biological_process 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. regulation of response to stimulus Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is 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. GOC:jid Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is 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. up regulation of response to stimulus up-regulation of response to stimulus upregulation of response to stimulus activation of response to stimulus stimulation of response to stimulus biological_process 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. positive regulation of response to stimulus Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is 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. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is 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. down regulation of response to stimulus down-regulation of response to stimulus downregulation of response to stimulus inhibition of response to stimulus biological_process 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. negative regulation of response to stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is 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. GOC:jid The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. formation of an anatomical structure involved in morphogenesis biological_process Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense. anatomical structure formation involved in morphogenesis The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GOC:dph GOC:jid GOC:tb formation of an anatomical structure involved in morphogenesis GOC:dph GOC:tb The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. biological_process system development The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. GOC:dph GOC:jid The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. development of an anatomical structure biological_process anatomical structure development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GO_REF:0000021 The process in which the anatomical structures of a cell projection are generated and organized. biological_process cell projection morphogenesis The process in which the anatomical structures of a cell projection are generated and organized. GO_REF:0000021 A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. biological_process cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. GOC:isa_complete Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. cell locomotion movement of a cell biological_process cell movement cell motility Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. GOC:dgh GOC:dph GOC:isa_complete GOC:mlg Any process in which a chromosome is transported to, or maintained in, a specific location. chromosome localisation establishment and maintenance of chromosome localization establishment and maintenance of chromosome position biological_process chromosome localization Any process in which a chromosome is transported to, or maintained in, a specific location. GOC:ai chromosome localisation GOC:mah The directed movement of nucleic acids, single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process nucleic acid transport The directed movement of nucleic acids, single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information, 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 The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process RNA transport The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of mRNA processing, those processes involved in the conversion of a primary mRNA transcript into a mature mRNA prior to its translation into polypeptide. biological_process regulation of mRNA processing Any process that modulates the frequency, rate or extent of mRNA processing, those processes involved in the conversion of a primary mRNA transcript into a mature mRNA prior to its translation into polypeptide. GOC:ai Any process that activates or increases the frequency, rate or extent of mRNA processing. up regulation of mRNA processing up-regulation of mRNA processing upregulation of mRNA processing activation of mRNA processing stimulation of mRNA processing biological_process positive regulation of mRNA processing Any process that activates or increases the frequency, rate or extent of mRNA processing. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of mRNA processing. down regulation of mRNA processing down-regulation of mRNA processing downregulation of mRNA processing inhibition of mRNA processing biological_process negative regulation of mRNA processing Any process that stops, prevents, or reduces the frequency, rate or extent of mRNA processing. GOC:ai Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell. biological_process regulation of protein secretion Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell. down regulation of protein secretion down-regulation of protein secretion downregulation of protein secretion inhibition of protein secretion biological_process negative regulation of protein secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. up regulation of protein secretion up-regulation of protein secretion upregulation of protein secretion activation of protein secretion stimulation of protein secretion biological_process positive regulation of protein secretion Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai 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. GO:0050791 regulation of physiological process biological_process regulation of biological process 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 Any process that modulates the activity of an enzyme. GO:0048552 regulation of enzyme activity regulation of metalloenzyme activity biological_process regulation of catalytic activity Any process that modulates the activity of an enzyme. GOC:ai GOC:ebc GOC:vw Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). biological_process regulation of developmental process Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:go_curators Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051244 regulation of cellular physiological process biological_process regulation of cellular process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators Interacting selectively and non-covalently with a component of the extracellular matrix. extracellular matrix constituent binding molecular_function adhesive extracellular matrix constituent extracellular matrix binding Interacting selectively and non-covalently with a component of the extracellular matrix. GOC:ai A organ system process carried out by any of the organs or tissues of neurological system. https://github.com/geneontology/go-ontology/issues/13824 neurological system process neurophysiological process biological_process pan-neural process nervous system process A organ system process carried out by any of the organs or tissues of neurological system. GOC:ai GOC:mtg_cardio 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. GO:0051869 physiological response to stimulus biological_process 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. response to stimulus 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 Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids. regulation of lipid breakdown regulation of lipid catabolism regulation of lipid degradation biological_process regulation of lipid catabolic process Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. down regulation of lipid catabolic process down-regulation of lipid catabolic process downregulation of lipid catabolic process negative regulation of lipid breakdown negative regulation of lipid catabolism negative regulation of lipid degradation inhibition of lipid catabolic process biological_process negative regulation of lipid catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. positive regulation of lipid breakdown positive regulation of lipid catabolism positive regulation of lipid degradation up regulation of lipid catabolic process up-regulation of lipid catabolic process upregulation of lipid catabolic process activation of lipid catabolic process stimulation of lipid catabolic process biological_process positive regulation of lipid catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. GOC:ai The directed movement of RNA, deoxyribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process DNA transport The directed movement of RNA, deoxyribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process mRNA transport The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of rRNA, ribosomal ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process rRNA transport The directed movement of rRNA, ribosomal ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of tRNA, transfer ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process tRNA transport The directed movement of tRNA, transfer ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Enables the transfer of nucleic acids from one side of a membrane to the other. Nucleic acids are single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information. molecular_function nucleic acid transmembrane transporter activity Enables the transfer of nucleic acids from one side of a membrane to the other. Nucleic acids are single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information. GOC:ai Enables the transfer of RNA, ribonucleic acid, from one side of a membrane to the other. Reactome:R-HSA-203906 molecular_function RNA transmembrane transporter activity Enables the transfer of RNA, ribonucleic acid, from one side of a membrane to the other. GOC:ai Reactome:R-HSA-203906 Exportin complex translocates pre-miRNA to cytosol Enables the transfer of tRNA, transfer ribonucleic acid, from one side of a membrane to the other. molecular_function tRNA transmembrane transporter activity Enables the transfer of tRNA, transfer ribonucleic acid, from one side of a membrane to the other. GOC:ai Enables the transfer of DNA, deoxyribonucleic acid, from one side of a membrane to the other. molecular_function DNA transmembrane transporter activity Enables the transfer of DNA, deoxyribonucleic acid, from one side of a membrane to the other. GOC:ai Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. biological_process regulation of secretion Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. up regulation of secretion up-regulation of secretion upregulation of secretion activation of secretion stimulation of secretion biological_process positive regulation of secretion Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. down regulation of secretion down-regulation of secretion downregulation of secretion inhibition of secretion biological_process negative regulation of secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process regulation of transport Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of transport up-regulation of transport upregulation of transport activation of transport stimulation of transport biological_process positive regulation of transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of transport down-regulation of transport downregulation of transport inhibition of transport biological_process negative regulation of transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. regulation of DNA metabolism biological_process regulation of DNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA. down regulation of DNA metabolic process down-regulation of DNA metabolic process downregulation of DNA metabolic process negative regulation of DNA metabolism inhibition of DNA metabolic process biological_process negative regulation of DNA metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. positive regulation of DNA metabolism up regulation of DNA metabolic process up-regulation of DNA metabolic process upregulation of DNA metabolic process activation of DNA metabolic process stimulation of DNA metabolic process biological_process positive regulation of DNA metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. down regulation of lipid biosynthetic process down-regulation of lipid biosynthetic process downregulation of lipid biosynthetic process negative regulation of lipid anabolism negative regulation of lipid biosynthesis negative regulation of lipid formation negative regulation of lipid synthesis negative regulation of lipogenesis inhibition of lipid biosynthetic process biological_process negative regulation of lipid biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GOC:ai negative regulation of lipogenesis GOC:sl The controlled breakdown of the nuclear envelope in the context of a normal process. nuclear envelope breakdown nuclear envelope catabolism nuclear envelope degradation biological_process nuclear envelope disassembly The controlled breakdown of the nuclear envelope in the context of a normal process. GOC:ai Interacting selectively and non-covalently with an unfolded protein. binding unfolded ER proteins fimbrium-specific chaperone activity glycoprotein-specific chaperone activity histone-specific chaperone activity ribosomal chaperone activity tubulin-specific chaperone activity molecular_function chaperone activity unfolded protein binding Interacting selectively and non-covalently with an unfolded protein. GOC:ai Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription. GO:1904167 GO:2000823 regulation of transcription factor activity regulation of DNA binding transcription factor activity regulation of sequence-specific DNA binding transcription factor activity regulation of androgen receptor activity regulation of thyroid hormone receptor activity biological_process regulation of DNA-binding transcription factor activity Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription. GOC:ai regulation of transcription factor activity GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription. rph 2015-04-22T12:22:16Z GO:1904169 positive regulation of transcription factor activity positive regulation of DNA binding transcription factor activity positive regulation of sequence-specific DNA binding transcription factor activity up regulation of transcription factor activity up-regulation of transcription factor activity upregulation of transcription factor activity activation of transcription factor activity positive regulation of thyroid hormone receptor activity stimulation of transcription factor activity biological_process positive regulation of DNA-binding transcription factor activity Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription. GOC:ai positive regulation of transcription factor activity GOC:dph GOC:tb Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). down regulation of developmental process down-regulation of developmental process downregulation of developmental process inhibition of developmental process biological_process negative regulation of developmental process Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:ai Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). up regulation of developmental process up-regulation of developmental process upregulation of developmental process activation of developmental process stimulation of developmental process biological_process positive regulation of developmental process Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:ai Any process that modulates the frequency, rate or extent of helicase activity. biological_process regulation of helicase activity Any process that modulates the frequency, rate or extent of helicase activity. GOC:ai Any process that activates or increases the activity of a helicase. up regulation of helicase activity up-regulation of helicase activity upregulation of helicase activity activation of helicase activity stimulation of helicase activity biological_process positive regulation of helicase activity Any process that activates or increases the activity of a helicase. GOC:ai Any process that stops or reduces the activity of a helicase. down regulation of helicase activity down-regulation of helicase activity downregulation of helicase activity inhibition of helicase activity biological_process negative regulation of helicase activity Any process that stops or reduces the activity of a helicase. GOC:ai Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. biological_process regulation of binding Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. up regulation of binding up-regulation of binding upregulation of binding activation of binding stimulation of binding biological_process positive regulation of binding Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. down regulation of binding down-regulation of binding downregulation of binding inhibition of binding biological_process negative regulation of binding Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). biological_process regulation of DNA binding Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid). GOC:ai GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. regulation of cellular component organisation biological_process regulation of cell organisation regulation of cell organization regulation of cellular component organization and biogenesis regulation of cellular component organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai regulation of cell organisation GOC:mah regulation of cell organization GOC:mah regulation of cellular component organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. down regulation of cell organization down-regulation of cell organization downregulation of cell organization inhibition of cell organization biological_process negative regulation of cell organisation negative regulation of cellular component organization and biogenesis negative regulation of cellular component organization Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai negative regulation of cell organisation GOC:mah negative regulation of cellular component organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. positive regulation of cell organisation up regulation of cell organization up-regulation of cell organization upregulation of cell organization activation of cell organization stimulation of cell organization biological_process positive regulation of cellular component organization and biogenesis positive regulation of cellular component organization Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai positive regulation of cellular component organization and biogenesis GOC:mah The directed movement of substances out of the nucleus. export from nucleus nucleus export substance nuclear export biological_process nuclear export The directed movement of substances out of the nucleus. GOC:ai The directed movement of substances into, out of, or within the nucleus. Wikipedia:Nuclear_transport nucleus transport biological_process nuclear transport The directed movement of substances into, out of, or within the nucleus. GOC:ai The directed movement of substances into the nucleus. jl 2013-12-19T15:26:34Z GO:1902593 nuclear import single organism nuclear import substance nuclear import biological_process single-organism nuclear import import into nucleus The directed movement of substances into the nucleus. GOC:ai single organism nuclear import GOC:TermGenie Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. regulation of nitrogen metabolic process regulation of nitrogen metabolism biological_process regulation of nitrogen compound metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb regulation of nitrogen metabolic process GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. down regulation of nitrogen metabolic process down-regulation of nitrogen metabolic process downregulation of nitrogen metabolic process negative regulation of nitrogen metabolic process negative regulation of nitrogen metabolism inhibition of nitrogen metabolic process biological_process negative regulation of nitrogen compound metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb negative regulation of nitrogen metabolic process GOC:tb Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. positive regulation of nitrogen metabolic process positive regulation of nitrogen metabolism up regulation of nitrogen metabolic process up-regulation of nitrogen metabolic process upregulation of nitrogen metabolic process activation of nitrogen metabolic process stimulation of nitrogen metabolic process biological_process positive regulation of nitrogen compound metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb positive regulation of nitrogen metabolic process GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. down regulation of sulfur metabolic process down-regulation of sulfur metabolic process downregulation of sulfur metabolic process negative regulation of sulfur metabolism negative regulation of sulphur metabolic process negative regulation of sulphur metabolism inhibition of sulfur metabolic process biological_process negative regulation of sulfur metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. positive regulation of sulfur metabolism positive regulation of sulphur metabolic process positive regulation of sulphur metabolism up regulation of sulfur metabolic process up-regulation of sulfur metabolic process upregulation of sulfur metabolic process activation of sulfur metabolic process stimulation of sulfur metabolic process biological_process positive regulation of sulfur metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. GOC:ai 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. jl 2013-12-18T13:51:04Z GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process single organism localization single-organism localization localization 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 localisation GOC:mah single organism localization GOC:TermGenie 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. vitamin or cofactor transport biological_process cofactor transport 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 Enables the transfer of a cofactor from one side of a membrane to the other. A cofactor is a substance that is required for the activity of an enzyme or other protein. vitamin or cofactor transporter activity molecular_function cofactor transporter activity cofactor transmembrane transporter activity GO_REF:0000090 Enables the transfer of a cofactor from one side of a membrane to the other. A cofactor is a substance that is required for the activity of an enzyme or other protein. GOC:ai 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. cofactor metabolism biological_process cofactor metabolic process 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 The chemical reactions and pathways resulting in the breakdown of a cofactor, a substance that is required for the activity of an enzyme or other protein. cofactor breakdown cofactor catabolism cofactor degradation biological_process cofactor catabolic process The chemical reactions and pathways resulting in the breakdown of a cofactor, a substance that is required for the activity of an enzyme or other protein. GOC:ai The chemical reactions and pathways resulting in the formation of a cofactor, a substance that is required for the activity of an enzyme or other protein. cofactor anabolism cofactor biosynthesis cofactor formation cofactor synthesis biological_process cofactor biosynthetic process The chemical reactions and pathways resulting in the formation of a cofactor, a substance that is required for the activity of an enzyme or other protein. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a cofactor. regulation of cofactor metabolism biological_process regulation of cofactor metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a cofactor. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a cofactor. positive regulation of cofactor metabolism up regulation of cofactor metabolic process up-regulation of cofactor metabolic process upregulation of cofactor metabolic process activation of cofactor metabolic process stimulation of cofactor metabolic process biological_process positive regulation of cofactor metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a cofactor. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a cofactor. down regulation of cofactor metabolic process down-regulation of cofactor metabolic process downregulation of cofactor metabolic process negative regulation of cofactor metabolism inhibition of cofactor metabolic process biological_process negative regulation of cofactor metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a cofactor. GOC:ai Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of protein transport up-regulation of protein transport upregulation of protein transport activation of protein transport stimulation of protein transport biological_process positive regulation of protein transport Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process regulation of protein transport Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of protein transport down-regulation of protein transport downregulation of protein transport inhibition of protein transport biological_process negative regulation of protein transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation biological_process establishment of localization Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos establishment of localisation GOC:mah The directed movement of RNA to a specific location. RNA positioning RNA recruitment establishment of RNA localisation biological_process establishment of RNA localization The directed movement of RNA to a specific location. GOC:ai establishment of RNA localisation GOC:mah Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. biological_process regulation of multicellular organismal process Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. up regulation of multicellular organismal process up-regulation of multicellular organismal process upregulation of multicellular organismal process activation of multicellular organismal process stimulation of multicellular organismal process biological_process positive regulation of multicellular organismal process Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. down regulation of multicellular organismal process down-regulation of multicellular organismal process downregulation of multicellular organismal process inhibition of multicellular organismal process biological_process negative regulation of multicellular organismal process Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. regulation of protein metabolism biological_process regulation of protein metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein. positive regulation of protein metabolism up regulation of protein metabolic process up-regulation of protein metabolic process upregulation of protein metabolic process activation of protein metabolic process stimulation of protein metabolic process biological_process positive regulation of protein metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. down regulation of protein metabolic process down-regulation of protein metabolic process downregulation of protein metabolic process negative regulation of protein metabolism inhibition of protein metabolic process biological_process negative regulation of protein metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA. regulation of RNA metabolism biological_process regulation of RNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA. down regulation of RNA metabolic process down-regulation of RNA metabolic process downregulation of RNA metabolic process negative regulation of RNA metabolism inhibition of RNA metabolic process biological_process negative regulation of RNA metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA. positive regulation of RNA metabolism up regulation of RNA metabolic process up-regulation of RNA metabolic process upregulation of RNA metabolic process activation of RNA metabolic process stimulation of RNA metabolic process biological_process positive regulation of RNA metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai 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. protein polymer biosynthesis protein polymer biosynthetic process protein polymer formation biological_process protein polymerization 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 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. protein polymer breakdown protein polymer catabolic process protein polymer catabolism protein polymer degradation biological_process protein depolymerization 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 Any process that modulates the frequency, rate or extent of the movement of a cellular component. regulation of cellular component motion biological_process regulation of cell movement regulation of cellular component movement Any process that modulates the frequency, rate or extent of the movement of a cellular component. GOC:ai GOC:dph GOC:jl regulation of cellular component motion GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component. negative regulation of cellular component motion biological_process negative regulation of cellular component movement Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component. GOC:ai GOC:dph GOC:jl negative regulation of cellular component motion GOC:mah Any process that activates or increases the frequency, rate or extent of the movement of a cellular component. positive regulation of cellular component motion biological_process positive regulation of cellular component movement Any process that activates or increases the frequency, rate or extent of the movement of a cellular component. GOC:ai GOC:dph GOC:jl positive regulation of cellular component motion GOC:mah 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. GO:0007001 GO:0051277 chromosome organisation biological_process chromosome organization and biogenesis maintenance of genome integrity nuclear genome maintenance chromosome organization 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 chromosome organization and biogenesis GOC:mah 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. Wikipedia:Cell_division biological_process Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division 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 Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells. biological_process regulation of cell division Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells. GOC:go_curators The directed movement of a chromosome to a specific location. chromosome positioning establishment of chromosome localisation biological_process establishment of chromosome localization The directed movement of a chromosome to a specific location. GOC:ai establishment of chromosome localisation GOC:mah Any process that modulates the frequency, rate or extent of hydrolase activity, the 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. hydrolase regulator biological_process regulation of hydrolase activity Any process that modulates the frequency, rate or extent of hydrolase activity, the 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. EC:3.-.-.- GOC:ai Any process that modulates the frequency, rate or extent of transferase activity, the 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. transferase regulator biological_process This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. regulation of transferase activity Any process that modulates the frequency, rate or extent of transferase activity, the 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. EC:2.-.-.- GOC:ai Any process that modulates the frequency, rate or extent of lyase activity, the 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. lyase regulator biological_process regulation of lyase activity Any process that modulates the frequency, rate or extent of lyase activity, the 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.-.-.- GOC:ai Any process that modulates the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. Ligase is the systematic name for any enzyme of EC class 6. ligase regulator biological_process regulation of ligase activity Any process that modulates the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. Ligase is the systematic name for any enzyme of EC class 6. EC:6.-.-.- GOC:ai Any process that modulates the frequency, rate or extent of oxidoreductase activity, the 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. oxidoreductase regulator biological_process regulation of oxidoreductase activity Any process that modulates the frequency, rate or extent of oxidoreductase activity, the 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. EC:1.-.-.- GOC:ai Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds. hydrolase activator up regulation of hydrolase activity up-regulation of hydrolase activity upregulation of hydrolase activity activation of hydrolase activity stimulation of hydrolase activity biological_process positive regulation of hydrolase activity Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds. GOC:ai Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds. down regulation of hydrolase activity down-regulation of hydrolase activity downregulation of hydrolase activity hydrolase inhibitor inhibition of hydrolase activity biological_process negative regulation of hydrolase activity Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds. GOC:ai Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. transferase activator up regulation of transferase activity up-regulation of transferase activity upregulation of transferase activity activation of transferase activity stimulation of transferase activity biological_process This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. positive regulation of transferase activity Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. GOC:ai Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. down regulation of transferase activity down-regulation of transferase activity downregulation of transferase activity transferase inhibitor inhibition of transferase activity biological_process This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. negative regulation of transferase activity Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. GOC:ai Any process that activates or increases the frequency, rate or extent of lyase activity, the 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. lyase activator up regulation of lyase activity up-regulation of lyase activity upregulation of lyase activity activation of lyase activity stimulation of lyase activity biological_process positive regulation of lyase activity Any process that activates or increases the frequency, rate or extent of lyase activity, the 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. GOC:ai Any process that stops or reduces the rate of lyase activity, the 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. down regulation of lyase activity down-regulation of lyase activity downregulation of lyase activity lyase inhibitor inhibition of lyase activity biological_process negative regulation of lyase activity Any process that stops or reduces the rate of lyase activity, the 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. GOC:ai Any process that activates or increases the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. ligase activator up regulation of ligase activity up-regulation of ligase activity upregulation of ligase activity activation of ligase activity stimulation of ligase activity biological_process positive regulation of ligase activity Any process that activates or increases the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. GOC:ai Any process that stops or reduces the rate of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. down regulation of ligase activity down-regulation of ligase activity downregulation of ligase activity ligase inhibitor inhibition of ligase activity biological_process negative regulation of ligase activity Any process that stops or reduces the rate of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. GOC:ai Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the 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. GO:0009391 oxidoreductase activator up regulation of oxidoreductase activity up-regulation of oxidoreductase activity upregulation of oxidoreductase activity activation of oxidoreductase activity ribonucleotide reductase activating enzyme activity stimulation of oxidoreductase activity biological_process positive regulation of oxidoreductase activity Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the 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. GOC:ai Any process that stops or reduces the rate of oxidoreductase activity, the 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. down regulation of oxidoreductase activity down-regulation of oxidoreductase activity downregulation of oxidoreductase activity oxidoreductase inhibitor inhibition of oxidoreductase activity biological_process negative regulation of oxidoreductase activity Any process that stops or reduces the rate of oxidoreductase activity, the 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. GOC:ai The 'de novo' formation of a microtubule, mediated by the microtubule organizing center. MTOC-mediated microtubule nucleation microtubule nucleation by MTOC microtubule nucleation by microtubule organising centre microtubule organizing center-mediated microtubule nucleation biological_process microtubule nucleation by microtubule organizing center The 'de novo' formation of a microtubule, mediated by the microtubule organizing center. GOC:ai The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole. GO:0042146 biological_process heterotypic vacuole fusion (non-autophagic) heterotypic vacuole fusion, non-autophagic vesicle fusion with vacuole The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole. GOC:ai Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. regulation of cytoskeleton organisation biological_process regulation of cytoskeleton organization and biogenesis regulation of cytoskeleton organization Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai regulation of cytoskeleton organisation GOC:mah regulation of cytoskeleton organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. down regulation of cytoskeleton organization down-regulation of cytoskeleton organization downregulation of cytoskeleton organization negative regulation of cytoskeleton organisation inhibition of cytoskeleton organization biological_process negative regulation of cytoskeleton organization and biogenesis negative regulation of cytoskeleton organization Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai negative regulation of cytoskeleton organisation GOC:mah negative regulation of cytoskeleton organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. positive regulation of cytoskeleton organisation up regulation of cytoskeleton organization up-regulation of cytoskeleton organization upregulation of cytoskeleton organization activation of cytoskeleton organization stimulation of cytoskeleton organization biological_process positive regulation of cytoskeleton organization and biogenesis positive regulation of cytoskeleton organization Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai positive regulation of cytoskeleton organisation GOC:mah positive regulation of cytoskeleton organization and biogenesis GOC:mah The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells. peptidolysis involved in cellular protein catabolic process peptidolysis involved in cellular protein catabolism biological_process peptidolysis during cellular protein catabolic process peptidolysis during cellular protein catabolism proteolysis during cellular protein catabolic process proteolysis during cellular protein catabolism proteolysis involved in cellular protein catabolic process The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells. GOC:ai GOC:dph GOC:tb Any process leading to the attainment of the full functional capacity of a protein. biological_process protein maturation Any process leading to the attainment of the full functional capacity of a protein. GOC:ai Any process in which an organelle is transported to, and/or maintained in, a specific location. establishment and maintenance of organelle localization organelle localisation biological_process organelle localization Any process in which an organelle is transported to, and/or maintained in, a specific location. GOC:ai organelle localisation GOC:mah 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. jl 2013-12-18T14:04:32Z GO:1902580 cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane single organism cellular localization intracellular localization localization within cell biological_process single-organism cellular localization cellular localization 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 cellular localisation GOC:mah single organism cellular localization GOC:TermGenie Any process in which endoplasmic reticulum is transported to, and/or maintained in, a specific location within the cell. ER localization endoplasmic reticulum localisation establishment and maintenance of ER localization biological_process endoplasmic reticulum localization Any process in which endoplasmic reticulum is transported to, and/or maintained in, a specific location within the cell. GOC:ai ER localization GOC:dph endoplasmic reticulum localisation GOC:mah Any process in which a plastid is transported to, and/or maintained in, a specific location within the cell. establishment and maintenance of plastid localization plastid localisation biological_process plastid localization Any process in which a plastid is transported to, and/or maintained in, a specific location within the cell. GOC:ai plastid localisation GOC:mah Any process in which the Golgi is transported to, and/or maintained in, a specific location within the cell. Golgi apparatus localization Golgi body localization Golgi localisation establishment and maintenance of Golgi localization biological_process Golgi localization Any process in which the Golgi is transported to, and/or maintained in, a specific location within the cell. GOC:ai Golgi localisation GOC:mah Any process in which a mitochondrion or mitochondria are transported to, and/or maintained in, a specific location within the cell. establishment and maintenance of mitochondria localization establishment and maintenance of mitochondrion localization localization of mitochondria localization of mitochondrion mitochondria localization mitochondrial localization mitochondrion localisation biological_process mitochondrion localization Any process in which a mitochondrion or mitochondria are transported to, and/or maintained in, a specific location within the cell. GOC:ai mitochondrion localisation GOC:mah Any process in which the nucleus is transported to, and/or maintained in, a specific location within the cell. cell nucleus localization establishment and maintenance of nucleus localization localization of nucleus nucleus localisation biological_process nucleus localization Any process in which the nucleus is transported to, and/or maintained in, a specific location within the cell. GOC:ai nucleus localisation GOC:mah Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. cytoplasmic vesicle localization establishment and maintenance of vesicle localization vesicle localisation biological_process vesicle localization Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. GOC:ai vesicle localisation GOC:mah Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation in cell establishment of intracellular localization establishment of localization within cell positioning within cell biological_process establishment of cellular localization establishment of localization in cell Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos GOC:dph GOC:tb establishment of localisation in cell GOC:mah establishment of cellular localization GOC:dph GOC:tb The directed movement of a vesicle to a specific location. establishment of vesicle localisation biological_process establishment of vesicle localization The directed movement of a vesicle to a specific location. GOC:ai establishment of vesicle localisation GOC:mah The directed movement of the mitochondrion to a specific location. establishment of mitochondria localization establishment of mitochondrion localisation mitochondria positioning mitochondrial migration mitochondrion positioning biological_process establishment of mitochondrion localization The directed movement of the mitochondrion to a specific location. GOC:ai establishment of mitochondrion localisation GOC:mah The directed movement of an organelle to a specific location. establishment of organelle localisation biological_process establishment of organelle localization The directed movement of an organelle to a specific location. GOC:ai establishment of organelle localisation GOC:mah The directed movement of a plastid to a specific location in the cell. establishment of plastid localisation biological_process establishment of plastid localization The directed movement of a plastid to a specific location in the cell. GOC:ai establishment of plastid localisation GOC:mah Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane. establishment and maintenance of localization in membrane establishment and maintenance of position in membrane localisation within membrane localization to membrane positioning within membrane biological_process localization within membrane Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane. GOC:ai localisation within membrane GOC:mah Any process in which a cell is transported to, and/or maintained in, a specific location. cell localization establishment and maintenance of cell localization establishment and maintenance of localization of cell localisation of cell biological_process localization of cell Any process in which a cell is transported to, and/or maintained in, a specific location. GOC:ai localisation of cell GOC:mah The directed movement of the Golgi to a specific location. establishment of Golgi apparatus localization establishment of Golgi body localization establishment of Golgi localisation biological_process establishment of Golgi localization The directed movement of the Golgi to a specific location. GOC:ai establishment of Golgi localisation GOC:mah The directed movement of the endoplasmic reticulum to a specific location. establishment of ER localisation establishment of endoplasmic reticulum localization biological_process establishment of ER localization The directed movement of the endoplasmic reticulum to a specific location. GOC:ai establishment of ER localisation GOC:mah A biological process which involves another organism of the same or different species. GO:0051706 interaction between organisms physiological interaction between organisms physiological interaction with other organism biological_process multi-organism process A biological process which involves another organism of the same or different species. GOC:jl Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. biological_process 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. cellular response to stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. GOC:bf GOC:jl Any process that modulates the rate or extent of progression through the cell cycle. GO:0000074 cell cycle modulation cell cycle regulation control of cell cycle progression modulation of cell cycle progression regulation of cell cycle progression regulation of progression through cell cycle biological_process cell cycle regulator tumor suppressor regulation of cell cycle Any process that modulates the rate or extent of progression through the cell cycle. GOC:ai GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of cell division. up regulation of cell division up-regulation of cell division upregulation of cell division activation of cell division stimulation of cell division biological_process positive regulation of cell division Any process that activates or increases the frequency, rate or extent of cell division. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of cell division. down regulation of cell division down-regulation of cell division downregulation of cell division inhibition of cell division biological_process negative regulation of cell division Any process that stops, prevents, or reduces the frequency, rate or extent of cell division. GOC:ai Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. biological_process regulation of nuclear division Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. down regulation of nuclear division down-regulation of nuclear division downregulation of nuclear division inhibition of nuclear division biological_process negative regulation of nuclear division Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. up regulation of nuclear division up-regulation of nuclear division upregulation of nuclear division activation of nuclear division stimulation of nuclear division biological_process positive regulation of nuclear division Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process regulation of amine transport Any process that modulates the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of amine transport down-regulation of amine transport downregulation of amine transport inhibition of amine transport biological_process negative regulation of amine transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of amine transport up-regulation of amine transport upregulation of amine transport activation of amine transport stimulation of amine transport biological_process positive regulation of amine transport Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. biological_process regulation of nervous system development Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. down regulation of nervous system development down-regulation of nervous system development downregulation of nervous system development inhibition of nervous system development biological_process negative regulation of nervous system development Any process that stops, prevents, or reduces the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. GOC:ai Any process that activates, maintains or increases the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. up regulation of nervous system development up-regulation of nervous system development upregulation of nervous system development activation of nervous system development stimulation of nervous system development biological_process positive regulation of nervous system development Any process that activates, maintains or increases the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. GOC:ai Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. biological_process regulation of chromosome segregation Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. up regulation of chromosome segregation up-regulation of chromosome segregation upregulation of chromosome segregation activation of chromosome segregation stimulation of chromosome segregation biological_process positive regulation of chromosome segregation Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. down regulation of chromosome segregation down-regulation of chromosome segregation downregulation of chromosome segregation inhibition of chromosome segregation biological_process negative regulation of chromosome segregation Any process that stops, prevents, or reduces the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai Any process that modulates the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins. biological_process peptidase regulator activity regulation of peptidase activity Any process that modulates the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins. GOC:ai Any process that modulates the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. protease regulator activity biological_process regulation of endopeptidase activity Any process that modulates the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins. GOC:ai GOC:hjd The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. tanyaberardini 2015-10-21T13:22:47Z GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. transmembrane transport The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GOC:dph GOC:jid 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. Wikipedia:Redox oxidation reduction oxidoreductase process biological_process oxidation-reduction process 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 oxidoreductase process 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. GO:0032947 binding, bridging molecular_function protein complex scaffold activity protein-containing complex scaffold activity molecular adaptor activity 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 Any process in which a peroxisome is transported to, and/or maintained in, a specific location. A peroxisome is a small membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules. peroxisome localisation biological_process peroxisome localization Any process in which a peroxisome is transported to, and/or maintained in, a specific location. A peroxisome is a small membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules. GOC:dph PMID:16449325 peroxisome localisation GOC:mah The microtubule-based process in which a peroxisome is transported to, and/or maintained in, a specific location. A peroxisome is a small membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules. microtubule-based peroxisome localisation biological_process microtubule-based peroxisome localization The microtubule-based process in which a peroxisome is transported to, and/or maintained in, a specific location. A peroxisome is a small membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules. GOC:dph PMID:16449325 microtubule-based peroxisome localisation GOC:mah Any process that modulates the frequency, rate or extent of 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. biological_process regulation of macromolecule metabolic process Any process that modulates the frequency, rate or extent of 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. GOC:dph GOC:tb The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GO:0042384 Reactome:R-HSA-5617833.2 ciliogenesis cilium assembly cilium formation microtubule-based flagellum assembly biological_process cilium biogenesis cilium morphogenesis cilium organization Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium assembly The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GOC:BHF GOC:cilia GOC:dph GOC:kmv GOC:pr GOC:vw ISBN:0198506732 PMID:13978319 PMID:27350441 Reactome:R-HSA-5617833.2 cilium biogenesis GOC:mah cilium organization GOC:dph Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process regulation of cell development Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. regulation of cellular localisation biological_process regulation of cellular localization Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. GOC:dph GOC:tb regulation of cellular localisation GOC:mah The removal of tubulin heterodimers from one or both ends of an axonemal microtubule. An axonemal microtubule is a microtubule in the axoneme of a cilium or flagellum; an axoneme contains nine modified doublet microtubules surrounding a pair of single microtubules. biological_process axonemal microtubule depolymerization The removal of tubulin heterodimers from one or both ends of an axonemal microtubule. An axonemal microtubule is a microtubule in the axoneme of a cilium or flagellum; an axoneme contains nine modified doublet microtubules surrounding a pair of single microtubules. GOC:cilia GOC:dph GOC:krc GOC:tb Any process that modulates the rate, frequency, or extent of cell projection assembly. biological_process regulation of cell projection formation regulation of cell projection assembly Any process that modulates the rate, frequency, or extent of cell projection assembly. GOC:dph GOC:tb regulation of cell projection formation GOC:dph GOC:tb Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. dph 2009-04-13T01:56:10Z biological_process negative regulation of cell death Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. GOC:BHF GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. dph 2009-05-18T02:29:43Z biological_process regulation of vesicle-mediated transport Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of ER to Golgi vesicle-mediated transport, the directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi. dph 2009-05-18T02:37:00Z biological_process regulation of ER to Golgi vesicle-mediated transport Any process that modulates the rate, frequency, or extent of ER to Golgi vesicle-mediated transport, the directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins. dph 2009-05-18T03:07:02Z biological_process regulation of microtubule-based movement Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of a mRNA catabolic process, the chemical reactions and pathways resulting in the breakdown of 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. dph 2010-01-29T01:48:10Z biological_process regulation of mRNA decay regulation of mRNA catabolic process Any process that modulates the rate, frequency, or extent of a mRNA catabolic process, the chemical reactions and pathways resulting in the breakdown of 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. GOC:ascb_2009 GOC:dph GOC:tb regulation of mRNA decay GOC:ascb_2009 GOC:dph GOC:tb Any process that increases the rate, frequency, or extent of a mRNA catabolic process, the chemical reactions and pathways resulting in the breakdown of 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. dph 2010-01-29T01:58:03Z biological_process positive regulation of mRNA decay positive regulation of mRNA catabolic process Any process that increases the rate, frequency, or extent of a mRNA catabolic process, the chemical reactions and pathways resulting in the breakdown of 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. GOC:ascb_2009 GOC:dph GOC:tb positive regulation of mRNA decay GOC:ascb_2009 GOC:dph GOC:tb 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. janelomax 2010-02-08T02:43:11Z GO:0016044 GO:0044802 cellular membrane organisation cellular membrane organization membrane organisation biological_process membrane organization and biogenesis single-organism membrane organization membrane organization 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 membrane organisation GOC:mah membrane organization and biogenesis GOC:mah The membrane organization process that joins two lipid bilayers to form a single membrane. janelomax 2010-02-08T02:48:06Z GO:0006944 GO:0044801 Wikipedia:Lipid_bilayer_fusion cellular membrane fusion biological_process single-organism membrane fusion membrane fusion The membrane organization process that joins two lipid bilayers to form a single membrane. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome. dph 2010-05-17T01:33:20Z biological_process regulation of proteasomal protein catabolic process Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome. GOC:dph GOC:tb A process in which a protein is transported to, or maintained in, a location within a lysosome. dph 2012-10-05T10:50:51Z biological_process protein localization to lysosome A process in which a protein is transported to, or maintained in, a location within a lysosome. GOC:dph A process in which a protein is transported to, or maintained in, a location within a cilium. dph 2013-03-22T15:41:44Z biological_process protein localization to cilium A process in which a protein is transported to, or maintained in, a location within a cilium. GOC:dph A cellular process that results in the breakdown of a cilium. dph 2013-04-18T14:59:59Z cilium resorption biological_process Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium disassembly A cellular process that results in the breakdown of a cilium. GOC:cilia GOC:dph PMID:17604723 PMID:27350441 cilium resorption GOC:dph Combining with a nuclear import signal (NIS) on a cargo to be transported, to mediate transport of the cargo through the nuclear pore, from the cytoplasm to the nuclear lumen. The cargo can be either a RNA or a protein. https://github.com/geneontology/go-ontology/issues/14336 dph 2014-03-03T07:58:18Z molecular_function importin activity nuclear import signal receptor activity Combining with a nuclear import signal (NIS) on a cargo to be transported, to mediate transport of the cargo through the nuclear pore, from the cytoplasm to the nuclear lumen. The cargo can be either a RNA or a protein. GOC:dph GOC:pg GOC:vw PMID:28713609 Wikipedia:Nuclear_transport The aggregation, arrangement and bonding together of the mitochondrial ribosome and of its subunits. dph 2014-11-07T15:32:20Z biological_process mitochondrial ribosome assembly The aggregation, arrangement and bonding together of the mitochondrial ribosome and of its subunits. GOC:dph A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). dph 2015-05-06T11:22:38Z cellular_component transferase complex, transferring phosphorus-containing groups A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GOC:bhm GOC:dph The chemical reactions and pathways resulting in the breakdown of lipid droplets and hydrolysis of stored triglycerides occurring through the orchestrated activation of cytosolic lipases. dph 2015-07-08T13:42:15Z biological_process cytosolic lipolysis The chemical reactions and pathways resulting in the breakdown of lipid droplets and hydrolysis of stored triglycerides occurring through the orchestrated activation of cytosolic lipases. GOC:autophagy The disaggregation of a mitochondrion into its constituent components. dph 2015-07-08T13:59:16Z mitochondrion degradation biological_process mitochondrion disassembly The disaggregation of a mitochondrion into its constituent components. GOC:autophagy PMID:25009776 mitochondrion degradation GOC:autophagy Any process in which the microtubule organizing center is transported to, and/or maintained in, a specific location within the cell. MTOC localization MTOC polarity microtubule organizing center polarity biological_process microtubule organizing center localization Any process in which the microtubule organizing center is transported to, and/or maintained in, a specific location within the cell. PMID:21281821 A cellular process involving delivery of a portion of the cytoplasm to lysosomes or to the plant or fungal vacuole that does not involve direct transport through the endocytic or vacuolar protein sorting (Vps) pathways. This process typically leads to degradation of the cargo; however, it can also be used to deliver resident proteins, such as in the cytoplasm-to-vacuole targeting (Cvt) pathway. dph 2017-07-13T19:42:14Z biological_process process utilizing autophagic mechanism A cellular process involving delivery of a portion of the cytoplasm to lysosomes or to the plant or fungal vacuole that does not involve direct transport through the endocytic or vacuolar protein sorting (Vps) pathways. This process typically leads to degradation of the cargo; however, it can also be used to deliver resident proteins, such as in the cytoplasm-to-vacuole targeting (Cvt) pathway. PMID:21997368 PMID:22966490 PMID:28596378 The directed movement of a protein to a specific location in a plasma membrane. dph 2017-10-26T12:55:15Z biological_process establishment of protein localization to plasma membrane The directed movement of a protein to a specific location in a plasma membrane. GOC:dph GOC:vw Any process that modulates the rate, frequency or extent of a small molecule metabolic process. dph 2018-03-19T14:11:54Z regulation of small molecule metabolism biological_process regulation of small molecule metabolic process Any process that modulates the rate, frequency or extent of a small molecule metabolic process. GOC:vw Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process. dph 2018-03-19T14:25:10Z positive regulation of small molecule metabolism biological_process positive regulation of small molecule metabolic process Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process. GOC:vw Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process. dph 2018-03-19T14:27:23Z negative regulation of small molecule metabolism biological_process negative regulation of small molecule metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process. GOC:vw Any process that modulates the frequency, rate or extent of mitochondrial gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). dph 2019-05-30T16:45:04Z biological_process regulation of mitochondrial gene expression Any process that modulates the frequency, rate or extent of mitochondrial gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). PMID:28285835 The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore. intracellular membrane translocation of a protein intracellular protein membrane transport intracellular protein transport across a membrane biological_process Note that this term is not intended for use in annotating lateral movement within membranes. intracellular protein transmembrane transport The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore. GOC:isa_complete The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. GO:0006461 biological_process chaperone activity macromolecular complex assembly macromolecule complex assembly protein complex assembly protein complex formation protein-containing complex assembly The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. GOC:jl Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process biological regulation 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 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. regulation of biological attribute regulation of biological characteristic biological_process regulation of biological quality 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 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. regulation of a molecular function biological_process regulation of molecular function 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 Catalysis of the hydrolysis of peptide bonds formed between L-amino acids. Reactome:R-HSA-3065958 Reactome:R-HSA-3065959 Reactome:R-HSA-4167501 Reactome:R-HSA-6803060 molecular_function peptidase activity, acting on L-amino acid peptides Catalysis of the hydrolysis of peptide bonds formed between L-amino acids. GOC:mah Reactome:R-HSA-3065958 An unknown protease degrades ACACA Reactome:R-HSA-3065959 An unknown protease degrades hCBXs Reactome:R-HSA-4167501 An unknown protease degrades ACACB Reactome:R-HSA-6803060 DCD(63-110) is processed to DCD(63-109) An organelle lumen that is part of an intracellular organelle. cellular_component intracellular organelle lumen An organelle lumen that is part of an intracellular organelle. GOC:mah The process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA. mitochondrial translation initiation biological_process mitochondrial translational initiation The process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA. GOC:mah mitochondrial translation initiation GOC:mah The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in a mitochondrion. mitochondrial translation elongation biological_process mitochondrial translational elongation The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in a mitochondrion. GOC:mah mitochondrial translation elongation GOC:mah The process resulting in the release of a polypeptide chain from the ribosome in a mitochondrion, usually in response to a termination codon (note that mitochondria use variants of the universal genetic code that differ between different taxa). mitochondrial translation termination biological_process mitochondrial translational termination The process resulting in the release of a polypeptide chain from the ribosome in a mitochondrion, usually in response to a termination codon (note that mitochondria use variants of the universal genetic code that differ between different taxa). GOC:mah http://mitogenome.org/index.php/Genetic_Code_of_mitochondria mitochondrial translation termination GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. regulation of mitochondrial protein anabolism regulation of mitochondrial protein biosynthesis regulation of mitochondrial protein formation regulation of mitochondrial protein synthesis biological_process regulation of mitochondrial translation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. GOC:mah regulation of mitochondrial protein anabolism GOC:mah regulation of mitochondrial protein biosynthesis GOC:mah regulation of mitochondrial protein formation GOC:mah regulation of mitochondrial protein synthesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. negative regulation of mitochondrial protein anabolism negative regulation of mitochondrial protein biosynthesis negative regulation of mitochondrial protein formation negative regulation of mitochondrial protein synthesis biological_process negative regulation of mitochondrial translation Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. GOC:mah negative regulation of mitochondrial protein anabolism GOC:mah negative regulation of mitochondrial protein biosynthesis GOC:mah negative regulation of mitochondrial protein formation GOC:mah negative regulation of mitochondrial protein synthesis GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. positive regulation of mitochondrial protein anabolism positive regulation of mitochondrial protein biosynthesis positive regulation of mitochondrial protein formation positive regulation of mitochondrial protein synthesis biological_process positive regulation of mitochondrial translation Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. GOC:mah positive regulation of mitochondrial protein anabolism GOC:mah positive regulation of mitochondrial protein biosynthesis GOC:mah positive regulation of mitochondrial protein formation GOC:mah positive regulation of mitochondrial protein synthesis GOC:mah Any process that modulates the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion. regulation of mitochondrial translation initiation biological_process regulation of mitochondrial translational initiation Any process that modulates the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion. GOC:mah regulation of mitochondrial translation initiation GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion. negative regulation of mitochondrial translation initiation biological_process negative regulation of mitochondrial translational initiation Any process that stops, prevents, or reduces the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion. GOC:mah negative regulation of mitochondrial translation initiation GOC:mah Any process that activates or increases the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion. positive regulation of mitochondrial translation initiation biological_process positive regulation of mitochondrial translational initiation Any process that activates or increases the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion. GOC:mah positive regulation of mitochondrial translation initiation GOC:mah The directed movement of a protein to a specific location on a chromosome. establishment of protein localisation to chromosome biological_process establishment of protein localization to chromosome The directed movement of a protein to a specific location on a chromosome. GOC:BHF GOC:mah establishment of protein localisation to chromosome GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. regulation of establishment of protein localisation biological_process regulation of establishment of protein localization Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. GOC:BHF GOC:mah regulation of establishment of protein localisation GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome. regulation of establishment of protein localisation to chromosome biological_process regulation of establishment of protein localization to chromosome Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome. GOC:BHF GOC:mah regulation of establishment of protein localisation to chromosome GOC:mah Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. regulation of microtubule cytoskeleton organisation regulation of microtubule dynamics biological_process regulation of microtubule cytoskeleton organization Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. GOC:mah regulation of microtubule cytoskeleton organisation GOC:mah regulation of microtubule dynamics GOC:dph GOC:tb A process in which a protein is transported to, or maintained in, a location within the mitochondrion. midori 2009-04-24T02:31:18Z protein localisation in mitochondrion protein localization in mitochondrion biological_process protein localization to mitochondrion A process in which a protein is transported to, or maintained in, a location within the mitochondrion. GOC:ecd protein localisation in mitochondrion GOC:mah The chemical reactions and pathways resulting in the formation of a macromolecule that is destined to form part of a specific cellular component. midori 2009-04-28T11:01:25Z cellular component macromolecule biosynthesis biological_process cellular component macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule that is destined to form part of a specific cellular component. GOC:mah cellular component macromolecule biosynthesis GOC:mah Interacting selectively and non-covalently with a proteasome, a large multisubunit protein complex that catalyzes protein degradation. midori 2009-05-01T04:38:58Z molecular_function proteasome binding Interacting selectively and non-covalently with a proteasome, a large multisubunit protein complex that catalyzes protein degradation. GOC:mah The aggregation, arrangement and bonding together of a cell wall. A cell wall is a rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells. midori 2009-06-16T03:58:20Z biological_process cell wall assembly The aggregation, arrangement and bonding together of a cell wall. A cell wall is a rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells. GOC:mah Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. midori 2009-06-16T04:08:29Z cellular macromolecule localisation biological_process cellular macromolecule localization Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:mah cellular macromolecule localisation GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of proteins from the endoplasmic reticulum. midori 2009-08-17T03:39:18Z regulation of protein exit from ER regulation of protein export from ER regulation of protein export from endoplasmic reticulum biological_process regulation of protein exit from endoplasmic reticulum Any process that modulates the frequency, rate or extent of the directed movement of proteins from the endoplasmic reticulum. GOC:mah regulation of protein exit from ER GOC:mah regulation of protein export from ER GOC:mah regulation of protein export from endoplasmic reticulum GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of proteins from the endoplasmic reticulum. midori 2009-08-17T03:45:56Z down regulation of protein exit from endoplasmic reticulum down-regulation of protein exit from endoplasmic reticulum downregulation of protein exit from endoplasmic reticulum negative regulation of protein exit from ER negative regulation of protein export from ER negative regulation of protein export from endoplasmic reticulum inhibition of protein exit from endoplasmic reticulum biological_process negative regulation of protein exit from endoplasmic reticulum Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of proteins from the endoplasmic reticulum. GOC:mah down regulation of protein exit from endoplasmic reticulum GOC:mah down-regulation of protein exit from endoplasmic reticulum GOC:mah downregulation of protein exit from endoplasmic reticulum GOC:mah negative regulation of protein exit from ER GOC:mah negative regulation of protein export from ER GOC:mah negative regulation of protein export from endoplasmic reticulum GOC:mah inhibition of protein exit from endoplasmic reticulum GOC:mah Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the endoplasmic reticulum. midori 2009-08-17T03:50:04Z positive regulation of protein exit from ER positive regulation of protein export from ER positive regulation of protein export from endoplasmic reticulum up regulation of protein exit from endoplasmic reticulum up-regulation of protein exit from endoplasmic reticulum upregulation of protein exit from endoplasmic reticulum activation of protein exit from endoplasmic reticulum stimulation of protein exit from endoplasmic reticulum biological_process positive regulation of protein exit from endoplasmic reticulum Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the endoplasmic reticulum. GOC:mah positive regulation of protein exit from ER GOC:mah positive regulation of protein export from ER GOC:mah positive regulation of protein export from endoplasmic reticulum GOC:mah up regulation of protein exit from endoplasmic reticulum GOC:mah up-regulation of protein exit from endoplasmic reticulum GOC:mah upregulation of protein exit from endoplasmic reticulum GOC:mah activation of protein exit from endoplasmic reticulum GOC:mah stimulation of protein exit from endoplasmic reticulum GOC:mah The chemical reactions and pathways that result in the breakdown of macromolecules that form part of a cell wall, and contributes to the breakdown of the cell wall. midori 2009-09-09T02:40:57Z biological_process cell wall macromolecule catabolic process involved in cell wall disassembly The chemical reactions and pathways that result in the breakdown of macromolecules that form part of a cell wall, and contributes to the breakdown of the cell wall. GOC:mah The aggregation, arrangement and bonding together of a set of components to form an organelle. 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. midori 2009-09-15T03:00:51Z biological_process organelle assembly The aggregation, arrangement and bonding together of a set of components to form an organelle. 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 A process in which a protein is transported to, or maintained in, a location within the endoplasmic reticulum. midori 2009-10-02T12:43:34Z protein localisation in endoplasmic reticulum protein localization in ER protein localization in endoplasmic reticulum biological_process protein localization to endoplasmic reticulum A process in which a protein is transported to, or maintained in, a location within the endoplasmic reticulum. GOC:mah protein localisation in endoplasmic reticulum GOC:mah protein localization in ER GOC:mah The process of directing proteins towards the vacuole using signals contained within the protein, occurring as part of autophagy, the process in which cells digest parts of their own cytoplasm. midori 2009-11-25T02:25:27Z biological_process protein targeting to autophagosome protein targeting to vacuole involved in autophagy The process of directing proteins towards the vacuole using signals contained within the protein, occurring as part of autophagy, the process in which cells digest parts of their own cytoplasm. GOC:mah protein targeting to autophagosome GOC:pad A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cell wall. midori 2010-01-13T03:19:38Z GO:0070882 cell wall organisation or biogenesis cell wall organization or biogenesis at cellular level cellular cell wall organisation or biogenesis cellular cell wall organization or biogenesis biological_process cell wall organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cell wall. GOC:mah cell wall organisation or biogenesis GOC:mah cell wall organization or biogenesis at cellular level GOC:mah cellular cell wall organisation or biogenesis GOC:mah 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. midori 2010-01-13T03:33:07Z GO:0007047 GO:0044234 cell wall organisation cell wall organisation in other organism cell wall organization at cellular level cell wall organization in other organism cellular cell wall organisation cellular cell wall organization biological_process cell wall organization and biogenesis cell wall organization 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 cell wall organisation in other organism GOC:mah cell wall organization at cellular level GOC:mah cell wall organization and biogenesis GOC:mah Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location. midori 2010-02-25T04:00:13Z protein localisation in extracellular region protein localization in extracellular region biological_process protein localization to extracellular region Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location. GOC:mah protein localisation in extracellular region GOC:mah The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. midori 2010-03-08T02:15:14Z biological_process organic substance transport The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. GOC:mah The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. midori 2010-03-08T03:32:18Z organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism biological_process organic substance metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. GOC:mah The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. midori 2010-03-08T03:56:28Z biological_process nitrogen compound transport The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah The aggregation, arrangement and bonding together of a set of components to form a membrane. midori 2010-03-10T11:19:17Z biological_process membrane assembly The aggregation, arrangement and bonding together of a set of components to form a membrane. GOC:mah The process in which a protein is transported across a membrane. midori 2010-09-03T02:54:26Z protein membrane transport biological_process Note that this term is not intended for use in annotating lateral movement within membranes. protein transmembrane transport The process in which a protein is transported across a membrane. GOC:mah GOC:vw Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. midori 2010-09-08T10:10:35Z RNA-protein complex subunit organization protein-RNA complex subunit organization ribonucleoprotein complex subunit organisation biological_process ribonucleoprotein complex subunit organization Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. GOC:mah RNA-protein complex subunit organization GOC:mah protein-RNA complex subunit organization GOC:mah ribonucleoprotein complex subunit organisation GOC:mah A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. midori 2010-09-10T01:39:16Z GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level biological_process cellular component organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:mah cellular component organisation or biogenesis GOC:mah cellular component organisation or biogenesis at cellular level GOC:mah The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. midori 2010-09-15T02:14:33Z DNA anabolism DNA biosynthesis DNA formation DNA synthesis biological_process DNA biosynthetic process The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. GOC:mah DNA anabolism GOC:mah DNA biosynthesis GOC:mah DNA formation GOC:mah