# statements

stanza: BFO:0000051
subject: BFO:0000051
predicate: IAO:0000115
datatype: xsd:string
value:
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.


stanza: BFO:0000062
subject: BFO:0000062
predicate: IAO:0000115
language: en
value:
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.


stanza: BFO:0000062
subject: BFO:0000062
predicate: IAO:0000115
datatype: xsd:string
value:
The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P.


stanza: BFO:0000063
subject: BFO:0000063
predicate: IAO:0000115
language: en
value:
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.


stanza: BFO:0000066
subject: BFO:0000066
predicate: IAO:0000115
language: en
value:
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t


stanza: BFO:0000067
subject: BFO:0000067
predicate: IAO:0000115
language: en
value:
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t


stanza: RO:0000052
subject: RO:0000052
predicate: IAO:0000115
language: en
value:
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence


stanza: RO:0000053
subject: RO:0000053
predicate: IAO:0000115
language: en
value:
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence


stanza: RO:0000056
subject: RO:0000056
predicate: IAO:0000115
language: en
value:
a relation between a continuant and a process, in which the continuant is somehow involved in the process


stanza: RO:0000057
subject: RO:0000057
predicate: IAO:0000115
language: en
value:
a relation between a process and a continuant, in which the continuant is somehow involved in the process


stanza: RO:0000081
subject: RO:0000081
predicate: IAO:0000115
language: en
value:
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence


stanza: RO:0000087
subject: RO:0000087
predicate: IAO:0000115
language: en
value:
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence


stanza: RO:0002013
subject: RO:0002013
predicate: IAO:0000115
value:
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.


stanza: RO:0002014
subject: RO:0002014
predicate: IAO:0000115
value:
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.


stanza: RO:0002015
subject: RO:0002015
predicate: IAO:0000115
value:
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.


stanza: RO:0002018
subject: RO:0002018
predicate: IAO:0000115
value:
w 'has process component' p if p and w are processes,  w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.


stanza: RO:0002023
subject: RO:0002023
predicate: IAO:0000115
value:
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.


stanza: RO:0002024
subject: RO:0002024
predicate: IAO:0000115
value:
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.


stanza: RO:0002025
subject: RO:0002025
predicate: IAO:0000115
value:
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674),  A 'has component activity' B and B is the effector (output function) of B.  Each compound function has only one effector activity.


stanza: RO:0002160
subject: RO:0002160
predicate: IAO:0000115
value:
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.


stanza: RO:0002160
subject: RO:0002160
predicate: IAO:0000115
datatype: xsd:string
value:
U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon.


stanza: RO:0002162
subject: RO:0002162
predicate: IAO:0000115
value:
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.


stanza: RO:0002180
subject: RO:0002180
predicate: IAO:0000115
value:
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.


stanza: RO:0002211
subject: RO:0002211
predicate: IAO:0000115
value:
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.


stanza: RO:0002212
subject: RO:0002212
predicate: IAO:0000115
value:
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.


stanza: RO:0002213
subject: RO:0002213
predicate: IAO:0000115
value:
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.


stanza: RO:0002215
subject: RO:0002215
predicate: IAO:0000115
value:
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.


stanza: RO:0002216
subject: RO:0002216
predicate: IAO:0000115
value:
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.


stanza: RO:0002233
subject: RO:0002233
predicate: IAO:0000115
value:
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.


stanza: RO:0002263
subject: RO:0002263
predicate: IAO:0000115
value:
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.


stanza: RO:0002264
subject: RO:0002264
predicate: IAO:0000115
value:
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.


stanza: RO:0002328
subject: RO:0002328
predicate: IAO:0000115
value:
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.


stanza: RO:0002410
subject: RO:0002410
predicate: IAO:0000115
value:
This relation groups causal relations between material entities and causal relations between processes


stanza: RO:0002412
subject: RO:0002412
predicate: IAO:0000115
value:
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p  must be an input of q.


stanza: RO:0002418
subject: RO:0002418
predicate: IAO:0000115
value:
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.


stanza: RO:0002431
subject: RO:0002431
predicate: IAO:0000115
value:
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p


stanza: RO:0002432
subject: RO:0002432
predicate: IAO:0000115
value:
c executes activity in d if and only if c enables p and p occurs_in d.  Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.


stanza: RO:0002434
subject: RO:0002434
predicate: IAO:0000115
value:
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.


stanza: RO:0002436
subject: RO:0002436
predicate: IAO:0000115
value:
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.


stanza: RO:0002448
subject: RO:0002448
predicate: IAO:0000115
value:
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.

A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.


stanza: RO:0002449
subject: RO:0002449
predicate: IAO:0000115
value:
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. 
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.


stanza: RO:0002450
subject: RO:0002450
predicate: IAO:0000115
value:
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. 
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.


stanza: RO:0002479
subject: RO:0002479
predicate: IAO:0000115
value:
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.


stanza: RO:0002500
subject: RO:0002500
predicate: IAO:0000115
value:
A relationship between a material entity and a process where the material entity has some causal role that influences the process


stanza: RO:0002501
subject: RO:0002501
predicate: IAO:0000115
value:
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.


stanza: RO:0002566
subject: RO:0002566
predicate: IAO:0000115
value:
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).


stanza: RO:0002578
subject: RO:0002578
predicate: IAO:0000115
value:
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  regulates the kinase activity (P2) of protein B then P1 directly regulates P2.


stanza: RO:0002584
subject: RO:0002584
predicate: IAO:0000115
value:
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p


stanza: RO:0002595
subject: RO:0002595
predicate: IAO:0000115
value:
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.


stanza: RO:0002629
subject: RO:0002629
predicate: IAO:0000115
value:
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.


stanza: RO:0002630
subject: RO:0002630
predicate: IAO:0000115
value:
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.


stanza: RO:0004007
subject: RO:0004007
predicate: IAO:0000115
value:
p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.


stanza: RO:0004031
subject: RO:0004031
predicate: IAO:0000115
value:
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.


stanza: RO:0004034
subject: RO:0004034
predicate: IAO:0000115
value:
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive


stanza: RO:0004035
subject: RO:0004035
predicate: IAO:0000115
value:
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative


stanza: RO:0011002
subject: RO:0011002
predicate: IAO:0000115
value:
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.


stanza: BFO:0000002
subject: BFO:0000002
predicate: IAO:0000115
language: en
value:
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.


stanza: BFO:0000004
subject: BFO:0000004
predicate: IAO:0000115
language: en
value:
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.


stanza: BFO:0000015
subject: BFO:0000015
predicate: IAO:0000115
language: en
value:
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.


stanza: BFO:0000017
subject: BFO:0000017
predicate: IAO:0000115
language: en
value:
A specifically dependent continuant  that inheres in continuant  entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.


stanza: BFO:0000020
subject: BFO:0000020
predicate: IAO:0000115
language: en
value:
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.


stanza: BFO:0000023
subject: BFO:0000023
predicate: IAO:0000115
language: en
value:
A realizable entity  the manifestation of which brings about some result or end that is not essential to a continuant  in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant  in some kinds of natural, social or institutional contexts.


stanza: BFO:0000040
subject: BFO:0000040
predicate: IAO:0000115
language: en
value:
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.


stanza: CL:0000000
subject: CL:0000000
predicate: IAO:0000115
datatype: xsd:string
value:
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.


stanza: GO:0003674
subject: GO:0003674
predicate: rdfs:comment
datatype: xsd:string
value:
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.


stanza: GO:0003674
subject: GO:0003674
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0003824
subject: GO:0003824
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0005575
subject: GO:0005575
predicate: rdfs:comment
datatype: xsd:string
value:
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.


stanza: GO:0005575
subject: GO:0005575
predicate: IAO:0000115
datatype: xsd:string
value:
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).


stanza: GO:0005622
subject: GO:0005622
predicate: IAO:0000115
datatype: xsd:string
value:
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.


stanza: GO:0005634
subject: GO:0005634
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0005635
subject: GO:0005635
predicate: IAO:0000115
datatype: xsd:string
value:
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).


stanza: GO:0005737
subject: GO:0005737
predicate: IAO:0000115
datatype: xsd:string
value:
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.


stanza: GO:0005773
subject: GO:0005773
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0005886
subject: GO:0005886
predicate: IAO:0000115
datatype: xsd:string
value:
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.


stanza: GO:0005938
subject: GO:0005938
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0006793
subject: GO:0006793
predicate: IAO:0000115
datatype: xsd:string
value:
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).


stanza: GO:0006796
subject: GO:0006796
predicate: IAO:0000115
datatype: xsd:string
value:
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.


stanza: GO:0008150
subject: GO:0008150
predicate: rdfs:comment
datatype: xsd:string
value:
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.


stanza: GO:0008150
subject: GO:0008150
predicate: IAO:0000115
datatype: xsd:string
value:
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.


stanza: GO:0008152
subject: GO:0008152
predicate: rdfs:comment
datatype: xsd:string
value:
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.


stanza: GO:0008152
subject: GO:0008152
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0009892
subject: GO:0009892
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.


stanza: GO:0009893
subject: GO:0009893
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.


stanza: GO:0009987
subject: GO:0009987
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0010562
subject: GO:0010562
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.


stanza: GO:0010563
subject: GO:0010563
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.


stanza: GO:0012505
subject: GO:0012505
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0016301
subject: GO:0016301
predicate: rdfs:comment
datatype: xsd:string
value:
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.


stanza: GO:0016310
subject: GO:0016310
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0016740
subject: GO:0016740
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0016740
subject: _:riog00000514
predicate: rdfs:label
datatype: xsd:string
value:
TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248


stanza: GO:0016772
subject: GO:0016772
predicate: rdfs:comment
datatype: xsd:string
value:
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.


stanza: GO:0016772
subject: GO:0016772
predicate: IAO:0000115
datatype: xsd:string
value:
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).


stanza: GO:0019207
subject: GO:0019207
predicate: IAO:0000115
datatype: xsd:string
value:
Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.


stanza: GO:0019209
subject: GO:0019209
predicate: IAO:0000115
datatype: xsd:string
value:
Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.


stanza: GO:0019220
subject: GO:0019220
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.


stanza: GO:0019222
subject: GO:0019222
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.


stanza: GO:0031090
subject: GO:0031090
predicate: IAO:0000115
datatype: xsd:string
value:
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.


stanza: GO:0031323
subject: GO:0031323
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.


stanza: GO:0031324
subject: GO:0031324
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0031325
subject: GO:0031325
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.


stanza: GO:0031965
subject: GO:0031965
predicate: IAO:0000115
datatype: xsd:string
value:
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.


stanza: GO:0031967
subject: GO:0031967
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0031975
subject: GO:0031975
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0033673
subject: GO:0033673
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0033674
subject: GO:0033674
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0042325
subject: GO:0042325
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.


stanza: GO:0042326
subject: GO:0042326
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.


stanza: GO:0042327
subject: GO:0042327
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.


stanza: GO:0043226
subject: GO:0043226
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0043227
subject: GO:0043227
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0043229
subject: GO:0043229
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0043231
subject: GO:0043231
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0043549
subject: GO:0043549
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0044092
subject: GO:0044092
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0044093
subject: GO:0044093
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0045936
subject: GO:0045936
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates.


stanza: GO:0045937
subject: GO:0045937
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.


stanza: GO:0048518
subject: GO:0048518
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0048519
subject: GO:0048519
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0048522
subject: GO:0048522
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0048523
subject: GO:0048523
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0050789
subject: GO:0050789
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0050794
subject: GO:0050794
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0051174
subject: GO:0051174
predicate: IAO:0000115
datatype: xsd:string
value:
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.


stanza: GO:0051338
subject: GO:0051338
predicate: rdfs:comment
datatype: xsd:string
value:
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.


stanza: GO:0051338
subject: GO:0051338
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0051347
subject: GO:0051347
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0051348
subject: GO:0051348
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0065009
subject: GO:0065009
predicate: IAO:0000115
datatype: xsd:string
value:
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.


stanza: GO:0071944
subject: GO:0071944
predicate: IAO:0000115
datatype: xsd:string
value:
The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.


stanza: GO:0098590
subject: GO:0098590
predicate: rdfs:comment
datatype: xsd:string
value:
Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.


stanza: GO:0099568
subject: GO:0099568
predicate: IAO:0000115
datatype: xsd:string
value:
Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.


stanza: GO:0110165
subject: GO:0110165
predicate: IAO:0000115
datatype: xsd:string
value:
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.


stanza: NCBITaxon:Union_0000024
subject: NCBITaxon:Union_0000024
predicate: IAO:0000115
datatype: xsd:string
value:
The unikonts have a triple-gene fusion that is lacking in the bikonts. The three genes that are fused together in the unikonts but not bacteria or bikonts encode enzymes for synthesis of the pyrimidine nucleotides: carbamoyl phosphate synthase, dihydroorotase, aspartate carbamoyltransferase. This must have involved a double fusion, a rare pair of events, supporting the shared ancestry of Opisthokonta and Amoebozoa.


stanza: PATO:0000001
subject: PATO:0000001
predicate: IAO:0000115
datatype: xsd:string
value:
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities


stanza: IAO:0000103
subject: IAO:0000103
predicate: IAO:0000115
language: en
value:
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job


stanza: IAO:0000120
subject: IAO:0000120
predicate: IAO:0000115
language: en
value:
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.


stanza: IAO:0000121
subject: IAO:0000121
predicate: IAO:0000115
language: en
value:
term created to ease viewing/sort terms for development purpose, and will not be included in a release


stanza: IAO:0000122
subject: IAO:0000122
predicate: IAO:0000115
language: en
value:
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release.  Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."


stanza: IAO:0000123
subject: IAO:0000123
predicate: IAO:0000115
language: en
value:
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.


stanza: IAO:0000125
subject: IAO:0000125
predicate: IAO:0000115
language: en
value:
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.


stanza: IAO:0000224
subject: IAO:0000224
predicate: IAO:0000115
language: en
value:
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.


stanza: IAO:0000420
subject: IAO:0000420
predicate: IAO:0000115
datatype: xsd:string
value:
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal


stanza: IAO:0000421
subject: IAO:0000421
predicate: IAO:0000115
datatype: xsd:string
value:
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.


stanza: IAO:0000428
subject: IAO:0000428
predicate: IAO:0000115
language: en
value:
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.


