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mobio-full.obo
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format-version: 1.2
data-version: mobio/releases/2023-04-13/mobio-full.owl
subsetdef: gocheck_do_not_annotate ""
subsetdef: gocheck_do_not_manually_annotate ""
subsetdef: goslim_agr ""
subsetdef: goslim_candida ""
subsetdef: goslim_chembl ""
subsetdef: goslim_drosophila ""
subsetdef: goslim_flybase_ribbon ""
subsetdef: goslim_generic ""
subsetdef: goslim_metagenomics ""
subsetdef: goslim_pir ""
subsetdef: goslim_plant ""
subsetdef: goslim_pombe ""
subsetdef: goslim_yeast ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
subsetdef: prokaryote_subset ""
subsetdef: ro-eco ""
subsetdef: RO:0002259 ""
subsetdef: SOFA ""
ontology: mobio/mobio-full
property_value: http://purl.org/dc/terms/description "None" xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
property_value: http://purl.org/dc/terms/title "Mobilome Ontology" xsd:string
property_value: owl:versionInfo "2023-04-13" xsd:string
[Term]
id: BFO:0000001
name: entity
property_value: BFO:0000179 "entity" xsd:string
property_value: BFO:0000180 "Entity" xsd:string
property_value: IAO:0000112 "Julius Caesar" xsd:string
property_value: IAO:0000112 "the Second World War" xsd:string
property_value: IAO:0000112 "Verdi’s Requiem" xsd:string
property_value: IAO:0000112 "your body mass index" xsd:string
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"}
property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000002
name: continuant
def: "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." []
is_a: BFO:0000001 ! entity
disjoint_from: BFO:0000003 ! occurrent
relationship: part_of BFO:0000002 {all_only="true"} ! continuant
property_value: BFO:0000179 "continuant" xsd:string
property_value: BFO:0000180 "Continuant" xsd:string
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"}
property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000003
name: occurrent
def: "An entity that has temporal parts and that happens, unfolds or develops through time." []
is_a: BFO:0000001 ! entity
relationship: part_of BFO:0000003 {all_only="true"} ! occurrent
property_value: BFO:0000179 "occurrent" xsd:string
property_value: BFO:0000180 "Occurrent" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string
property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"}
property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"}
property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"}
property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"}
property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"}
property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"}
property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000004
name: independent continuant
def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." []
def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant
relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant
property_value: BFO:0000179 "ic" xsd:string
property_value: BFO:0000180 "IndependentContinuant" xsd:string
property_value: IAO:0000112 "a chair" xsd:string
property_value: IAO:0000112 "a heart" xsd:string
property_value: IAO:0000112 "a leg" xsd:string
property_value: IAO:0000112 "a molecule" xsd:string
property_value: IAO:0000112 "a spatial region" xsd:string
property_value: IAO:0000112 "an atom" xsd:string
property_value: IAO:0000112 "an orchestra." xsd:string
property_value: IAO:0000112 "an organism" xsd:string
property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string
property_value: IAO:0000112 "the interior of your mouth" xsd:string
property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"}
property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"}
property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"}
property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"}
property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000015
name: process
def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." []
def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
is_a: BFO:0000003 ! occurrent
property_value: BFO:0000179 "process" xsd:string
property_value: BFO:0000180 "Process" xsd:string
property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string
property_value: IAO:0000112 "a process of meiosis" xsd:string
property_value: IAO:0000112 "a process of sleeping" xsd:string
property_value: IAO:0000112 "the course of a disease" xsd:string
property_value: IAO:0000112 "the flight of a bird" xsd:string
property_value: IAO:0000112 "the life of an organism" xsd:string
property_value: IAO:0000112 "your process of aging." xsd:string
property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string
property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000016
name: disposition
is_a: BFO:0000017 ! realizable entity
disjoint_from: BFO:0000023 ! role
[Term]
id: BFO:0000017
name: realizable entity
def: "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." []
is_a: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000019 ! quality
relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity
[Term]
id: BFO:0000019
name: quality
is_a: BFO:0000020 ! specifically dependent continuant
relationship: part_of BFO:0000019 {all_only="true"} ! quality
[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "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." []
is_a: BFO:0000002 ! continuant
relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant
[Term]
id: BFO:0000023
name: role
def: "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." []
is_a: BFO:0000017 ! realizable entity
[Term]
id: BFO:0000030
name: object
is_a: BFO:0000040 ! material entity
property_value: BFO:0000179 "object" xsd:string
property_value: BFO:0000180 "Object" xsd:string
property_value: IAO:0000112 "atom" xsd:string
property_value: IAO:0000112 "cell" xsd:string
property_value: IAO:0000112 "cells and organisms" xsd:string
property_value: IAO:0000112 "engineered artifacts" xsd:string
property_value: IAO:0000112 "grain of sand" xsd:string
property_value: IAO:0000112 "molecule" xsd:string
property_value: IAO:0000112 "organelle" xsd:string
property_value: IAO:0000112 "organism" xsd:string
property_value: IAO:0000112 "planet" xsd:string
property_value: IAO:0000112 "solid portions of matter" xsd:string
property_value: IAO:0000112 "star" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: an object is a maximal causally unified material entity" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting." xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)." xsd:string
property_value: IAO:0000116 "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74" xsd:string
property_value: IAO:0000600 "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: BFO:0000034
name: function
is_a: BFO:0000016 ! disposition
[Term]
id: BFO:0000040
name: material entity
def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." []
is_a: BFO:0000004 ! independent continuant
property_value: BFO:0000179 "material" xsd:string
property_value: BFO:0000180 "MaterialEntity" xsd:string
property_value: IAO:0000112 "a flame" xsd:string
property_value: IAO:0000112 "a forest fire" xsd:string
property_value: IAO:0000112 "a human being" xsd:string
property_value: IAO:0000112 "a hurricane" xsd:string
property_value: IAO:0000112 "a photon" xsd:string
property_value: IAO:0000112 "a puff of smoke" xsd:string
property_value: IAO:0000112 "a sea wave" xsd:string
property_value: IAO:0000112 "a tornado" xsd:string
property_value: IAO:0000112 "an aggregate of human beings." xsd:string
property_value: IAO:0000112 "an energy wave" xsd:string
property_value: IAO:0000112 "an epidemic" xsd:string
property_value: IAO:0000112 "the undetached arm of a human being" xsd:string
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"}
property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"}
property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"}
property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"}
property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"}
property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Term]
id: GO:0000150
name: DNA strand exchange activity
namespace: molecular_function
def: "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC:elh]
comment: Note that this term represents activities that do not break or form phosphodiester bonds, and is therefore not a parent of 'site-specific recombinase activity ; GO:0009009'.
subset: goslim_metagenomics
synonym: "RecA-family recombinase activity" RELATED []
synonym: "recombinase activity" EXACT []
synonym: "strand exchange activity" RELATED []
synonym: "strand transferase" NARROW []
xref: Reactome:R-HSA-912458 "Formation of meiotic heteroduplex"
is_a: GO:0140097 ! catalytic activity, acting on DNA
relationship: part_of GO:0006310 ! DNA recombination
property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20964" xsd:anyURI
[Term]
id: GO:0003674
name: molecular_function
namespace: molecular_function
alt_id: GO:0005554
def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt]
def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [GOC:pdt]
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "molecular function" EXACT []
[Term]
id: GO:0003824
name: catalytic activity
namespace: molecular_function
def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb]
xref: Wikipedia:Enzyme
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0004803
name: transposase activity
namespace: molecular_function
alt_id: GO:0004804
def: "Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element." [GOC:bm, ISBN:0198506732]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "P-element encoded transposase activity" NARROW []
is_a: GO:0140097 ! catalytic activity, acting on DNA
[Term]
id: GO:0006139
name: nucleobase-containing compound metabolic process
namespace: biological_process
alt_id: GO:0055134
def: "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai]
subset: goslim_pir
subset: goslim_plant
synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT []
synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT []
synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED []
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb]
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT []
is_a: GO:0006725 ! cellular aromatic compound metabolic process
is_a: GO:0034641 ! cellular nitrogen compound metabolic process
is_a: GO:0044238 ! primary metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
[Term]
id: GO:0006259
name: DNA metabolic process
namespace: biological_process
alt_id: GO:0055132
def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "cellular DNA metabolism" EXACT []
synonym: "DNA metabolism" EXACT []
is_a: GO:0090304 ! nucleic acid metabolic process
[Term]
id: GO:0006310
name: DNA recombination
namespace: biological_process
def: "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN:0198506732]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
subset: prokaryote_subset
is_a: GO:0006259 ! DNA metabolic process
[Term]
id: GO:0006725
name: cellular aromatic compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells." [GOC:ai, ISBN:0198506732]
subset: goslim_pir
synonym: "aromatic compound metabolism" EXACT []
synonym: "aromatic hydrocarbon metabolic process" NARROW []
synonym: "aromatic hydrocarbon metabolism" NARROW []
is_a: GO:0044237 ! cellular metabolic process
[Term]
id: GO:0006807
name: nitrogen compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen." [GOC:jl, ISBN:0198506732]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "nitrogen compound metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
alt_id: GO:0000004
alt_id: GO:0007582
alt_id: GO:0044699
def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
synonym: "biological process" EXACT []
synonym: "physiological process" EXACT []
synonym: "single organism process" RELATED []
synonym: "single-organism process" RELATED []
xref: Wikipedia:Biological_process
property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI
created_by: jl
creation_date: 2012-09-19T15:05:24Z
[Term]
id: GO:0008152
name: metabolic process
namespace: biological_process
alt_id: GO:0044236
alt_id: GO:0044710
def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684]
comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
subset: gocheck_do_not_manually_annotate
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "metabolic process resulting in cell growth" NARROW []
synonym: "metabolism" EXACT []
synonym: "metabolism resulting in cell growth" NARROW []
synonym: "multicellular organism metabolic process" NARROW []
synonym: "single-organism metabolic process" RELATED []
xref: Wikipedia:Metabolism
is_a: GO:0008150 ! biological_process
created_by: jl
creation_date: 2012-10-17T15:46:40Z
[Term]
id: GO:0009987
name: cellular process
namespace: biological_process
alt_id: GO:0008151
alt_id: GO:0044763
alt_id: GO:0050875
def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete]
comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
subset: gocheck_do_not_annotate
subset: goslim_plant
synonym: "cell growth and/or maintenance" NARROW []
synonym: "cell physiology" EXACT []
synonym: "cellular physiological process" EXACT []
synonym: "single-organism cellular process" RELATED []
is_a: GO:0008150 ! biological_process
created_by: jl
creation_date: 2012-12-11T16:56:55Z
[Term]
id: GO:0016301
name: kinase activity
def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732]
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
synonym: "phosphokinase activity" EXACT []
xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm"
xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines"
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0034641
name: cellular nitrogen compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah]
subset: goslim_chembl
synonym: "cellular nitrogen compound metabolism" EXACT []
is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0044237 ! cellular metabolic process
[Term]
id: GO:0043170
name: macromolecule metabolic process
namespace: biological_process
alt_id: GO:0034960
alt_id: GO:0043283
alt_id: GO:0044259
def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah]
subset: goslim_pir
synonym: "biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09]
synonym: "macromolecule metabolism" EXACT []
synonym: "multicellular organismal macromolecule metabolic process" NARROW []
synonym: "organismal macromolecule metabolism" EXACT []
is_a: GO:0071704 ! organic substance metabolic process
[Term]
id: GO:0044237
name: cellular metabolic process
namespace: biological_process
def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators]
comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
subset: gocheck_do_not_annotate
synonym: "cellular metabolism" EXACT []
synonym: "intermediary metabolism" RELATED [GOC:mah]
is_a: GO:0008152 ! metabolic process
is_a: GO:0009987 ! cellular process
[Term]
id: GO:0044238
name: primary metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org]
subset: goslim_pir
synonym: "primary metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
[Term]
id: GO:0046483
name: heterocycle metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [ISBN:0198506732]
subset: goslim_pir
synonym: "heterocycle metabolism" EXACT []
is_a: GO:0044237 ! cellular metabolic process
[Term]
id: GO:0071704
name: organic substance metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah]
synonym: "organic molecular entity metabolic process" EXACT []
synonym: "organic molecular entity metabolism" EXACT []
synonym: "organic substance metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
created_by: mah
creation_date: 2010-03-08T03:32:18Z
[Term]
id: GO:0090304
name: nucleic acid metabolic process
namespace: biological_process
def: "Any cellular metabolic process involving nucleic acids." [GOC:dph, GOC:tb]
is_a: GO:0006139 ! nucleobase-containing compound metabolic process
is_a: GO:0043170 ! macromolecule metabolic process
created_by: tb
creation_date: 2010-04-07T10:18:47Z
[Term]
id: GO:0140097
name: catalytic activity, acting on DNA
namespace: molecular_function
def: "Catalytic activity that acts to modify DNA." [GOC:molecular_function_refactoring, GOC:pdt]
subset: goslim_generic
subset: prokaryote_subset
is_a: GO:0140640 ! catalytic activity, acting on a nucleic acid
property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI
created_by: pg
creation_date: 2017-09-14T12:03:51Z
[Term]
id: GO:0140640
name: catalytic activity, acting on a nucleic acid
namespace: molecular_function
def: "Catalytic activity that acts to modify a nucleic acid." [GOC:pg]
is_a: GO:0003824 ! catalytic activity
property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/21402" xsd:anyURI
created_by: pg
creation_date: 2021-05-11T06:31:07Z
[Term]
id: GO:1901360
name: organic cyclic compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving organic cyclic compound." [GOC:TermGenie]
synonym: "organic cyclic compound metabolism" EXACT [GOC:TermGenie]
is_a: GO:0071704 ! organic substance metabolic process
created_by: bf
creation_date: 2012-09-14T09:03:51Z
[Term]
id: MOBIO:0000001
name: mobile genetic element
def: "Mobile genetic elements (MGEs) are a type of genetic material, a segment of DNA or RNA, that is capable of movement around a genome or that can be transferred from one species or replicon to another. These include transposons, plasmids, bacteriophages, and genomic islands. The mechanism of movement may be self-encoded or may rely on other enzymes and structures, such as a pilus. In bacteria, MGEs are often associated with the movement of antibiotic resistance genes and virulence factors from one species to another, for example by plasmid-mediated transfer." []
is_a: BFO:0000030 ! object
[Term]
id: MOBIO:0000002
name: plasmid
def: "A plasmid is a small, circular, double-stranded DNA molecule that is distinct from a cell's chromosomal DNA. Plasmids naturally exist in bacterial cells, and they also occur in some eukaryotes. Often, the genes carried in plasmids provide bacteria with genetic advantages, such as antibiotic resistance. Plasmids have a wide range of lengths, from roughly one thousand DNA base pairs to hundreds of thousands of base pairs." []
is_a: MOBIO:0000001 ! mobile genetic element
[Term]
id: MOBIO:0000003
name: transposable element
def: "A transposable element (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genome size. Transposition often results in duplication of the same genetic material. Transposons were originally discovered as \"jumping genes\" by Barbara McClintock." []
synonym: "transposon" EXACT []
is_a: MOBIO:0000001 ! mobile genetic element
relationship: part_of MOBIO:0000002 ! plasmid
[Term]
id: MOBIO:0000004
name: bacteriophage
def: "Bacteriophage are viral infectious agents with bacterial host organisms. Bacteriophage infect and replicate inside bacterial host cells, causing cell lysis as viral particles replicate. Bacteriophage are involved in DNA transfer between host organisms at low frequency through transduction: when segments of host DNA is accidentally packaged with the viral DNA, then integrated into a new host genome and later inherited." []
is_a: MOBIO:0000001 ! mobile genetic element
[Term]
id: MOBIO:0000006
name: Col Plasmids
def: "These plasmids contain genes that code for bacteriocins, proteins that can kill other bacteria." []
is_a: MOBIO:0000002 ! plasmid
[Term]
id: MOBIO:0000007
name: Fertility F-Plasmids
def: "Fertility F-plasmids contain tra genes and are capable of conjugation resulting in the expression of sex pilli." []
is_a: MOBIO:0000002 ! plasmid
[Term]
id: MOBIO:0000008
name: Resistance Plasmids
def: "These plasmids contain genes that provide resistance against antibiotics or poisons. Historically known as R-factors, before the nature of plasmids was understood." []
is_a: MOBIO:0000002 ! plasmid
[Term]
id: MOBIO:0000009
name: Degradative Plasmids
def: "These plasmids enable the digestion of unusual substances, e.g. toluene and salicylic acid." []
is_a: MOBIO:0000002 ! plasmid
[Term]
id: MOBIO:0000010
name: Virulence Plasmids
def: "which turn the bacterium into a pathogen" []
is_a: MOBIO:0000002 ! plasmid
[Term]
id: MOBIO:0000011
name: mechanism of plasmid maintenance
def: "The set of specific processes that needed for plasmid partition, stability, replication, and mobility. These are all processes that allow for the plasmid to move between organisms." []
is_a: BFO:0000015 ! process
[Term]
id: MOBIO:0000012
name: mechanism of replication
def: "Any process or set of processes through which plasmid replication is initiated." []
is_a: MOBIO:0000011 ! mechanism of plasmid maintenance
[Term]
id: MOBIO:0000013
name: theta type
def: "Replication by the Theta Mechanism - opening of the strands followed by RNA priming" []
is_a: MOBIO:0000012 ! mechanism of replication
[Term]
id: MOBIO:0000014
name: strand displacement
def: "strand displacement replication. Opening of the strands followed by RNA priming" []
is_a: MOBIO:0000012 ! mechanism of replication
[Term]
id: MOBIO:0000015
name: rolling circle replication
def: "A mechanism of plasmid replication in which the two strands are asynchronously copied, with one strand initially forming a single-stranded circle." []
is_a: MOBIO:0000012 ! mechanism of replication
[Term]
id: MOBIO:0000016
name: process or mechanism of genetic mobility
def: "Molecular mechanisms involved in the intracellular and intercellular transfer, integration, stabilization and recombination of mobile genetic elements." []
is_a: BFO:0000015 ! process
[Term]
id: MOBIO:0000017
name: conjugative transfer
def: "Conjugation is the process by which one bacterium transfers genetic material to another through direct contact. During conjugation, one bacterium serves as the donor of the genetic material, and the other serves as the recipient." []
synonym: "Conjugation" EXACT []
is_a: MOBIO:0000196 ! mechanism of plasmid mobility
[Term]
id: MOBIO:0000019
name: mechanism of stabilization
def: "Stabilization mechanisms facilitate and promote the survival of plasmids in their host cells. This includes mechanisms that allow for the survival of the host cell itself in harsh conditions." []
is_a: MOBIO:0000011 ! mechanism of plasmid maintenance
[Term]
id: MOBIO:0000020
name: transformation
def: "Transformation refers to process of free DNA uptake by competent cells and subsequent integration and functional expression of genes. Extracellular DNA continually enters the environment upon release from decomposing cells, disrupted cells, viral particles or excretion from living cells." []
is_a: MOBIO:0000016 ! process or mechanism of genetic mobility
[Term]
id: MOBIO:0000021
name: Toxin-antitoxin system
def: "A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a protein 'poison' and a corresponding 'antidote'. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable anti-toxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK)." []
[Term]
id: MOBIO:0000022
name: Type I TA System
def: "Type I toxin-antitoxin systems rely on the base-pairing of complementary antitoxin RNA with the toxin's mRNA. Translation of the mRNA is then inhibited either by degradation via RNase III or by occluding the Shine-Dalgarno sequence or ribosome binding site." []
is_a: MOBIO:0000021 ! Toxin-antitoxin system
[Term]
id: MOBIO:0000023
name: Type II TA System
def: "In this system a labile protein antitoxin tightly binds and inhibits the activity of a stable toxin. Type II systems are organised in operons with the antitoxin protein typically being located upstream of the toxin. The antitoxin inhibits the toxin by downregulating its expression." []
is_a: MOBIO:0000021 ! Toxin-antitoxin system
[Term]
id: MOBIO:0000024
name: Type III TA System
def: "Type III toxin-antitoxin systems rely on direct interaction between a toxic protein and an RNA antitoxin. The toxic effects of the protein are neutralised by the RNA gene." []
is_a: MOBIO:0000021 ! Toxin-antitoxin system
[Term]
id: MOBIO:0000025
name: conjugal transfer subunit or complex
def: "The process of conjugation requires several different types of subunits and complexes." []
is_a: MOBIO:0000185 ! complex or subunit involved in plasmid maitenance
[Term]
id: MOBIO:0000026
name: pilX7
def: "Protein involved in the conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli." [PMID:18375554, PMID:19717626]
is_a: MOBIO:0000025 ! conjugal transfer subunit or complex
[Term]
id: MOBIO:0000027
name: pilX8
def: "Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli." [PMID:18375554, PMID:19717626]
is_a: MOBIO:0000025 ! conjugal transfer subunit or complex
[Term]
id: MOBIO:0000028
name: colicin immunity protein
def: "Colicin immunity proteins are plasmid encoded proteins necessary for protecting the cell against colicins. Colicins are toxins released by bacteria during times of stress" []
is_a: MOBIO:0000188 ! subunit or complex involved in stabilization
relationship: part_of MOBIO:0000006 ! Col Plasmids
[Term]
id: MOBIO:0000029
name: pilX9
def: "Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli.\n" [PMID:18375554, PMID:19717626]
is_a: MOBIO:0000025 ! conjugal transfer subunit or complex
[Term]
id: MOBIO:0000030
name: pilX10
def: "Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. It is homologous to type IV secretory pathway VirB10 protein" [PMID:18375554, PMID:19717626]
is_a: MOBIO:0000025 ! conjugal transfer subunit or complex
[Term]
id: MOBIO:0000031
name: pilX11
def: "Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. It is homologous to P-type DNA transfer ATPase VirB11." [PMID:18375554, PMID:19717626]
is_a: MOBIO:0000025 ! conjugal transfer subunit or complex
[Term]
id: MOBIO:0000032
name: taxB
def: "conjugal transfer protein - conjugal transfer protein TraG" [PMID:18375554]
is_a: MOBIO:0000181 ! conjugation coupling protein
[Term]
id: MOBIO:0000033
name: RelE
def: "Toxic component of a type II toxin-antitoxin (TA) module. A sequence-specific, ribosome-dependent mRNA endoribonuclease that inhibits translation during amino acid starvation (the stringent response). In vitro acts by cleaving mRNA with high codon specificity in the ribosomal A site between positions 2 and 3. The stop codon UAG is cleaved at a fast rate while UAA and UGA are cleaved with intermediate and slow rates. In vitro mRNA cleavage can also occur in the ribosomal E site after peptide release from peptidyl-tRNA in the P site as well as on free 30S subunits. In vivo cuts frequently in the first 100 codons, most frequently after the second and third base and rarely near the stop codon. Overexpression of RelE results in the inhibition of bacterial growth and a sharp decrease in colony-forming ability which is neutralized by the labile cognate antitoxin RelB. Overexpression also sharply increases persisters (cells that neither grow nor die in the presence of bactericidal agents and are largely responsible for high levels of biofilm tolerance to antimicrobials). Plays a role in dormancy when expressed in high-density cells in the absence of antitoxin RelB; amino acid starvation and an unidentified extracellular factor promote dormancy, while expression of antitoxin RelB restores cell culturability. Acts with RelB as a corepressor of relBE transcription, considerably increasing the repression of RelB alone. 2 RelB dimers bind to 2 operator sequences; DNA-binding and repression is stronger when complexed with toxin/corepressor RelE by conditional cooperativity." [PMID:12526800, PMID:15576765, PMID:18375554, PMID:21324908, PMID:22210768, PMID:9767574]
is_a: MOBIO:0000051 ! Type II toxin
relationship: part_of MOBIO:0000123 ! RelB/RelE Type II toxin-antitoxin system
[Term]
id: MOBIO:0000034
name: DNA topoisomerase
def: "Topoisomerases are enzymes that participate in the overwinding or underwinding of DNA. They bind to double-stranded DNA and cut the phosphate backbone of either one or both the DNA strands. " []
is_a: MOBIO:0000187 ! subunit or complex involved in plasmid DNA replication
relationship: RO:0000056 MOBIO:0000013 ! participates in theta type
relationship: RO:0000056 MOBIO:0000014 ! participates in strand displacement
relationship: RO:0000056 MOBIO:0000015 ! participates in rolling circle replication
[Term]
id: MOBIO:0000035
name: traE
def: "The traE gene, first identified in plasmid RP4, is a homologue of E. coli DNA topoisomerase III." [PMID:18375554]
is_a: MOBIO:0000034 ! DNA topoisomerase
[Term]
id: MOBIO:0000036
name: Molecular Chaperone
def: "Molecular chaperones are proteins that assist the covalent folding or unfolding and the assembly or disassembly of other macromolecular structures. Chaperones are present when the macromolecules perform their normal biological functions and have correctly completed the processes of folding and/or assembly. The chaperones are concerned primarily with protein folding. One major function of chaperones is to prevent both newly synthesized polypeptide chains and assembled subunits from aggregating into nonfunctional structures. Many chaperones are heat shock proteins because the tendency to aggregate increases as proteins are denatured by stress.\n\nMolecular chaperones have been shown to be involved in both the assembly and disassembly of DNA replication complexes." []
is_a: MOBIO:0000187 ! subunit or complex involved in plasmid DNA replication
relationship: RO:0000056 MOBIO:0000015 ! participates in rolling circle replication
[Term]
id: MOBIO:0000037
name: DnaJ
def: "Chaperone DnaJ, also known as Hsp40 (heat shock protein 40 kD), is a molecular chaperone protein. The J domain of DnaJ interacts with Hsp70 heat shock proteins. DnaJ heat-shock proteins play a role in regulating the ATPase activity of Hsp70 heat-shock proteins." [PMID:18375554]
synonym: "Hsp40" EXACT []
is_a: MOBIO:0000036 ! Molecular Chaperone
[Term]
id: MOBIO:0000038
name: transposase
def: "Class 2 transposons encode transposase, which is an enzyme that binds to the end of a transposon and catalyzes the movement of the transposon to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism.\n" []
is_a: MOBIO:0000190 ! subunit or complex involved in genetic mobility
relationship: part_of MOBIO:0000003 ! transposable element
[Term]
id: MOBIO:0000039
name: replication initiation protein RepC
def: "This protein is a specific topoisomerase involved in initiating replication. This protein is specifically required and may be rate-limiting for replication of the plasmid in vivo.\n" []
synonym: "repC" EXACT []
is_a: MOBIO:0000046 ! replication initiation protein
[Term]
id: MOBIO:0000040
name: Chromate transport protein
def: "These proteins reduce chromate accumulation and are essential for chromate resistance. They are composed of one or two copies of this region. The short-chain CHR proteins form heterodimer transporters which efflux chromate ions from the cytoplasm, while the long chain CHR proteins appear to have arisen from a gene fusion event of two short chain transporters" []
is_a: MOBIO:0000188 ! subunit or complex involved in stabilization
[Term]
id: MOBIO:0000041
name: Dihydrofolate reductase
def: "Dihydrofolate reductase converts dihydrofolate into tetrahydrofolate, a methyl group shuttle required for the de novo synthesis of purines, thymidylic acid, and certain amino acids." []
synonym: "DfrA" EXACT []
is_a: MOBIO:0000187 ! subunit or complex involved in plasmid DNA replication
relationship: RO:0000056 MOBIO:0000013 ! participates in theta type
relationship: RO:0000056 MOBIO:0000014 ! participates in strand displacement
relationship: RO:0000056 MOBIO:0000015 ! participates in rolling circle replication
[Term]
id: MOBIO:0000042
name: Class 1 Integrase
def: "Class 1 Integrase is a site-specific recombination enzyme that is part of the class 1 integron system. It recognizes the recombination site, attI1, which is where it will catalyze the insertion of gene casettes." [PMID:18193080, PMID:8574395]
synonym: "Intl1" EXACT []
is_a: MOBIO:0000104 ! recombinase
relationship: part_of MOBIO:0000043 ! integron
[Term]
id: MOBIO:0000043
name: integron
def: "Integrons are genetic mechanisms that allow bacteria to adapt and evolve rapidly through the acquisition, stockpiling and differential expression of new genes. Additionally, an integron will usually contain one or more gene cassettes that have been incorporated into it." []
is_a: MOBIO:0000001 ! mobile genetic element
relationship: part_of MOBIO:0000003 ! transposable element
[Term]
id: MOBIO:0000044
name: PadR family transcriptional regulator
def: "DNA-binding transcriptional regulator. Protein that is involved in negative regulation of phenolic acid metabolism." []
is_a: MOBIO:0000045 ! transcriptional regulator of operons found in MGEs
[Term]
id: MOBIO:0000045
name: transcriptional regulator of operons found in MGEs
def: "transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity." []
is_a: MOBIO:0000190 ! subunit or complex involved in genetic mobility
[Term]
id: MOBIO:0000046
name: replication initiation protein
def: "protein required for initiation of replication" []
is_a: MOBIO:0000187 ! subunit or complex involved in plasmid DNA replication
relationship: RO:0000056 MOBIO:0000013 ! participates in theta type
relationship: RO:0000056 MOBIO:0000014 ! participates in strand displacement
relationship: RO:0000056 MOBIO:0000015 ! participates in rolling circle replication
[Term]
id: MOBIO:0000047
name: replication initiation protein RepA
def: "This protein is essential for plasmid replication; it is involved in copy control functions" []
synonym: "RepA" EXACT []
is_a: MOBIO:0000046 ! replication initiation protein
[Term]
id: MOBIO:0000048
name: Major pili subunit operon regulatory protein papB
def: "papB may act as both positive and negative regulator of the pyelonephritis-associated pili (pap) pilin gene transcription. It is found in the pap operon." []
is_a: MOBIO:0000025 ! conjugal transfer subunit or complex
relationship: RO:0000056 MOBIO:0000017 ! participates in conjugative transfer
[Term]
id: MOBIO:0000049
name: Type II post-segregation antitoxin
def: "Type II systems are organised in operons with the antitoxin protein typically being located upstream of the toxin. The antitoxin inhibits the toxin by downregulating its expression. " []
synonym: "antitoxin" EXACT []
is_a: MOBIO:0000191 ! component of a TA system
relationship: part_of MOBIO:0000023 ! Type II TA System
[Term]
id: MOBIO:0000050
name: C protein
def: "transcriptional regulator" []
is_a: MOBIO:0000045 ! transcriptional regulator of operons found in MGEs
[Term]
id: MOBIO:0000051
name: Type II toxin
def: "Type II systems are organised in operons with the antitoxin protein typically being located upstream of the toxin. The antitoxin inhibits the toxin by downregulating its expression. " []
is_a: MOBIO:0000191 ! component of a TA system
relationship: part_of MOBIO:0000023 ! Type II TA System
[Term]
id: MOBIO:0000052
name: CcdA
def: "Antitoxin component of a toxin-antitoxin (TA) module which inhibits the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Labile antitoxin with a half-life of about 1 hour in the presence of CcdB. Binds to and blocks the activity of CcdB; will also remove bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. The N-terminal 36 residues are not required for rejuventation. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdB." [PMID:27357537]
is_a: MOBIO:0000049 ! Type II post-segregation antitoxin
relationship: part_of MOBIO:0000079 ! CcdA/CcdB Type II Toxin-antitoxin system
[Term]
id: MOBIO:0000053
name: CcdB
def: "Toxic component of a toxin-antitoxin (TA) module, functioning in plasmid maintainence. Responsible for the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Half-life of over 2 hours. Cell killing by CcdB is accompanied by filamentation, defects in chromosome and plasmid segregation, defects in cell division, formation of anucleate cells, decreased DNA synthesis and plasmid loss. Interferes with the activity of DNA gyrase, inducing it to form a covalent GyrA-DNA complex that cannot be resolved, thus promoting breakage of plasmid and chromosomal DNA. DNA breakage requires hydrolyzable ATP. Toxicity is inhibited by labile antitoxin CcdA, which blocks the activity of CcdB; CcdA also removes bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Also acts to inhibit partitioning of the chromosomal DNA. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdA." []
is_a: MOBIO:0000051 ! Type II toxin
relationship: part_of MOBIO:0000079 ! CcdA/CcdB Type II Toxin-antitoxin system
[Term]
id: MOBIO:0000054
name: replication initiation protein RepE
def: "Replication initiator in the monomeric form, and autogenous repressor in the dimeric form." []
synonym: "RepE" EXACT []
is_a: MOBIO:0000046 ! replication initiation protein
[Term]
id: MOBIO:0000055
name: plasmid partition system
def: "A plasmid partition system is the mechanism that assures the stable transmission of plasmids during bacterial cell division. Each plasmid has its independent replication system which control the number of copy of a plasmid in a cell." []
is_a: MOBIO:0000011 ! mechanism of plasmid maintenance
[Term]
id: MOBIO:0000056
name: Type I Partition System
def: "This system is also used by most bacteria for chromosome segregation. Type I partition system are composed of an ATPase which contains Walker motifs and a CBP which is structurally distinct in type Ia and Ib. ATPases and CBP from type Ia are longer than the one from type Ib, but both CBPs contain an arginine finger in their N-terminal part. ParA proteins from different plasmids and bacterial species show 25 to 30% of sequence identity to the protein ParA of the plasmid P1. The partition of type I system uses a \"diffusion-ratchet\" mechanism. " []
synonym: "Type 1 Partition System" EXACT []
is_a: MOBIO:0000055 ! plasmid partition system
[Term]
id: MOBIO:0000057
name: Type Ia Partition System
def: "def" []
is_a: MOBIO:0000056 ! Type I Partition System
[Term]
id: MOBIO:0000058
name: Type Ib partition system
def: "partition system" []
[Term]
id: MOBIO:0000059
name: Type II Partition System
def: "This system is composed of an actin-like ATPase, ParM, and a CBP called ParR. The centromere-like site, parC contains two sets of five 11 base pair direct repeats separated by the parMR promoter. The amino-acid sequence identity can go down to 15% between ParM and other actin-like ATPase." []
is_a: MOBIO:0000055 ! plasmid partition system
[Term]
id: MOBIO:0000060
name: Type III Partition System
def: "This mechanism is composed of tubulin-like GTPase termed TubZ, and the CBP is termed TubR. Amino-acid sequence identity can go down to 21% for TubZ proteins" []
is_a: MOBIO:0000055 ! plasmid partition system
[Term]
id: MOBIO:0000061
name: R388 Partition System
def: "The partition system of the plasmid R388 has been found within the stb operon. This operon is composed of three genes, stbA, stbB and stbC" []
is_a: MOBIO:0000055 ! plasmid partition system
[Term]
id: MOBIO:0000062
name: pSK1 partition system
def: "pSK1 is plasmid from Staphylococcus aureus. This plasmid has a partition system determined by a single gene, par, previously known as orf245. This gene has effect neither on the plasmid copy number nor on the growth rate (excluding its implication in a post-segregational killing system). A centromere-like binding sequence is present upstream the par gene, and is composed of seven direct repeats and one inverted repeat." []
is_a: MOBIO:0000055 ! plasmid partition system
[Term]
id: MOBIO:0000063
name: ParA
def: "Partitioning protein - ATPase" []
is_a: MOBIO:0000186 ! partitioning protein
relationship: part_of MOBIO:0000058 ! Type Ib partition system
[Term]
id: MOBIO:0000064
name: pifA
def: "PifA is encoded on plasmid F and is responsible for the exclusion of phage T7. E. coli cells that carry plasmid F inhibit the growth of bacteriophage T7. " [PMID:7883717]
is_a: MOBIO:0000193 ! protein conferring phage resistance
[Term]
id: MOBIO:0000065
name: replication initiation protein RepB
def: "Is essential for plasmid replication. Nicks the positive strand at the plus origin of replication." [PMID:18375554]
synonym: "Pi protein" EXACT []
synonym: "pir" EXACT []
synonym: "RepB" EXACT []
is_a: MOBIO:0000046 ! replication initiation protein
[Term]
id: MOBIO:0000066
name: replication regulatory protein
def: "regulates replication" []
is_a: MOBIO:0000187 ! subunit or complex involved in plasmid DNA replication
[Term]
id: MOBIO:0000067
name: repA2
def: "This protein is involved in the determination of copy number in gene replication. It binds to the repA promoter thus inhibiting the synthesis of the mRNA for the initiator protein RepA." []
is_a: MOBIO:0000066 ! replication regulatory protein
[Term]
id: MOBIO:0000068
name: SopA
def: "This protein is essential for plasmid partition. It ensures the proper distribution of newly replicated plasmids to daughter cells during cell division. SopA is trans-acting and binds to a sequence in the sopAB operon, thus regulating the expression of the operon. " [PMID:25753630, PMID:2670941]
is_a: MOBIO:0000186 ! partitioning protein
relationship: part_of MOBIO:0000058 ! Type Ib partition system
[Term]
id: MOBIO:0000069
name: SopB
def: "SopB is involved in the control of plasmid partitioning. It is trans-acting and binds specifically with the DNA segment containing the sopC region. The presence of SopB in the SopAB complex enhances SopA binding to the target DNA sequence." [PMID:25753630, PMID:2670941]
is_a: MOBIO:0000186 ! partitioning protein
relationship: part_of MOBIO:0000058 ! Type Ib partition system
[Term]
id: MOBIO:0000070
name: antirestriction protein KlcA
def: "Bacterial cells often contain type I DNA and restriction modification (RM) systems that degrade foreign DNA during bacterial conjugation. KlcA could be involved in inhibiting the RM systems and enhancing the success of conjugation." [PMID:20007596]
is_a: MOBIO:0000025 ! conjugal transfer subunit or complex
[Term]
id: MOBIO:0000071
name: group II intron reverse transcriptase/maturase
def: "Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain followed by an RNA-binding maturase domain. These proteins play a role in site-specific DNA insertion." []
is_a: MOBIO:0000190 ! subunit or complex involved in genetic mobility
[Term]
id: MOBIO:0000072
name: hydrolase
def: "An enzyme that catalyzes the hydrolysis of a particular substrate. Many hydrolases participate in the inactivation of antibiotics." [PMID:25753630]
is_a: MOBIO:0000188 ! subunit or complex involved in stabilization
[Term]
id: MOBIO:0000073
name: single stranded DNA binding protein
def: "Single-strand DNA-binding protein (SSB) binds to single-stranded regions of deoxyribonucleic acid (DNA). Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination, and repair." [PMID:25753630]
is_a: MOBIO:0000187 ! subunit or complex involved in plasmid DNA replication
[Term]
id: MOBIO:0000074