Alan Ruttenberg
This is the release of December 12, 2015. It will always be available at http://purl.obolibrary.org/ncro/2015-12-10/ncro.owl. While current, this ontology is also available at http://purl.obolibrary.org/obo/ncro.owl This file is a merge of NCRO and any imported ontologies or terms. You can access the ontology that existed before the merge, with imports intact, at http://purl.obolibrary.org/obo/ncro/YYYY-MM-DD/ncro.owl or, for the current version, http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl
This ontology is currently undergoing changes. ID deprecation policies will start in the next couple of months. In the mean time, identifiers may be deleted and not marked obsolete.
BFO OWL specification label
Really of interest to developers only
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
BFO CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
editor preferred label
editor preferred term
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
example
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
relates an class defined in an ontology, to the type of it's denotator
is denotator type
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
expand assertion to
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
Chris Mungall
ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
use boolean value xsd:true to indicate that the property is an antisymmetric property
OBO foundry unique label
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
An alternative name for a class or property which is unique across the OBO Foundry.
GROUP:OBO Foundry <http://obofoundry.org/>
PERSON:Bjoern Peters
PERSON:Chris Mungall
has ID digit count
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
has ID range allocated to
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
has ID prefix
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
elucidation
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
person:Alan Ruttenberg
has associated axiom(nl)
An axiom associated with a term expressed using natural language
Person:Alan Ruttenberg
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
is allocated id range
Add as annotation triples in the granting ontology
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
has axiom label
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom id
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
part of
a core relation that holds between a part and its whole
part_of
preceded by
is preceded by
preceded_by
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.
precedes
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.
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
occurs_in
unfolds in
unfolds_in
participates in
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has_participant
derives from
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives_from
regulates
x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y
negatively regulates
x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
positively regulates
x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y
member of
is member of is a mereological relation between a item and a collection.
has member
has member is a mereological relation between a collection and an item.
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
Similarity that results from common evolutionary origin.
in non functional homology relationship with
Structural homology that involves a pseudogenic feature and its functional ancestor.
entity
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
continuant
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
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])
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
occurrent
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
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
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.
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
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])
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.
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.
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
independent continuant
(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]
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
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])
the bottom right portion of a human torso
the interior of your mouth
spatial region
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
temporal region
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
two-dimensional spatial region
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
spatiotemporal region
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
process
(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]
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)
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
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])
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
disposition
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
an atom of element X has the disposition to decay to an atom of element Y
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
realizable entity
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
zero-dimensional spatial region
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
quality
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
specifically dependent continuant
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
role
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
fiat object part
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
one-dimensional spatial region
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
an edge of a cube-shaped portion of space.
object aggregate
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
three-dimensional spatial region
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
a cube-shaped region of space
a sphere-shaped region of space,
site
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
object
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.
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).
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
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
atom
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])
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
generically dependent continuant
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
function
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
process boundary
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
the boundary between the 2nd and 3rd year of your life.
one-dimensional temporal region
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
the temporal region during which a process occurs.
material entity
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
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])
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
the undetached arm of a human being
continuant fiat boundary
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
immaterial entity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
one-dimensional continuant fiat boundary
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
The Equator
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
process profile
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
relational quality
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
a marriage bond, an instance of love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
two-dimensional continuant fiat boundary
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
zero-dimensional continuant fiat boundary
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
zero-dimensional temporal region
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
a temporal region that is occupied by a process boundary
right now
temporal instant.
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
history
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
A single-stranded RNA molecule containing about 70-90 nucleotides, folded by intrastrand base pairing into a characteristic secondary ('cloverleaf') structure that carries a specific amino acid and matches it to its corresponding codon on an mRNA during protein synthesis.
tRNA
RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis.
rRNA
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
Any substituent group or skeleton containing carbon.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
RNA
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
A class of small RNA molecules which are comprised of approximately 150 nucleotides and which are found within the nucleus of eukaryotic cells.
snRNA
circRNA
cell line
A disease that is characterized by abnormally rapid cell division.
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
negative regulation of transcription from RNA polymerase II promoter
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
down regulation of transcription from RNA polymerase II promoter
down-regulation of transcription from RNA polymerase II promoter
downregulation of transcription from RNA polymerase II promoter
inhibition of transcription from RNA polymerase II promoter
negative regulation of transcription from Pol II promoter
Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
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.
Catalysis of the hydrolysis of ester linkages within nucleic acids.
Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of an RNA molecule.
Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
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.
That part of the nuclear content other than the chromosomes or the nucleolus.
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
nucleobase-containing compound metabolic process
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
The cellular synthesis of RNA on a template of DNA.
regulation of transcription, DNA-templated
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
regulation of cellular transcription, DNA-dependent
regulation of transcription, DNA-dependent
regulation of transcription from RNA polymerase II promoter
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of transcription from Pol II promoter
Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
A process in which RNA is transported to, or maintained in, a specific location.
establishment and maintenance of RNA localization
The directed movement of RNA from the nucleus to the cytoplasm.
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome.
The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.
cellular aromatic compound metabolic process
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.
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
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.
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
negative regulation of biosynthetic process
Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances.
positive regulation of biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
negative regulation of metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
positive regulation of metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances.
negative regulation of catabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.
positive regulation of catabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.
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.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
production of ta-siRNAs involved in RNA interference
Cleavage of double-stranded RNA to form trans-acting small interfering RNA molecules (siRNAs) of 21-23 nucleotides. ta-siRNAs arise from PolII genes and function like miRNAs to guide cleavage of target mRNAs.
RNA interference, production of ta-siRNAs
A small round nuclear body, measuring 0.2-0.8 microns in diameter that is diffusely distributed throughout the nucleoplasm. Several proteins known to be involved in miRNA processing have been localized to these structures. D-bodies are thought to be involved in primary-miRNA processing and/or storage/assembly of miRNA processing complexes.
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
regulation of macromolecule biosynthetic process
Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
positive regulation of macromolecule biosynthetic process
Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
negative regulation of macromolecule biosynthetic process
Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
The chemical reactions and pathways involving miRNA, microRNA, a class of single-stranded RNA molecules of about 21-23 nucleotides in length, which regulates gene expression.
The chemical reactions and pathways resulting in the breakdown of miRNA, microRNA, a class of single-stranded RNA molecules of about 21-23 nucleotides in length, which regulates gene expression.
positive regulation of macromolecule metabolic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
negative regulation of macromolecule metabolic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
posttranscriptional regulation of gene expression
Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.
posttranscriptional gene silencing by siRNA
The inactivation of gene expression by a posttranscriptional mechanism.
A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation.
Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, postranscriptional repression of gene expression.
endoribonuclease activity, producing 5'-phosphomonoesters
Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
exoribonuclease activity, producing 5'-phosphomonoesters
Catalysis of the hydrolysis of ester linkages within ribonucleic acids by removing nucleotide residues from the 3' or 5' end to yield 5' phosphomonoesters.
exoribonuclease activity, producing 5' phosphomonoesters
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.
down regulation of protein biosynthetic process
down-regulation of protein biosynthetic process
downregulation of protein biosynthetic process
negative regulation of protein anabolism
negative regulation of protein biosynthesis
negative regulation of protein biosynthetic process
negative regulation of protein formation
negative regulation of protein synthesis
The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
regulation of nucleobase-containing compound metabolic process
Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
protein metabolic process and modification
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.
ribonucleoprotein complex biogenesis and assembly
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
production of siRNA involved in RNA interference
Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference.
RNA interference, production of guide RNAs
production of guide RNAs involved in RNA interference
A macromolecular complex containing both protein and RNA molecules.
Cleavage of double-stranded RNA molecules by an RNaseIII-family enzyme to produce small RNAs (generally 20-30 nucleotides, depending on species) with biological function.
Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule.
Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
regulation of cellular metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
negative regulation of cellular metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
down regulation of cellular metabolic process
down-regulation of cellular metabolic process
downregulation of cellular metabolic process
negative regulation of cellular metabolism
positive regulation of cellular metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
positive regulation of cellular metabolism
up regulation of cellular metabolic process
up-regulation of cellular metabolic process
upregulation of cellular metabolic process
regulation of cellular biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
negative regulation of cellular biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
down regulation of cellular biosynthetic process
down-regulation of cellular biosynthetic process
downregulation of cellular biosynthetic process
negative regulation of cellular anabolism
negative regulation of cellular biosynthesis
negative regulation of cellular formation
negative regulation of cellular synthesis
positive regulation of cellular biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
positive regulation of cellular anabolism
positive regulation of cellular biosynthesis
positive regulation of cellular formation
positive regulation of cellular synthesis
up regulation of cellular biosynthetic process
up-regulation of cellular biosynthetic process
upregulation of cellular biosynthetic process
regulation of cellular catabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
negative regulation of cellular catabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
down regulation of cellular catabolic process
down-regulation of cellular catabolic process
downregulation of cellular catabolic process
negative regulation of cellular breakdown
negative regulation of cellular catabolism
negative regulation of cellular degradation
positive regulation of cellular catabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
positive regulation of cellular breakdown
positive regulation of cellular catabolism
positive regulation of cellular degradation
up regulation of cellular catabolic process
up-regulation of cellular catabolic process
upregulation of cellular catabolic process
The volume enclosed by the nuclear inner membrane.
regulation of cellular protein metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
regulation of cellular protein metabolism
negative regulation of cellular protein metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
down regulation of cellular protein metabolic process
down-regulation of cellular protein metabolic process
downregulation of cellular protein metabolic process
negative regulation of cellular protein metabolism
The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.
A ribonucleoprotein complex found in the cytoplasm of male germ cells, composed of exceedingly thin filaments that are consolidated into a compact mass or into dense strands of varying thickness that branch to form an irregular network. Contains mRNAs, miRNAs, and protein components involved in miRNA processing (such as Argonaute proteins and the endonuclease Dicer) and in RNA decay (such as the decapping enzyme DCP1a and GW182).
Any process that results in the conversion of one or more primary non-coding RNA (ncRNA) transcripts into one or more mature ncRNA molecules.
cellular nitrogen compound metabolic process
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular macromolecule biosynthetic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells.
cellular biopolymer biosynthetic process
nucleobase-containing compound biosynthetic process
The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid anabolism
nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis
nucleobase, nucleoside, nucleotide and nucleic acid formation
nucleobase-containing compound catabolic process
The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid breakdown
nucleobase, nucleoside, nucleotide and nucleic acid catabolism
nucleobase, nucleoside, nucleotide and nucleic acid degradation
The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs).
The chemical reactions and pathways resulting in the breakdown of non-coding RNA transcripts (ncRNAs). Includes the breakdown of cryptic unstable transcripts (CUTs).
A complex containing both protein and micro-RNA (miRNA) molecules. miRNAs are approximately 22 nucleotide noncoding RNAs derived from endogenous genes; they are processed from the stem of a longer hairpin like structure termed a pre-miRNA.
posttranscriptional gene silencing by RNA
Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation.
RNA-mediated posttranscriptional gene silencing
Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: endolytic cleavage of mRNA cleavage or translational repression, usually accompanied by poly-A tail shortgening and subsequent degredation of the mRNA.
production of miRNAs involved in gene silencing by miRNA
Cleavage of stem-loop RNA precursors into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein.
gene silencing by miRNA, production of miRNAs
miRNA-mediated gene silencing, production of miRNAs
microRNA-mediated gene silencing, production of microRNAs
production of microRNAs involved in gene silencing by microRNA
Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes.
negative regulation of translation involved in gene silencing by miRNA
The process in which microRNAs (miRNAs) block the translation of target mRNAs into proteins. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA will typically repress translation if the miRNA imperfectly base-pairs with the 3' untranslated regions of target mRNAs.
down regulation of translation involved in gene silencing by miRNA
down-regulation of translation involved in gene silencing by miRNA
downregulation of translation involved in gene silencing by miRNA
gene silencing by miRNA, negative regulation of translation
negative regulation of translation involved in gene silencing by microRNA
mRNA cleavage involved in gene silencing by miRNA
The process in which microRNAs (miRNAs) direct the cleavage of target mRNAs. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA base pairing with near-perfect complementarity to the target mRNA will typically direct targeted endonucleolytic cleavage of the mRNA. Many plant miRNAs downregulate gene expression through this mechanism.
mRNA cleavage involved in gene silencing by microRNA
miRNA-mediated gene silencing, mRNA cleavage
miRNA loading onto RISC involved in gene silencing by miRNA
The transfer of a microRNA (miRNA) strand from a miRNA:miRNA duplex onto the RNA-initiated silencing complex (RISC).
gene silencing by miRNA, miRNA loading onto RISC
miRNA-mediated gene silencing, miRNA loading onto RISC
microRNA loading onto RISC involved in gene silencing by microRNA
Transport of pre-microRNAs (pre-miRNAs) from the nucleus to the cytoplasm. Pre-miRNAs are a ~60-70 nucleotide stem loop intermediate in miRNA production, produced by the nuclear cleavage of a primary miRNA (pri-mRNA) transcript. Pre-miRNAs are transported from the nucleus to the cytoplasm where further cleavage occurs to produce a mature miRNA product.
pre-microRNA transport from nucleus to cytoplasm
A non-membranous macromolecular complex containing proteins and translationally silenced mRNAs. RNA granules contain proteins that control the localization, stability, and translation of their RNA cargo. Different types of RNA granules (RGs) exist, depending on the cell type and cellular conditions.
A ribonucleoprotein granule located in the cytoplasm.
negative regulation of translation, ncRNA-mediated
Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein.
down regulation of mRNA translation, ncRNA-mediated
down-regulation of mRNA translation, ncRNA-mediated
downregulation of mRNA translation, ncRNA-mediated
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
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.
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.
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.
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
intracellular membrane-enclosed organelle
intracellular non-membrane-bounded organelle
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.
intracellular non-membrane-enclosed organelle
The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a double-stranded RNA stimulus.
Any process involved in forming the mature 3' end of a non-coding RNA molecule.
macromolecular complex subunit organization
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a macromolecular complex.
cellular macromolecular complex organization
cellular macromolecular complex subunit organisation
cellular macromolecular complex subunit organization
macromolecular complex subunit organisation
The chemical reactions and pathways by which individual cells transform chemical substances.
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.
The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
cellular macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
cellular macromolecule catabolic process
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells.
The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
cellular nitrogen compound catabolic process
The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds.
cellular nitrogen compound biosynthetic process
The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.
Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane.
Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.
Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane.
Any constituent part of the nucleoplasm, that part of the nuclear content other than the chromosomes or the nucleolus.
Any constituent part of a cell, the basic structural and functional unit of all organisms.
A biological process that involves only one organism.
A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism.
Any process involved in forming distinct miRNA isoforms from a mature miRNA that differ at their 3'-ends.
3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing
Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule that contributes to forming distinct miRNA isoforms from a mature miRNA.
Any process that is carried out at the cellular level, occurring within a single organism.
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism.
negative regulation of transcription, DNA-templated
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
down regulation of transcription, DNA-dependent
down-regulation of transcription, DNA-dependent
downregulation of transcription, DNA-dependent
negative regulation of cellular transcription, DNA-dependent
negative regulation of transcription, DNA-dependent
positive regulation of transcription, DNA-templated
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
positive regulation of cellular transcription, DNA-dependent
positive regulation of transcription, DNA-dependent
up regulation of transcription, DNA-dependent
up-regulation of transcription, DNA-dependent
upregulation of transcription, DNA-dependent
negative regulation of nucleobase-containing compound metabolic process
Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
positive regulation of nucleobase-containing compound metabolic process
Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
positive regulation of transcription from RNA polymerase II promoter
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
activation of transcription from RNA polymerase II promoter
positive regulation of transcription from Pol II promoter
stimulation of transcription from RNA polymerase II promoter
up regulation of transcription from RNA polymerase II promoter
up-regulation of transcription from RNA polymerase II promoter
upregulation of transcription from RNA polymerase II promoter
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).
The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
The directed movement of substances within a cell.
positive regulation of biological process
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
positive regulation of physiological process
negative regulation of biological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
negative regulation of physiological process
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
positive regulation of cellular physiological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
negative regulation of cellular physiological process
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
positive regulation of response to stimulus
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
negative regulation of response to stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
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.
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.
regulation of cellular physiological process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
The directed movement of substances out of the nucleus.
regulation of nitrogen compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
regulation of nitrogen metabolic process
negative regulation of nitrogen compound metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
down regulation of nitrogen metabolic process
down-regulation of nitrogen metabolic process
downregulation of nitrogen metabolic process
negative regulation of nitrogen metabolic process
negative regulation of nitrogen metabolism
positive regulation of nitrogen compound metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
positive regulation of nitrogen metabolic process
positive regulation of nitrogen metabolism
up regulation of nitrogen metabolic process
up-regulation of nitrogen metabolic process
upregulation of nitrogen metabolic process
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to or maintained in a specific location.
establishment and maintenance of localization
establishment and maintenance of position
The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.
The directed movement of RNA to a specific location.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein.
negative regulation of protein metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein.
down regulation of protein metabolic process
down-regulation of protein metabolic process
downregulation of protein metabolic process
negative regulation of protein metabolism
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.
negative regulation of RNA metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA.
down regulation of RNA metabolic process
down-regulation of RNA metabolic process
positive regulation of RNA metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
regulation of posttranscriptional gene silencing
Any process that modulates the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism.
positive regulation of posttranscriptional gene silencing
Any process that increases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism.
negative regulation of posttranscriptional gene silencing
Any process that decreases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism.
regulation of macromolecule metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
Any process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
regulation of gene silencing by microRNA
negative regulation of gene silencing by miRNA
Any process that decreases the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
negative regulation of gene silencing by microRNA
Any process that regulates the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes.
negative regulation of gene silencing by RNA
Any process that decreases the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes.
Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
Any process that decreases the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
pri-miRNA transcription from RNA polymerase II promoter
The cellular synthesis of primary microRNA (pri-miRNA) transcripts from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. pri-miRNA transcripts are subsequently processed to produce the ~22nt miRNAs that function in gene regulation.
The aggregation, arrangement and bonding together of a set of macromolecules to form a complex.
An organelle lumen that is part of an intracellular organelle.
A trimeric ribonucleoprotein complex that and is required for the formation of a mature RNA induced silencing complex (RISC). In humans the complex is composed of the endonuclease Dicer (DICER1) and TRBP (TARBP2) in association with the Argonaute protein Ago2 (EIF2C2/AGO2). Within the complex, Dicer and TRBP are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto Ago2. Ago2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from Dicer and TRBP. This complex has endorobonuclease activity.
A protein complex that binds to heme and to pri-miRNAs, and is required for the formation of a pre-microRNA (pre-miRNA), the initial step of microRNA (miRNA) biogenesis. The complex is composed of the double-stranded-RNA-specific RNase Drosha (also called RNASEN) and the RNA-binding protein DGCR8 (heme-free or heme-bound forms). Within the complex, DGCR8 function as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs RNASEN/Drosha to cleave the 3' and 5' strands of a stem-loop to release hairpin-shaped pre-miRNAs.
Interacting selectively and non-covalently with a primary microRNA (pri-miRNA) transcript, an RNA molecule that is processed into a short hairpin-shaped structure called a pre-miRNA and finally into a functional miRNA. Both double-stranded and single-stranded regions of a pri-miRNA are required for binding.
Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
production of small RNA involved in gene silencing by RNA
The process in which a double-stranded RNA precursor is processed into short (20-30 nt) fragments. RNA cleavage is catalyzed by a Dicer endonuclease.
gene silencing by RNA, production of guide RNA
gene silencing by RNA, production of small RNA
regulation of production of small RNA involved in gene silencing by RNA
Any process that modulates the frequency, rate or extent of the production of small RNA involved in gene silencing by RNA.
regulation of gene silencing by RNA, production of guide RNA
regulation of gene silencing by RNA, production of small RNA
Any process in which a ribonucleoprotein complex is transported to, or maintained in, a specific location within a cell.
cellular ribonucleoprotein complex localization
establishment and maintenance of ribonucleoprotein complex localization
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a double-stranded RNA stimulus.
cellular response to double-stranded RNA
cellular response to organic cyclic compound
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
cellular response to organic cyclic substance
ribonucleoprotein complex export from nucleus
The directed movement of a ribonucleoprotein complex from the nucleus to the cytoplasm.
ribonucleoprotein complex export from cell nucleus
ribonucleoprotein complex nucleus export
ribonucleoprotein complex transport from nucleus to cytoplasm
pre-miRNA-containing ribonucleoprotein complex export from nucleus
The directed movement of a ribonucleoprotein complex that contains pre-microRNA from the nucleus to the cytoplasm.
pre-microRNA-containing RNP export from nucleus
pre-microRNA-containing ribonucleoprotein complex export from cell nucleus
pre-microRNA-containing ribonucleoprotein complex export from nucleus
pre-microRNA-containing ribonucleoprotein complex nucleus export
pre-microRNA-containing ribonucleoprotein complex transport from nucleus to cytoplasm
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic molecular entity metabolic process
cellular component organization or biogenesis
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
Any cellular metabolic process involving nucleic acids.
nucleic acid phosphodiester bond hydrolysis
The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
RNA phosphodiester bond hydrolysis, endonucleolytic
The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
RNA phosphodiester bond hydrolysis, exonucleolytic
The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
endoribonuclease activity, cleaving miRNA-paired mRNA
Catalysis of the endonucleolytic cleavage of the mRNA in a double-stranded RNA molecule formed by the base pairing of an mRNA with an miRNA.
Enables the directed movement of pre-miRNAs between the nucleus and the cytoplasm of a cell.
organic cyclic compound metabolic process
The chemical reactions and pathways involving organic cyclic compound.
organic cyclic compound catabolic process
The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.
organic cyclic compound biosynthetic process
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.
organic molecular entity catabolic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
organic molecular entity biosynthetic process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.
cellular response to nitrogen molecular entity
negative regulation of RNA catabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process.
down regulation of RNA catabolic process
down-regulation of RNA catabolic process
A localization which involves only one organism.
An intracellular transport which involves only one organism.
negative regulation of RNA biosynthetic process
Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process.
down regulation of RNA biosynthetic process
down-regulation of RNA biosynthetic process
downregulation of RNA biosynthetic process
positive regulation of RNA biosynthetic process
Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process.
up regulation of RNA biosynthetic process
up-regulation of RNA biosynthetic process
upregulation of RNA biosynthetic process
regulation of pri-miRNA transcription from RNA polymerase II promoter
Any process that modulates the frequency, rate or extent of pri-miRNA transcription from RNA polymerase II promoter.
negative regulation of pri-miRNA transcription from RNA polymerase II promoter
Any process that stops, prevents or reduces the frequency, rate or extent of pri-miRNA transcription from RNA polymerase II promoter.
down regulation of pri-miRNA transcription from RNA polymerase II promoter
down-regulation of pri-miRNA transcription from RNA polymerase II promoter
downregulation of pri-miRNA transcription from RNA polymerase II promoter
positive regulation of pri-miRNA transcription from RNA polymerase II promoter
Any process that activates or increases the frequency, rate or extent of pri-miRNA transcription from RNA polymerase II promoter.
up regulation of pri-miRNA transcription from RNA polymerase II promoter
up-regulation of pri-miRNA transcription from RNA polymerase II promoter
upregulation of pri-miRNA transcription from RNA polymerase II promoter
regulation of nucleic acid-templated transcription
Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription.
negative regulation of nucleic acid-templated transcription
Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
down regulation of nucleic acid-templated transcription
down-regulation of nucleic acid-templated transcription
downregulation of nucleic acid-templated transcription
positive regulation of nucleic acid-templated transcription
Any process that activates or increases the frequency, rate or extent of nucleic acid-templated transcription.
up regulation of nucleic acid-templated transcription
up-regulation of nucleic acid-templated transcription
upregulation of nucleic acid-templated transcription
regulation of production of miRNAs involved in gene silencing by miRNA
Any process that modulates the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA.
regulation of gene silencing by miRNA, production of miRNAs
regulation of miRNA-mediated gene silencing, production of miRNAs
regulation of microRNA-mediated gene silencing, production of microRNAs
regulation of production of microRNAs involved in gene silencing by microRNA
negative regulation of production of miRNAs involved in gene silencing by miRNA
Any process that stops, prevents or reduces the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA.
down regulation of gene silencing by miRNA, production of miRNAs
down regulation of miRNA-mediated gene silencing, production of miRNAs
down regulation of microRNA-mediated gene silencing, production of microRNAs
down regulation of production of miRNAs involved in gene silencing by miRNA
down regulation of production of microRNAs involved in gene silencing by microRNA
down-regulation of gene silencing by miRNA, production of miRNAs
down-regulation of miRNA-mediated gene silencing, production of miRNAs
down-regulation of microRNA-mediated gene silencing, production of microRNAs
down-regulation of production of miRNAs involved in gene silencing by miRNA
down-regulation of production of microRNAs involved in gene silencing by microRNA
downregulation of gene silencing by miRNA, production of miRNAs
downregulation of miRNA-mediated gene silencing, production of miRNAs
downregulation of microRNA-mediated gene silencing, production of microRNAs
downregulation of production of miRNAs involved in gene silencing by miRNA
downregulation of production of microRNAs involved in gene silencing by microRNA
negative regulation of gene silencing by miRNA, production of miRNAs
negative regulation of miRNA-mediated gene silencing, production of miRNAs
negative regulation of microRNA-mediated gene silencing, production of microRNAs
negative regulation of production of microRNAs involved in gene silencing by microRNA
positive regulation of production of miRNAs involved in gene silencing by miRNA
Any process that activates or increases the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA.
positive regulation of gene silencing by miRNA, production of miRNAs
positive regulation of miRNA-mediated gene silencing, production of miRNAs
positive regulation of microRNA-mediated gene silencing, production of microRNAs
positive regulation of production of microRNAs involved in gene silencing by microRNA
up regulation of gene silencing by miRNA, production of miRNAs
up regulation of miRNA-mediated gene silencing, production of miRNAs
up regulation of microRNA-mediated gene silencing, production of microRNAs
up regulation of production of miRNAs involved in gene silencing by miRNA
up regulation of production of microRNAs involved in gene silencing by microRNA
up-regulation of gene silencing by miRNA, production of miRNAs
up-regulation of miRNA-mediated gene silencing, production of miRNAs
up-regulation of microRNA-mediated gene silencing, production of microRNAs
up-regulation of production of miRNAs involved in gene silencing by miRNA
up-regulation of production of microRNAs involved in gene silencing by microRNA
upregulation of gene silencing by miRNA, production of miRNAs
upregulation of miRNA-mediated gene silencing, production of miRNAs
upregulation of microRNA-mediated gene silencing, production of microRNAs
upregulation of production of miRNAs involved in gene silencing by miRNA
upregulation of production of microRNAs involved in gene silencing by microRNA
The directed movement of microRNA (miRNA) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
A macromolecular complex containing separate protein, lipid and RNA molecules. Separate in this context means not covalently bound to each other.
HDL-containing protein-lipid-RNA complex
A protein-lipid-RNA complex containing separate high-density lipoprotein (HDL), lipid and RNA molecules. Separate in this context means not covalently bound to each other.
LDL-containing protein-lipid-RNA complex
A protein-lipid-RNA complex containing separate low-density lipoprotein (LDL), lipid and RNA molecules. Separate in this context means not covalently bound to each other.
The covalent alteration of one or more nucleotides within a primary miRNA molecule to produce a primary miRNA molecule with a sequence that differs from that coded genetically.
regulation of cellular macromolecule biosynthetic process
Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process.
regulation of cellular biopolymer biosynthetic process
regulation of cellular macromolecule anabolism
regulation of cellular macromolecule biosynthesis
regulation of cellular macromolecule formation
regulation of cellular macromolecule synthesis
negative regulation of cellular macromolecule biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process.
negative regulation of cellular biopolymer biosynthetic process
negative regulation of cellular macromolecule anabolism
negative regulation of cellular macromolecule biosynthesis
negative regulation of cellular macromolecule formation
negative regulation of cellular macromolecule synthesis
Any process that modulates the frequency, rate or extent of miRNA catabolic process.
regulation of microRNA catabolic process
negative regulation of miRNA catabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of miRNA catabolic process.
negative regulation of microRNA catabolic process
positive regulation of miRNA catabolic process
Any process that activates or increases the frequency, rate or extent of miRNA catabolic process.
positive regulation of microRNA catabolic process
Any process that modulates the frequency, rate or extent of miRNA metabolic process.
regulation of microRNA metabolic process
negative regulation of miRNA metabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of miRNA metabolic process.
negative regulation of microRNA metabolic process
positive regulation of miRNA metabolic process
Any process that activates or increases the frequency, rate or extent of miRNA metabolic process.
positive regulation of microRNA metabolic process
Any process that modulates the frequency, rate or extent of pre-microRNA processing.
negative regulation of pre-miRNA processing
Any process that stops, prevents or reduces the frequency, rate or extent of pre-microRNA processing.
negative regulation of pre-microRNA processing
positive regulation of pre-miRNA processing
Any process that activates or increases the frequency, rate or extent of pre-microRNA processing.
positive regulation of pre-microRNA processing
Any process that modulates the frequency, rate or extent of primary microRNA processing.
regulation of primary microRNA processing
negative regulation of primary miRNA processing
Any process that stops, prevents or reduces the frequency, rate or extent of primary microRNA processing.
negative regulation of pri-miRNA processing
negative regulation of primary microRNA processing
positive regulation of primary miRNA processing
Any process that activates or increases the frequency, rate or extent of primary microRNA processing.
positive regulation of pri-miRNA processing
positive regulation of primary microRNA processing
positive regulation of gene silencing by miRNA
Any process that activates or increases the frequency, rate or extent of gene silencing by miRNA.
positive regulation of miRNA-mediated gene silencing
positive regulation of microRNA-mediated gene silencing
Any process that modulates the frequency, rate or extent of RNA biosynthetic process.
data item
information content entity
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
A generically dependent continuant that is about some thing.
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
PERSON: Chris Stoeckert
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
obsolescence reason specification
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
A denotator type indicates how a term should be interpreted from an ontological perspective.
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
An experimental variable is the variable that is used in an experiment and is known as the dependent variable that can be manipulated and is being studied
The ratio of force to the area over which that force is distributed
"A harmful role or activity realizeable by some agent in the human body"
""Germs" -- foreign microorganisms capable of causing disease"
The potential capacity of certain species of microbes to cause a disease
The ability or tendency to produce cancer.
Small infectious agent that replicates only inside the living cells of other organisms
"Tissues existing in the early embryonic stages of development"
"Tissues originating from mesoderm and performing a structural or connective function between other tissues"
Tissue that connects, supports, binds, or separates other tissues or organs, typically having relatively few cells embedded in an amorphous matrix, often with collagen or other fibers, and including cartilaginous, fatty, and elastic tissues.
"Tissue lining body structures and forming glands"
Membranous tissue covering internal organs and other internal surfaces of the body.
"Tissue forming muscles - capable of generating movement of body structures"
Muscle tissue is one of four basic biological tissues present in animals. It is a soft tissue that composes muscles. It is formed during embryo development in a process known as myogenesis.
"Tissue forming nerves and neural structures like the brain and spinal cord, used for coordinating bodily functions."
A kind of body tissue containing stored fat that serves as a source of energy; it also cushions and insulates vital organs.
"Blood tissue, including red and white blood cells"
Bodily fluid in animals that delivers necessary substances such as nutrients and oxygen to the cells and transports metabolic waste products away.
"Bone tissue - provides structural framework for body with high compressive strength"
Rigid organs that constitute part of the endoskeleton of vertebrates.
"Tough tissue that connects bones and gives form to many of the soft structures of the body"
A tough, elastic, fibrous connective tissue found in various parts of the body, such as the joints, outer ear, and larynx.
Type of involuntary striated muscle found in the walls and histological foundation of the heart.
"Muscle cells of skeletal muscle - those that execute voluntary movement of the skeleton"
Form of striated muscle tissue which is under the control of the somatic nervous system.
"Muscle cells of smooth muscle - found in digestive tract and blood vessels, execute involuntary movement"
Responsible for the contractility of hollow organs, such as blood vessels, the gastrointestinal tract, the bladder, or the uterus.
"The outer layer of cells in the early embryo"
Outermost of the three primary germ layers of an embryo, from which the epidermis, nervous tissue, and, in vertebrates, sense organs develop.
"The inner layer of cells in the early embryo"
Innermost of the three primary germ layers of an animal embryo, developing into the gastrointestinal tract, the lungs, and associated structures.
"The middle layer of cells in the early embryo"
Middle embryonic germ layer, lying between the ectoderm and the endoderm, from which connective tissue, muscle, bone, and the urogenital and circulatory systems develop.
A health care profession primarily concerned with the remediation of impairments and disabilities and the promotion of mobility, functional ability, quality of life and movement potential through examination, evaluation, diagnosis and physical intervention.
Branch of medicine that deals with the diagnosis and treatment of injury, deformity, and disease by manual and instrumental means.
Treatment of cancer with one or more cytotoxic antineoplastic drugs.
Immunosuppression involves an act that reduces the activation or efficacy of the immune system.
The treatment of disease, esp. cancer, using X-rays or similar forms of radiation.
An organism of microscopic or submicroscopic size, especially a bacterium or protozoan
microorganisms that are similar to bacteria in size and simplicity of structure but radically different in molecular organization. They are now believed to constitute an ancient intermediate group between the bacteria and eukaryotes
a member of a large group of unicellular microorganisms that have cell walls but lack organelles and an organized nucleus, including some that can cause diseas
non-coding RNA
A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein.
WEB:https://en.wikipedia.org/w/index.php?title=Non-coding_RNA&oldid=688555892#Non-coding RNA
ncRNA
genetic non-coding RNA
A genetic non-coding RNA is a non-coding RNA that is created by transcription in a cell
TODO: Add axiom linking GO transcription
synthesized non-coding RNA
TODO: Add axiom relating to OBI planned process and anything else from OBI that is relevant
a RNA that is manufactured in a planned process
long non-coding RNA
Long non-coding RNAs (long ncRNAs, lncRNA) are non-protein coding transcripts longer than 200 nucleotides.
Should requested and then imported from ChEBI
This somewhat arbitrary limit distinguishes long ncRNAs from small regulatory RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs
WEB:https://en.wikipedia.org/w/index.php?title=Long_non-coding_RNA&oldid=687562040#Long non-coding RNA
lncRNA
small interfering RNA
siRNA
small interfering RNA (siRNA) is a class of double-stranded RNA molecules, 20-25 base pairs in length. siRNA plays many roles, but it is most notable in the RNA interference (RNAi) pathway, where it interferes with thes expression of specific genes with complementary nucleotide sequences.
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
WEB: http://en.wikipedia.org/wiki/Organism
animal
fungus
plant
virus
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
A molecular entity that is a polymer of amino acids residues linked by peptide bonds.
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.
A gene located in mitochondrial sequence.
A plastid gene from leucoplast sequence.
A proviral gene with origin endogenous retrovirus.
A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
Any extent of continuous biological sequence.
A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.
A gene that is silenced by DNA modification.
A gene that is silenced by DNA methylation.
An epigenetically modified gene, rearranged at the DNA level.
The point at which one or more contiguous nucleotides were excised.
A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.
A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.
A transcript that in its initial state requires modification to be functional.
A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.
Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
The sequences extending on either side of a specific region.
Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
Removed axiom 'derives_from some miRNA_primary_transcript' pending review of status of SO terms. Changed relation of small regulatory ncRNA (superclass) into is about relationship
A transposable_element that is engineered and foreign.
engineered foreign transposable element gene
The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog).
The region of sequence surrounding a transposable element.
The junction where an insertion occurred.
The junction in a genome where a transposable_element has inserted.
A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
A recombinationally rearranged gene by inversion.
A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.
An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.
DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.
A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.
Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.
The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.
A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.
A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.
A gene that encodes a polyadenylated mRNA.
A gene that encodes an mRNA with a frameshift.
A gene that is recombinationally rearranged.
A gene with a transcript that is trans-spliced.
A non-functional descendant of a functional entity.
A primary transcript that is never translated into a protein.
A gene that encodes a transcript that is edited.
An unregulated promoter that allows continuous expression.
A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.
A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes.
A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).
Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
An mRNA that encodes multiple proteins from at least two non-overlapping regions.
A primary transcript encoding a micro RNA.
A mitochondrial gene located in a maxicircle.
An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
A region of sequence containing one or more repeat units.
The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
A gene that encodes a polycistronic transcript.
A gene that encodes a dicistronic transcript.
A gene that encodes an mRNA that is recoded.
A gene that encodes a transcript with stop codon readthrough.
A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.
gene with stop codon redefined as pyrrolysine
A sequence_feature with an extent of zero.
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
A gene encoding an mRNA that has the stop codon redefined as selenocysteine.
gene with stop codon redefined as selenocysteine
A gene with mRNA recoded by translational bypass.
gene with mRNA recoded by translational bypass
A gene encoding a transcript that has a translational frameshift.
gene with transcript with translational frameshift
An mRNA that has the quality dicistronic.
A gene that encodes a dicistronic primary transcript.
gene with dicistronic primary transcript
A gene that encodes a polycistronic mRNA.
gene with dicistronic processed transcript
The simplest repeated component of a repeat region. A single repeat.
A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network.
An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.
A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
TE that has been modified by manipulations in vitro.
Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
A gene that is post translationally regulated.
A gene that is positively autoregulated.
A gene that is translationally regulated.
A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.
A recombinationally rearranged gene of the vertebrate immune system.
recombinationally rearranged vertebrate immune system gene
A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
A regulatory_region that modulates the transcription of a gene or genes.
A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.
A region (DNA) to which RNA polymerase binds, to begin transcription.
A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.
A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.
A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.
A gene that is silenced by RNA interference.
A gene that is silenced by histone modification.
A gene that is silenced by histone methylation.
A gene that is silenced by histone deacetylation.
A region containing at least one unique origin of replication and a unique termination site.
A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
A sequence feature that corresponds to a single amino acid residue in a polypeptide.
A region defined by its disposition to be involved in a biological process.
A region that is defined according to its relations with other regions within the same sequence.
A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.
A gene that encodes for an piwi associated RNA.
A gene that encodes large intervening non-coding RNA.
A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.
A measurable sequence feature that varies within a population.
The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.
bacterial RNA polymerase promoter sigma 70
bacterial RNA polymerase promoter sigma54
A regulatory region that is involved in the control of the process of transcription.
A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.
restriction endonuclease recognition site
A terminal region of DNA sequence where the end of the region is not blunt ended.
An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.
A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence.
A gene with a start codon other than AUG.
A gene with a translational start codon of CUG.
A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA.
A gene suspected of being involved in the expression of a trait.
A candidate gene whose association with a trait is based on the gene's location on a chromosome.
A candidate gene whose function has something in common biologically with the trait under investigation.
A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome.
A CDS that is part of a transposable element.
A pseudogene contained within a transposable element.
A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation.
A region of sequence that is involved in the control of a biological process.
A gene that can be substituted for a related gene at a different site in the genome.
A sequence alteration where the length of the change in the variant is the same as that of the reference.
A continuous nucleotide sequence is inverted in the same position.
A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence.
The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.
A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.
A recoded_mRNA that was modified by an alteration of codon meaning.
Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
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.
organizational term
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
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."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
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.
core
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
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.
To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])