2015-12-10
He Zhang
Alan Ruttenberg
Alan Ruttenberg
Harrison Strachan
Jingshan Huang
Asiyah Yu Lin
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.
d
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
Person:Alan Ruttenberg
Really of interest to developers only
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
editor preferred term
editor preferred label
editor preferred term
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
editor preferred label
editor preferred term
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
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
example
example of usage
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
GROUP:OBI
OBI_0000277
in branch
has curation status
OBI_0000281
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
has curation status
definition
textual definition
definition
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.
definition
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
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.
definition
editor note
editor note
IAO:0000116
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.
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
PERSON:Daniel Schober
editor note
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.
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
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
PERSON:Daniel Schober
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
alternative term
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
definition source
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
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
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.
has obsolescence reason
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
is denotator type
Alan Ruttenberg
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
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
imported from
expand expression to
Chris Mungall
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 expression to
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)"
expand assertion to
first order logic expression
PERSON:Alan Ruttenberg
first order logic expression
antisymmetric property
antisymmetric property
Alan Ruttenberg
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/>
OBO foundry unique label
PERSON:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
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"
Person:Alan Ruttenberg
has ID range allocated to
Person:Alan Ruttenberg
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]
has ID policy for
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"
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
Person:Alan Ruttenberg
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.
Person:Alan Ruttenberg
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"
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
elucidation
person:Alan Ruttenberg
has associated axiom(nl)
An axiom associated with a term expressed using natural language
Person:Alan Ruttenberg
Person:Alan Ruttenberg
has associated axiom(nl)
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
Person:Alan Ruttenberg
Person:Alan Ruttenberg
has associated axiom(fol)
is allocated id range
Add as annotation triples in the granting ontology
PERSON:Alan Ruttenberg
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"
is allocated id range
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
Person:Alan Ruttenberg
Person:Alan Ruttenberg
has axiom id
term replaced by
Add as annotation triples in the granting ontology
Person:Alan Ruttenberg
Person:Alan Ruttenberg
Use on obsolete terms, relating the term to another term that can be used as a substitute
term replaced by
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
is_about_grouped_miRNA
2015-05-16T19:28:03Z
He_Zhang
is_about_miRNA
is_about_miRNA_target_gene
is_classified_into_gene_family_group
2015-05-16T19:27:05Z
He_Zhang
is_gene_template_of_mRNA
is_model_of_disease
is_predicted_target_of
2015-05-17T07:52:46Z
He_Zhang
miRNA_expressed_in_tissue
regulate_miRNA_transcription
regulate_mRNA_translation
has_predicted_target
2015-05-17T07:51:13Z
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
GO
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
David Hill
Tanya Berardini
Chris Mungall
negatively regulates
Chris Mungall
x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
positively regulates
Chris Mungall
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
SIO
is member of is a mereological relation between a item and a collection.
member part of
has member
SIO
has member is a mereological relation between a collection and an item.
in similarity relationship with
ECO:0000041
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
SO:similar_to
sameness
similar to
in homology relationship with
Similarity that results from common evolutionary origin.
homologous to
in non functional homology relationship with
SO:non_functional_homolog_of
Structural homology that involves a pseudogenic feature and its functional ancestor.
non functional homologous to
entity
entity
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
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
per discussion with Barry Smith
continuant
continuant
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])
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
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])
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])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
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
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
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])
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
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
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])
occurrent
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
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.
per discussion with Barry Smith
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.
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])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
independent continuant
IndependentContinuant
(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]
ic
(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
(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]
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])
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])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
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])
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
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])
s-region
SpatialRegion
(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.
per discussion with Barry Smith
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.
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])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(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])
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
TemporalRegion
t-region
(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])
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])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
per discussion with Barry Smith
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
two-dimensional spatial region
2d-s-region
TwoDimensionalSpatialRegion
(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
(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])
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])
st-region
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
SpatiotemporalRegion
(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
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
(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])
process
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])
process
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
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])
(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]
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]
Disposition
(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.
disposition
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
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])
(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]
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])
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])
RealizableEntity
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])
realizable
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
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])
(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])
(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]
zero-dimensional spatial region
0d-s-region
ZeroDimensionalSpatialRegion
(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])
(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]
quality
Quality
(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
(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]
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
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])
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])
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
SpecificallyDependentContinuant
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.
sdc
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
(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]
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])
per discussion with Barry Smith
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.
role
Role
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
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
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])
fiat object part
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
fiat-object-part
FiatObjectPart
(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
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])
(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]
one-dimensional spatial region
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
OneDimensionalSpatialRegion
1d-s-region
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.
(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])
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).
ObjectAggregate
object-aggregate
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
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.
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])
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
(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]
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
three-dimensional spatial region
ThreeDimensionalSpatialRegion
3d-s-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,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
site
site
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)
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])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
object
object
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
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])
generically dependent continuant
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
GenericallyDependentContinuant
gdc
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.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
function
function
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
Function
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
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])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
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]
p-boundary
ProcessBoundary
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.
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(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]
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])
one-dimensional temporal region
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
OneDimensionalTemporalRegion
1d-t-region
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.
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
material entity
material
(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])
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
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
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
continuant fiat boundary
cf-boundary
ContinuantFiatBoundary
(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])
(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]
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.
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
immaterial
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
ImmaterialEntity
one-dimensional continuant fiat boundary
OneDimensionalContinuantFiatBoundary
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
1d-cf-boundary
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
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])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
process profile
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.
ProcessProfile
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])
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])
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])
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
(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]
relational quality
r-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]
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.
RelationalQuality
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])
(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]
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]
TwoDimensionalContinuantFiatBoundary
2d-cf-boundary
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])
(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]
0d-cf-boundary
ZeroDimensionalContinuantFiatBoundary
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.
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])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
requested by Melanie Courtot
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]
ZeroDimensionalTemporalRegion
0d-t-region
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.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
history
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])
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])
transfer RNA
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.
ChemIDplus:9014-25-9
KEGG COMPOUND:C00066
transfer RNA
tRNA
ribosomal RNA
KEGG COMPOUND:C00240
RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis.
Ribosomal RNA
ribosomal RNA
rRNA
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entity
organic group
Any substituent group or skeleton containing carbon.
ribonucleic acid
ChemIDplus:63231-63-0
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
ribonucleic acid
ribonucleic acids
RNA
amino-acid residue
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
amino-acid residue
small nuclear RNA
A class of small RNA molecules which are comprised of approximately 150 nucleotides and which are found within the nucleus of eukaryotic cells.
CiteXplore:22907602
CiteXplore:23070852
CiteXplore:23190533
CiteXplore:23348838
CiteXplore:23394998
CiteXplore:23426875
CiteXplore:23727230
CiteXplore:23740936
Wikipedia:Small_nuclear_RNA
snRNA
RNA(circular)
KEGG COMPOUND:C02073
RNA(circular)
circRNA
cell line
MB, SS, JZ, MAH, BP, CS, YH
disease of cellular proliferation
A disease that is characterized by abnormally rapid cell division.
cell process disease
cancer
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
ICD10CM:C80
ICD10CM:C80.1
ICD9CM:199
MSH:D009369
NCI:C9305
SNOMEDCT_US_2015_03_01:154432008
SNOMEDCT_US_2015_03_01:154433003
SNOMEDCT_US_2015_03_01:154577008
SNOMEDCT_US_2015_03_01:187597000
SNOMEDCT_US_2015_03_01:188475001
SNOMEDCT_US_2015_03_01:188482002
SNOMEDCT_US_2015_03_01:190150006
SNOMEDCT_US_2015_03_01:269513004
SNOMEDCT_US_2015_03_01:269623003
SNOMEDCT_US_2015_03_01:269626006
SNOMEDCT_US_2015_03_01:269634000
SNOMEDCT_US_2015_03_01:363346000
SNOMEDCT_US_2015_03_01:38807002
UMLS_CUI:C0006826
malignant neoplasm
malignant tumor
primary cancer
disease
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.
MSH:D004194
NCI:C2991
SNOMEDCT_US_2015_03_01:64572001
UMLS_CUI:C0012634
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
3'-5'-exoribonuclease activity
3'-5' exoribonuclease activity
Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
EC:3.1.13.-
Reactome:REACT_102966
Reactome:REACT_108214
Reactome:REACT_20588
Reactome:REACT_33991
Reactome:REACT_34078
Reactome:REACT_78363
Reactome:REACT_82118
Reactome:REACT_88115
Reactome:REACT_89880
Reactome:REACT_92153
Reactome:REACT_93499
Reactome:REACT_95913
Reactome:REACT_95921
Reactome:REACT_96267
Reactome:REACT_99422
molecular_function
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.
molecular function
RNA binding
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
Reactome:REACT_101703
Reactome:REACT_103323
Reactome:REACT_106430
Reactome:REACT_107757
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catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Wikipedia:Enzyme
enzyme activity
nuclease activity
Catalysis of the hydrolysis of ester linkages within nucleic acids.
EC:3.1.-.-
endonuclease activity
Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
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endoribonuclease activity
Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
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Reactome:REACT_75787
exonuclease activity
Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
exoribonuclease activity
Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of an RNA molecule.
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ribonuclease activity
Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
transporter activity
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
Reactome:REACT_6315
binding
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Wikipedia:Binding_(molecular)
cellular_component
NIF_Subcellular:sao-1337158144
NIF_Subcellular:sao1337158144
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.
cell or subcellular entity
cellular component
intracellular
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
Wikipedia:Intracellular
internal to cell
protoplasm
cell
NIF_Subcellular:sao1813327414
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.
Wikipedia:Cell_(biology)
nucleus
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
NIF_Subcellular:sao1702920020
Wikipedia:Cell_nucleus
cell nucleus
nucleoplasm
NIF_Subcellular:sao661522542
That part of the nuclear content other than the chromosomes or the nucleolus.
Wikipedia:Nucleoplasm
cytoplasm
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
Wikipedia:Cytoplasm
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
transcription, DNA-templated
DNA-dependent transcription
The cellular synthesis of RNA on a template of DNA.
Wikipedia:Transcription_(genetics)
cellular transcription, DNA-dependent
transcription, DNA-dependent
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
mRNA cleavage
Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
RNA processing
Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
Wikipedia:Post-transcriptional_modification
mRNA processing
Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
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RNA catabolic process
RNA breakdown
RNA catabolism
RNA degradation
The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
RNA localization
A process in which RNA is transported to, or maintained in, a specific location.
RNA localisation
establishment and maintenance of RNA localization
RNA export from nucleus
RNA export from cell nucleus
RNA export out of nucleus
RNA transport from nucleus to cytoplasm
RNA-nucleus export
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The directed movement of RNA from the nucleus to the cytoplasm.
translation
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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.
Wikipedia:Translation_(genetics)
protein anabolism
protein biosynthesis
protein biosynthetic process
protein formation
protein synthesis
protein translation
translational elongation
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The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
translation elongation
regulation of translation
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.
regulation of protein anabolism
regulation of protein biosynthesis
regulation of protein formation
regulation of protein synthesis
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.
aromatic compound metabolism
transport
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
biological_process
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.
Wikipedia:Biological_process
biological process
physiological process
metabolic process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
Wikipedia:Metabolism
metabolism
catabolic process
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
Wikipedia:Catabolism
breakdown
catabolism
degradation
macromolecule catabolic process
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
biopolymer catabolic process
macromolecule breakdown
macromolecule catabolism
macromolecule degradation
biosynthetic process
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
Wikipedia:Anabolism
anabolism
biosynthesis
formation
synthesis
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.
biopolymer biosynthetic process
macromolecule anabolism
macromolecule biosynthesis
macromolecule formation
macromolecule synthesis
RNA modification
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.
Wikipedia:RNA_editing
regulation of biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
regulation of anabolism
regulation of biosynthesis
regulation of formation
regulation of synthesis
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.
down regulation of biosynthetic process
down-regulation of biosynthetic process
downregulation of biosynthetic process
negative regulation of anabolism
negative regulation of biosynthesis
negative regulation of formation
negative regulation of synthesis
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.
positive regulation of anabolism
positive regulation of biosynthesis
positive regulation of formation
positive regulation of synthesis
up regulation of biosynthetic process
up-regulation of biosynthetic process
upregulation of biosynthetic process
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.
down regulation of metabolic process
down-regulation of metabolic process
downregulation of metabolic process
negative regulation of metabolism
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.
positive regulation of metabolism
up regulation of metabolic process
up-regulation of metabolic process
upregulation of metabolic process
regulation of catabolic process
Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances.
regulation of breakdown
regulation of catabolism
regulation of degradation
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.
down regulation of catabolic process
down-regulation of catabolic process
downregulation of catabolic process
negative regulation of breakdown
negative regulation of catabolism
negative regulation of degradation
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.
positive regulation of breakdown
positive regulation of catabolism
positive regulation of degradation
up regulation of catabolic process
up-regulation of catabolic process
upregulation of catabolic process
cellular process
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
cell physiology
cellular physiological process
response to organic substance
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
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
nuclear dicing body
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.
D body
gene expression
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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.
Wikipedia:Gene_expression
regulation of gene expression
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (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.
Wikipedia:Regulation_of_gene_expression
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.
miRNA metabolic process
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.
microRNA metabolic process
miRNA catabolic process
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.
microRNA catabolic process
positive regulation of macromolecule metabolic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
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.
positive regulation of gene expression
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (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.
negative regulation of gene expression
Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (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.
response to organic cyclic compound
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
response to organic cyclic substance
cellular component organization
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
cell organisation
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
RNA metabolic process
RNA metabolism
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The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
RNA interference
RNAi
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.
Wikipedia:RNA_interference
posttranscriptional gene silencing by siRNA
posttranscriptional gene silencing
PTGS
The inactivation of gene expression by a posttranscriptional mechanism.
Wikipedia:Post_transcriptional_gene_silencing
post-transcriptional gene silencing
quelling
RISC complex
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.
RNA-induced silencing complex
Wikipedia:RNA-induced_silencing_complex
gene silencing
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.
Wikipedia:Gene_silencing
endoribonuclease activity, producing 5'-phosphomonoesters
Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
EC:3.1.26
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.
EC:3.1.13
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exoribonuclease activity, producing 5' phosphomonoesters
negative regulation of translation
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.
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
heterocycle biosynthetic process
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).
heterocycle anabolism
heterocycle biosynthesis
heterocycle formation
heterocycle synthesis
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
regulation of metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
regulation of metabolism
aromatic compound biosynthetic process
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
aromatic compound anabolism
aromatic compound biosynthesis
aromatic compound formation
aromatic compound synthesis
aromatic compound catabolic process
The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
aromatic compound breakdown
aromatic compound catabolism
aromatic compound degradation
protein metabolic process
The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
Wikipedia:Protein_metabolism
protein metabolic process and modification
protein metabolism
protein metabolism and modification
ribonucleoprotein complex biogenesis
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.
RNA-protein complex biogenesis
ribonucleoprotein complex biogenesis and assembly
ribonucleoprotein complex assembly
RNA-protein complex assembly
RNP complex assembly
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
protein-RNA complex assembly
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
RNA interference, production of siRNA
production of guide RNAs involved in RNA interference
ribonucleoprotein complex
A macromolecular complex containing both protein and RNA molecules.
RNA-protein complex
RNP
Wikipedia:Ribonucleoprotein
protein-RNA complex
ribonucleoprotein
dsRNA fragmentation
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.
double-stranded RNA fragmentation
primary miRNA processing
Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule.
pri-miRNA processing
primary microRNA processing
pre-miRNA processing
Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
pre-microRNA processing
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.
regulation of cellular metabolism
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.
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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.
regulation of cellular anabolism
regulation of cellular biosynthesis
regulation of cellular formation
regulation of cellular synthesis
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.
regulation of cellular breakdown
regulation of cellular catabolism
regulation of cellular degradation
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
nuclear lumen
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
RNA biosynthetic process
RNA anabolism
RNA biosynthesis
RNA formation
RNA synthesis
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.
macromolecular complex
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.
macromolecule complex
chromatoid body
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).
ncRNA processing
Any process that results in the conversion of one or more primary non-coding RNA (ncRNA) transcripts into one or more mature ncRNA molecules.
cellular nitrogen compound metabolic process
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The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolism
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
cellular macromolecule anabolism
cellular macromolecule biosynthesis
cellular macromolecule formation
cellular macromolecule synthesis
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
ncRNA metabolic process
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The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs).
ncRNA metabolism
ncRNA catabolic process
The chemical reactions and pathways resulting in the breakdown of non-coding RNA transcripts (ncRNAs). Includes the breakdown of cryptic unstable transcripts (CUTs).
ncRNA breakdown
ncRNA catabolism
ncRNA degradation
micro-ribonucleoprotein complex
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.
miRNP complex
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
gene silencing by miRNA
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.
gene silencing by microRNA
miRNA-mediated gene silencing
microRNA-mediated gene silencing
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 processing
miRNA-mediated gene silencing, production of miRNAs
microRNA-mediated gene silencing, production of microRNAs
production of microRNAs involved in gene silencing by microRNA
miRNA binding
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.
microRNA binding
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.
gene silencing by miRNA, mRNA cleavage
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
pre-miRNA export from nucleus
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 export from cell nucleus
pre-microRNA export out of nucleus
pre-microRNA transport from nucleus to cytoplasm
pre-microRNA-nucleus export
ribonucleoprotein granule
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.
RNP granule
mRNP granule
cytoplasmic ribonucleoprotein granule
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
response to chemical
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
response to chemical stimulus
response to chemical substance
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.
biopolymer metabolic process
macromolecule metabolism
organelle
NIF_Subcellular:sao1539965131
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.
Wikipedia:Organelle
intracellular organelle
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
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
organelle lumen
The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen.
response to dsRNA
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.
response to double-stranded RNA
ncRNA 3'-end processing
Any process involved in forming the mature 3' end of a non-coding RNA molecule.
ncRNA 3' end processing
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 organization
macromolecular complex subunit organisation
cellular metabolic process
The chemical reactions and pathways by which individual cells transform chemical substances.
cellular metabolism
primary metabolic process
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
primary metabolism
cellular catabolic process
The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
cellular breakdown
cellular catabolism
cellular degradation
cellular biosynthetic process
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
cellular anabolism
cellular biosynthesis
cellular formation
cellular synthesis
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 biopolymer metabolic process
cellular macromolecule metabolism
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.
cellular biopolymer catabolic process
cellular macromolecule breakdown
cellular macromolecule catabolism
cellular macromolecule degradation
cellular protein metabolic process
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The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
cellular protein metabolism
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.
organelle part
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.
intracellular part
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.
nuclear part
Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.
NIF_Subcellular:sao1499850686
nuclear subcomponent
nucleus component
cytoplasmic part
Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
cytoplasm component
intracellular organelle part
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.
nucleoplasm part
Any constituent part of the nucleoplasm, that part of the nuclear content other than the chromosomes or the nucleolus.
cell part
Any constituent part of a cell, the basic structural and functional unit of all organisms.
NIF_Subcellular:sao628508602
cellular subcomponent
single-organism process
A biological process that involves only one organism.
single organism process
single-organism metabolic process
A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism.
mature miRNA 3'-end processing
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.
single-organism cellular process
Any process that is carried out at the cellular level, occurring within a single organism.
single-organism transport
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving 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
heterocycle metabolic process
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).
heterocycle metabolism
heterocycle catabolic process
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).
heterocycle breakdown
heterocycle catabolism
heterocycle degradation
intracellular transport
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
up regulation of biological process
up-regulation of biological process
upregulation of biological process
negative regulation of biological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
down regulation of biological process
down-regulation of biological process
downregulation of biological process
negative regulation of physiological process
positive regulation of cellular process
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
positive regulation of cellular physiological process
up regulation of cellular process
up-regulation of cellular process
upregulation of cellular process
negative regulation of cellular process
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
down regulation of cellular process
down-regulation of cellular process
downregulation of cellular process
negative regulation of cellular physiological process
regulation of response to stimulus
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
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.
up regulation of response to stimulus
up-regulation of response to stimulus
upregulation of response to 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.
down regulation of response to stimulus
down-regulation of response to stimulus
downregulation of response to stimulus
RNA transport
The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
regulation of biological process
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
regulation of physiological process
regulation of cellular process
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
regulation of cellular physiological process
response to stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
physiological response to stimulus
nuclear export
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The directed movement of substances out of the nucleus.
export from nucleus
nucleus export
substance nuclear export
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
regulation of nitrogen metabolism
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
localization
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
localisation
establishment of localization
The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.
establishment of localisation
establishment of RNA localization
RNA positioning
RNA recruitment
The directed movement of RNA to a specific location.
establishment of RNA localisation
regulation of protein metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein.
regulation of protein metabolism
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
regulation of RNA metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.
regulation of RNA metabolism
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
downregulation of RNA metabolic process
negative regulation of RNA metabolism
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.
positive regulation of RNA metabolism
up regulation of RNA metabolic process
up-regulation of RNA metabolic process
upregulation of RNA metabolic process
cellular response to stimulus
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
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.
regulation of gene silencing by miRNA
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
regulation of gene silencing by RNA
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.
regulation of gene silencing
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.
negative regulation of gene silencing
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.
macromolecular complex assembly
The aggregation, arrangement and bonding together of a set of macromolecules to form a complex.
macromolecule complex assembly
intracellular organelle lumen
An organelle lumen that is part of an intracellular organelle.
RISC-loading complex
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.
miRLC
microRNA loading complex
microprocessor complex
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.
IntAct:EBI-9519039
IntAct:EBI-9519056
primary miRNA binding
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.
pri-miRNA binding
primary microRNA binding
pre-miRNA binding
Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA.
pre-microRNA binding
precursor microRNA binding
cellular response to chemical 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 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
ribonucleoprotein complex localization
Any process in which a ribonucleoprotein complex is transported to, or maintained in, a specific location within a cell.
RNP localization
cellular ribonucleoprotein complex localization
establishment and maintenance of ribonucleoprotein complex localization
ribonucleoprotein complex localisation
cellular response to organic substance
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.
cellular response to dsRNA
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
RNP 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
organic substance metabolic process
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic molecular entity metabolic process
organic molecular entity metabolism
organic substance metabolism
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
regulation of primary metabolic process
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.
nucleic acid metabolic process
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.
nucleic acid cleavage
RNA phosphodiester bond 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.
pre-miRNA transporter activity
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 metabolism
organic cyclic compound catabolic process
The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.
organic cyclic compound breakdown
organic cyclic compound catabolism
organic cyclic compound degradation
organic cyclic compound biosynthetic process
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
organic cyclic compound anabolism
organic cyclic compound biosynthesis
organic cyclic compound formation
organic cyclic compound synthesis
organic substance catabolic process
The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.
organic molecular entity breakdown
organic molecular entity catabolic process
organic molecular entity catabolism
organic molecular entity degradation
organic substance breakdown
organic substance catabolism
organic substance degradation
organic substance biosynthetic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
organic molecular entity anabolism
organic molecular entity biosynthesis
organic molecular entity biosynthetic process
organic molecular entity formation
organic molecular entity synthesis
organic substance anabolism
organic substance biosynthesis
organic substance formation
organic substance synthesis
response to nitrogen compound
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.
response to nitrogen molecular entity
cellular response to nitrogen 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 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 breakdown
down regulation of RNA catabolic process
down regulation of RNA catabolism
down regulation of RNA degradation
down-regulation of RNA breakdown
down-regulation of RNA catabolic process
down-regulation of RNA catabolism
down-regulation of RNA degradation
downregulation of RNA breakdown
downregulation of RNA catabolic process
downregulation of RNA catabolism
downregulation of RNA degradation
negative regulation of RNA breakdown
negative regulation of RNA catabolism
negative regulation of RNA degradation
single-organism localization
A localization which involves only one organism.
single organism localization
single-organism intracellular transport
An intracellular transport which involves only one organism.
single organism intracellular transport
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 anabolism
down regulation of RNA biosynthesis
down regulation of RNA biosynthetic process
down regulation of RNA formation
down regulation of RNA synthesis
down-regulation of RNA anabolism
down-regulation of RNA biosynthesis
down-regulation of RNA biosynthetic process
down-regulation of RNA formation
down-regulation of RNA synthesis
downregulation of RNA anabolism
downregulation of RNA biosynthesis
downregulation of RNA biosynthetic process
downregulation of RNA formation
downregulation of RNA synthesis
negative regulation of RNA anabolism
negative regulation of RNA biosynthesis
negative regulation of RNA formation
negative regulation of RNA synthesis
positive regulation of RNA biosynthetic process
Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process.
positive regulation of RNA anabolism
positive regulation of RNA biosynthesis
positive regulation of RNA formation
positive regulation of RNA synthesis
up regulation of RNA anabolism
up regulation of RNA biosynthesis
up regulation of RNA biosynthetic process
up regulation of RNA formation
up regulation of RNA synthesis
up-regulation of RNA anabolism
up-regulation of RNA biosynthesis
up-regulation of RNA biosynthetic process
up-regulation of RNA formation
up-regulation of RNA synthesis
upregulation of RNA anabolism
upregulation of RNA biosynthesis
upregulation of RNA biosynthetic process
upregulation of RNA formation
upregulation of RNA synthesis
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 processing
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 processing
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 processing
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 processing
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 processing
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 processing
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 processing
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 processing
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 processing
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
miRNA transport
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.
microRNA transport
protein-lipid-RNA complex
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.
primary miRNA modification
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
regulation of miRNA catabolic process
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
regulation of miRNA metabolic 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
regulation of pre-miRNA processing
Any process that modulates the frequency, rate or extent of pre-microRNA processing.
regulation 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
regulation of primary miRNA processing
Any process that modulates the frequency, rate or extent of primary microRNA processing.
regulation of pri-miRNA 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
regulation of RNA biosynthetic process
Any process that modulates the frequency, rate or extent of RNA biosynthetic process.
regulation of RNA anabolism
regulation of RNA biosynthesis
regulation of RNA formation
regulation of RNA synthesis
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.
OBI_0000142
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)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
PERSON:Bill Bug
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.
curation status specification
data about an ontology part
Person:Alan Ruttenberg
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.
obsolescence reason specification
denotator type
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
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.
miRNA_target_gene_primary_transcript
miRNA_target_gene_mRNA
miRNA_and_target_gene_binding
fly_miRNA
c_elegans_miRNA
bacterial_miRNA
virus_miRNA
non_mammalian_miRNA
mammalian_miRNA
miRNA_expression
protein_miRNA_promoter_binding
promoter_of_miRNA
miRNA_transcription_initiation
transcription_of_miRNA
animal_study_model
miRNA_target_gene
2015-05-25T15:37:18Z
environmental_variable
2013-09-28T19:15:26Z
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
HeZhang
gene_sequence
2013-09-28T19:15:26Z
HeZhang
pressure
2013-09-28T19:16:26Z
HeZhang
The ratio of force to the area over which that force is distributed
temperature
2013-09-28T19:16:26Z
HeZhang
Numerical measure of hot or cold
high_pressure
2013-09-28T19:17:41Z
HeZhang
low_pressure
2013-09-28T19:17:41Z
HeZhang
normal_pressure
2013-09-28T19:17:41Z
HeZhang
high_temperature
2013-09-28T19:18:33Z
HeZhang
low_temperature
2013-09-28T19:18:33Z
HeZhang
normal_temperature
2013-09-28T19:18:33Z
HeZhang
harmful_role
"A harmful role or activity realizeable by some agent in the human body"
2013-09-29T18:27:09Z
HeZhang
harmful_environmental_effect
"Harmful physical agents"
2013-09-29T18:29:20Z
HeZhang
pathogenicity
""Germs" -- foreign microorganisms capable of causing disease"
2013-09-29T18:29:20Z
HeZhang
The potential capacity of certain species of microbes to cause a disease
toxic_activity
"Harmful chemical agents"
2013-09-29T18:29:20Z
HeZhang
carcinogenicity
The ability or tendency to produce cancer.
2013-09-29T18:30:22Z
HeZhang
virus
2013-10-01T23:27:46Z
HeZhang
Small infectious agent that replicates only inside the living cells of other organisms
adult_tissue
2013-10-01T23:32:05Z
HeZhang
embryonic_tissue
"Tissues existing in the early embryonic stages of development"
2013-10-01T23:32:05Z
HeZhang
Tissue in an embryo
connective_tissue
"Tissues originating from mesoderm and performing a structural or connective function between other tissues"
2013-10-01T23:33:33Z
HeZhang
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.
epithelia_tissue
"Tissue lining body structures and forming glands"
2013-10-01T23:33:33Z
HeZhang
Membranous tissue covering internal organs and other internal surfaces of the body.
muscle_tissue
"Tissue forming muscles - capable of generating movement of body structures"
2013-10-01T23:33:33Z
HeZhang
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.
nerve_tissue
"Tissue forming nerves and neural structures like the brain and spinal cord, used for coordinating bodily functions."
2013-10-01T23:33:33Z
HeZhang
Tissue composed of neurons.
adipose_tissue
"Fat tissue"
2013-10-01T23:34:55Z
A kind of body tissue containing stored fat that serves as a source of energy; it also cushions and insulates vital organs.
HeZhang
blood
"Blood tissue, including red and white blood cells"
2013-10-01T23:34:55Z
Bodily fluid in animals that delivers necessary substances such as nutrients and oxygen to the cells and transports metabolic waste products away.
HeZhang
bone
"Bone tissue - provides structural framework for body with high compressive strength"
2013-10-01T23:34:55Z
HeZhang
Rigid organs that constitute part of the endoskeleton of vertebrates.
cartilage
"Tough tissue that connects bones and gives form to many of the soft structures of the body"
2013-10-01T23:34:55Z
A tough, elastic, fibrous connective tissue found in various parts of the body, such as the joints, outer ear, and larynx.
HeZhang
cardiac_muscle
"Muscle cells of the heart"
2013-10-01T23:36:04Z
HeZhang
Type of involuntary striated muscle found in the walls and histological foundation of the heart.
skeletal_muscle
"Muscle cells of skeletal muscle - those that execute voluntary movement of the skeleton"
2013-10-01T23:36:04Z
Form of striated muscle tissue which is under the control of the somatic nervous system.
HeZhang
smooth_muscle
"Muscle cells of smooth muscle - found in digestive tract and blood vessels, execute involuntary movement"
2013-10-01T23:36:04Z
HeZhang
Responsible for the contractility of hollow organs, such as blood vessels, the gastrointestinal tract, the bladder, or the uterus.
ectoderm
"The outer layer of cells in the early embryo"
2013-10-03T23:21:30Z
HeZhang
Outermost of the three primary germ layers of an embryo, from which the epidermis, nervous tissue, and, in vertebrates, sense organs develop.
endoderm
"The inner layer of cells in the early embryo"
2013-10-03T23:21:30Z
HeZhang
Innermost of the three primary germ layers of an animal embryo, developing into the gastrointestinal tract, the lungs, and associated structures.
mesoderm
"The middle layer of cells in the early embryo"
2013-10-03T23:21:30Z
HeZhang
Middle embryonic germ layer, lying between the ectoderm and the endoderm, from which connective tissue, muscle, bone, and the urogenital and circulatory systems develop.
treatment
2013-10-03T23:37:16Z
HeZhang
pharmaceutical_treatment
2013-10-04T20:10:02Z
physical_therapy
2013-10-04T20:10:02Z
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.
psychological_treatment
2013-10-04T20:10:02Z
surgery
2013-10-04T20:10:02Z
Branch of medicine that deals with the diagnosis and treatment of injury, deformity, and disease by manual and instrumental means.
analgesic_treatment
2013-10-04T20:19:18Z
antibiotic_treatment
2013-10-04T20:19:18Z
antihyperlipidemic_treatment
2013-10-04T20:19:18Z
antihypertensive_treatment
2013-10-04T20:19:18Z
chemotherapy
2013-10-04T20:19:18Z
Treatment of cancer with one or more cytotoxic antineoplastic drugs.
immunosuppressive_therapy
2013-10-04T20:19:18Z
Immunosuppression involves an act that reduces the activation or efficacy of the immune system.
radiation_release
2013-10-04T20:24:14Z
The treatment of disease, esp. cancer, using X-rays or similar forms of radiation.
cellular_organism
2013-10-07T00:19:58Z
An organism of microscopic or submicroscopic size, especially a bacterium or protozoan
archaea
2013-10-07T00:31:14Z
HeZhang
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
bacteria
2013-10-07T00:31:14Z
HeZhang
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
mouse_miRNA
TE_juxtaposition
2013-10-25T16:05:06Z
HeZhang
TE_insertion
2013-10-25T16:03:19Z
positive_strand_insertion
2013-10-25T16:17:26Z
HeZhang
negative_strand_insertion
2013-10-25T16:17:26Z
HeZhang
human_miRNA
2015-05-16T19:26:04Z
He_Zhang
hsa-mir-585
miRBase:MI0003592
hsa-mir-620
miRBase:MI0003634
hsa-mir-659
miRBase:MI0003683
hsa-mir-2113
miRBase:MI0003939
hsa-mir-1229
miRBase:MI0006319
hsa-mir-1234
miRBase:MI0006324
hsa-mir-548o
miRBase:MI0006402
hsa-mir-1279
miRBase:MI0006426
hsa-mir-1321
miRBase:MI0006652
hsa-mir-1470
miRBase:MI0007075
hsa-mir-1539
miRBase:MI0007260
hsa-mir-1973
miRBase:MI0009983
hsa-mir-2052
miRBase:MI0010486
hsa-mir-2053
miRBase:MI0010487
hsa-mir-2054
miRBase:MI0010488
hsa-mir-2115
miRBase:MI0010634
hsa-mir-2116
miRBase:MI0010635
hsa-mir-2117
miRBase:MI0010636
hsa-mir-2276
miRBase:MI0011282
hsa-mir-2277
miRBase:MI0011284
hsa-mir-2681
miRBase:MI0012062
hsa-mir-2682
miRBase:MI0012063
hsa-mir-2909
miRBase:MI0013083
hsa-mir-3115
miRBase:MI0014127
hsa-mir-3123
miRBase:MI0014139
hsa-mir-3124
miRBase:MI0014140
hsa-mir-3125
miRBase:MI0014142
hsa-mir-3128
miRBase:MI0014145
hsa-mir-3131
miRBase:MI0014151
hsa-mir-3133
miRBase:MI0014153
hsa-mir-3134
miRBase:MI0014155
hsa-mir-3137
miRBase:MI0014160
hsa-mir-3139
miRBase:MI0014162
hsa-mir-3141
miRBase:MI0014165
hsa-mir-3142
miRBase:MI0014166
hsa-mir-3143
miRBase:MI0014167
hsa-mir-3144
miRBase:MI0014169
hsa-mir-3147
miRBase:MI0014173
hsa-mir-3148
miRBase:MI0014175
hsa-mir-3152
miRBase:MI0014179
hsa-mir-3153
miRBase:MI0014180
hsa-mir-3157
miRBase:MI0014185
hsa-mir-3159
miRBase:MI0014188
hsa-mir-3161
miRBase:MI0014191
hsa-mir-3162
miRBase:MI0014192
hsa-mir-3163
miRBase:MI0014193
hsa-mir-3164
miRBase:MI0014194
hsa-mir-3166
miRBase:MI0014196
hsa-mir-3168
miRBase:MI0014199
hsa-mir-3169
miRBase:MI0014200
hsa-mir-3171
miRBase:MI0014202
hsa-mir-3118-4
miRBase:MI0014207
hsa-mir-3175
miRBase:MI0014209
hsa-mir-3176
miRBase:MI0014210
hsa-mir-3177
miRBase:MI0014211
hsa-mir-3178
miRBase:MI0014212
hsa-mir-3181
miRBase:MI0014223
hsa-mir-3182
miRBase:MI0014224
hsa-mir-3183
miRBase:MI0014225
hsa-mir-3184
miRBase:MI0014226
hsa-mir-3185
miRBase:MI0014227
hsa-mir-3186
miRBase:MI0014229
hsa-mir-3187
miRBase:MI0014231
hsa-mir-3189
miRBase:MI0014233
hsa-mir-3194
miRBase:MI0014239
hsa-mir-3195
miRBase:MI0014240
hsa-mir-3196
miRBase:MI0014241
hsa-mir-3197
miRBase:MI0014245
hsa-mir-3201
miRBase:MI0014250
hsa-mir-4295
miRBase:MI0015822
hsa-mir-4296
miRBase:MI0015823
hsa-mir-4297
miRBase:MI0015824
hsa-mir-378c
miRBase:MI0015825
hsa-mir-4293
miRBase:MI0015826
hsa-mir-4294
miRBase:MI0015827
hsa-mir-4301
miRBase:MI0015828
hsa-mir-4299
miRBase:MI0015829
hsa-mir-4298
miRBase:MI0015830
hsa-mir-4300
miRBase:MI0015831
hsa-mir-4304
miRBase:MI0015832
hsa-mir-4302
miRBase:MI0015833
hsa-mir-4303
miRBase:MI0015834
hsa-mir-4305
miRBase:MI0015835
hsa-mir-4306
miRBase:MI0015836
hsa-mir-4309
miRBase:MI0015837
hsa-mir-4307
miRBase:MI0015838
hsa-mir-4308
miRBase:MI0015839
hsa-mir-4310
miRBase:MI0015840
hsa-mir-4311
miRBase:MI0015841
hsa-mir-4312
miRBase:MI0015842
hsa-mir-4313
miRBase:MI0015843
hsa-mir-4316
miRBase:MI0015845
hsa-mir-4314
miRBase:MI0015846
hsa-mir-4318
miRBase:MI0015847
hsa-mir-4319
miRBase:MI0015848
hsa-mir-4320
miRBase:MI0015849
hsa-mir-4317
miRBase:MI0015850
hsa-mir-4322
miRBase:MI0015851
hsa-mir-4321
miRBase:MI0015852
hsa-mir-4323
miRBase:MI0015853
hsa-mir-4324
miRBase:MI0015854
hsa-mir-4256
miRBase:MI0015855
hsa-mir-4257
miRBase:MI0015856
hsa-mir-4258
miRBase:MI0015857
hsa-mir-4259
miRBase:MI0015858
hsa-mir-4260
miRBase:MI0015859
hsa-mir-4253
miRBase:MI0015860
hsa-mir-4251
miRBase:MI0015861
hsa-mir-4254
miRBase:MI0015862
hsa-mir-4255
miRBase:MI0015863
hsa-mir-4252
miRBase:MI0015864
hsa-mir-4325
miRBase:MI0015865
hsa-mir-4326
miRBase:MI0015866
hsa-mir-4327
miRBase:MI0015867
hsa-mir-4261
miRBase:MI0015868
hsa-mir-4265
miRBase:MI0015869
hsa-mir-4266
miRBase:MI0015870
hsa-mir-4267
miRBase:MI0015871
hsa-mir-4262
miRBase:MI0015872
hsa-mir-4268
miRBase:MI0015874
hsa-mir-4269
miRBase:MI0015875
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miRBase:MI0015876
hsa-mir-4264
miRBase:MI0015877
hsa-mir-4270
miRBase:MI0015878
hsa-mir-4271
miRBase:MI0015879
hsa-mir-4272
miRBase:MI0015880
hsa-mir-4273
miRBase:MI0015881
hsa-mir-4276
miRBase:MI0015882
hsa-mir-4275
miRBase:MI0015883
hsa-mir-4274
miRBase:MI0015884
hsa-mir-4281
miRBase:MI0015885
hsa-mir-4277
miRBase:MI0015886
hsa-mir-4279
miRBase:MI0015887
hsa-mir-4278
miRBase:MI0015888
hsa-mir-4280
miRBase:MI0015889
hsa-mir-4282
miRBase:MI0015890
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miRBase:MI0015891
hsa-mir-4284
miRBase:MI0015893
hsa-mir-4286
miRBase:MI0015894
hsa-mir-4287
miRBase:MI0015895
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miRBase:MI0015896
hsa-mir-4292
miRBase:MI0015897
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miRBase:MI0015898
hsa-mir-4290
miRBase:MI0015899
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miRBase:MI0015900
hsa-mir-4329
miRBase:MI0015901
hsa-mir-4330
miRBase:MI0015902
hsa-mir-4328
miRBase:MI0015904
hsa-mir-3606
miRBase:MI0015996
hsa-mir-3609
miRBase:MI0015999
hsa-mir-3610
miRBase:MI0016000
hsa-mir-3611
miRBase:MI0016001
hsa-mir-3614
miRBase:MI0016004
hsa-mir-3616
miRBase:MI0016006
hsa-mir-3619
miRBase:MI0016009
hsa-mir-3620
miRBase:MI0016011
hsa-mir-3621
miRBase:MI0016012
hsa-mir-3646
miRBase:MI0016046
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miRBase:MI0016049
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miRBase:MI0016050
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miRBase:MI0016051
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miRBase:MI0016052
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miRBase:MI0016053
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miRBase:MI0016054
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miRBase:MI0016055
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miRBase:MI0016056
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miRBase:MI0016057
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miRBase:MI0016058
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miRBase:MI0016060
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miRBase:MI0016063
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miRBase:MI0016064
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miRBase:MI0016066
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miRBase:MI0016067
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miRBase:MI0016068
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miRBase:MI0016069
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miRBase:MI0016072
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miRBase:MI0016073
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miRBase:MI0016075
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miRBase:MI0016076
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miRBase:MI0016078
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miRBase:MI0016079
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miRBase:MI0016080
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miRBase:MI0016082
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miRBase:MI0016083
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miRBase:MI0016084
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miRBase:MI0016085
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miRBase:MI0016086
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miRBase:MI0016087
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miRBase:MI0016092
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miRBase:MI0016093
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miRBase:MI0016134
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miRBase:MI0016135
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miRBase:MI0016410
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miRBase:MI0016412
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miRBase:MI0016413
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miRBase:MI0016415
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miRBase:MI0016420
hsa-mir-3916
miRBase:MI0016422
hsa-mir-3917
miRBase:MI0016423
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miRBase:MI0016424
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miRBase:MI0016425
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miRBase:MI0016427
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miRBase:MI0016428
hsa-mir-3922
miRBase:MI0016429
hsa-mir-3924
miRBase:MI0016432
hsa-mir-3925
miRBase:MI0016433
hsa-mir-3928
miRBase:MI0016438
hsa-mir-3929
miRBase:MI0016439
hsa-mir-3935
miRBase:MI0016591
hsa-mir-3936
miRBase:MI0016592
hsa-mir-3939
miRBase:MI0016596
hsa-mir-3941
miRBase:MI0016598
hsa-mir-3942
miRBase:MI0016599
hsa-mir-3944
miRBase:MI0016601
hsa-mir-3945
miRBase:MI0016602
hsa-mir-1268b
miRBase:MI0016748
hsa-mir-4417
miRBase:MI0016753
hsa-mir-4418
miRBase:MI0016754
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miRBase:MI0016755
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miRBase:MI0016756
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miRBase:MI0016757
hsa-mir-4422
miRBase:MI0016759
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miRBase:MI0016761
hsa-mir-4424
miRBase:MI0016763
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miRBase:MI0016764
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miRBase:MI0016765
hsa-mir-4430
miRBase:MI0016769
hsa-mir-4431
miRBase:MI0016771
hsa-mir-4432
miRBase:MI0016772
hsa-mir-4434
miRBase:MI0016774
hsa-mir-4437
miRBase:MI0016778
hsa-mir-4438
miRBase:MI0016781
hsa-mir-4439
miRBase:MI0016782
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miRBase:MI0016783
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miRBase:MI0016784
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miRBase:MI0016785
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miRBase:MI0016786
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miRBase:MI0016788
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miRBase:MI0016790
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miRBase:MI0016791
hsa-mir-4450
miRBase:MI0016795
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miRBase:MI0016798
hsa-mir-4453
miRBase:MI0016799
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miRBase:MI0016800
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miRBase:MI0016801
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miRBase:MI0016802
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miRBase:MI0016803
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miRBase:MI0016804
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miRBase:MI0016805
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miRBase:MI0016806
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miRBase:MI0016807
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miRBase:MI0016808
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miRBase:MI0016810
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miRBase:MI0016811
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miRBase:MI0016812
hsa-mir-4465
miRBase:MI0016816
hsa-mir-4466
miRBase:MI0016817
hsa-mir-4467
miRBase:MI0016818
hsa-mir-4468
miRBase:MI0016819
hsa-mir-4469
miRBase:MI0016820
hsa-mir-4470
miRBase:MI0016821
hsa-mir-4471
miRBase:MI0016822
hsa-mir-4472-1
miRBase:MI0016823
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miRBase:MI0016824
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miRBase:MI0016825
hsa-mir-4474
miRBase:MI0016826
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miRBase:MI0016827
hsa-mir-4476
miRBase:MI0016828
hsa-mir-4478
miRBase:MI0016831
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miRBase:MI0016838
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miRBase:MI0016841
hsa-mir-4481
miRBase:MI0016842
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miRBase:MI0016843
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miRBase:MI0016844
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miRBase:MI0016846
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miRBase:MI0016847
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miRBase:MI0016848
hsa-mir-4489
miRBase:MI0016850
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miRBase:MI0016852
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miRBase:MI0016853
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miRBase:MI0016854
hsa-mir-4493
miRBase:MI0016855
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miRBase:MI0016856
hsa-mir-4495
miRBase:MI0016857
hsa-mir-4496
miRBase:MI0016858
hsa-mir-4497
miRBase:MI0016859
hsa-mir-4498
miRBase:MI0016860
hsa-mir-4419b
miRBase:MI0016861
hsa-mir-4499
miRBase:MI0016862
hsa-mir-4500
miRBase:MI0016863
hsa-mir-4501
miRBase:MI0016864
hsa-mir-4502
miRBase:MI0016865
hsa-mir-4503
miRBase:MI0016866
hsa-mir-4505
miRBase:MI0016868
hsa-mir-4506
miRBase:MI0016869
hsa-mir-4507
miRBase:MI0016871
hsa-mir-4508
miRBase:MI0016872
hsa-mir-4511
miRBase:MI0016877
hsa-mir-4512
miRBase:MI0016878
hsa-mir-4513
miRBase:MI0016879
hsa-mir-4514
miRBase:MI0016880
hsa-mir-4516
miRBase:MI0016882
hsa-mir-4517
miRBase:MI0016883
hsa-mir-4518
miRBase:MI0016884
hsa-mir-4519
miRBase:MI0016885
hsa-mir-4521
miRBase:MI0016887
hsa-mir-1269b
miRBase:MI0016888
hsa-mir-4522
miRBase:MI0016889
hsa-mir-4525
miRBase:MI0016892
hsa-mir-4527
miRBase:MI0016894
hsa-mir-4528
miRBase:MI0016895
hsa-mir-4530
miRBase:MI0016897
hsa-mir-4531
miRBase:MI0016898
hsa-mir-4532
miRBase:MI0016899
hsa-mir-4533
miRBase:MI0016900
hsa-mir-4534
miRBase:MI0016901
hsa-mir-378i
miRBase:MI0016902
hsa-mir-4535
miRBase:MI0016903
hsa-mir-1587
miRBase:MI0016905
hsa-mir-4537
miRBase:MI0016908
hsa-mir-4538
miRBase:MI0016909
hsa-mir-4539
miRBase:MI0016910
hsa-mir-4540
miRBase:MI0016911
hsa-mir-3972
miRBase:MI0016990
hsa-mir-3973
miRBase:MI0016991
hsa-mir-3974
miRBase:MI0016992
hsa-mir-3975
miRBase:MI0016993
hsa-mir-3976
miRBase:MI0016994
hsa-mir-3977
miRBase:MI0016995
hsa-mir-3978
miRBase:MI0016996
hsa-mir-4632
miRBase:MI0017259
hsa-mir-4633
miRBase:MI0017260
hsa-mir-4634
miRBase:MI0017261
hsa-mir-4635
miRBase:MI0017262
hsa-mir-4636
miRBase:MI0017263
hsa-mir-4638
miRBase:MI0017265
hsa-mir-4639
miRBase:MI0017266
hsa-mir-4640
miRBase:MI0017267
hsa-mir-4641
miRBase:MI0017268
hsa-mir-4642
miRBase:MI0017269
hsa-mir-4643
miRBase:MI0017270
hsa-mir-4644
miRBase:MI0017271
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miRBase:MI0017272
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miRBase:MI0017273
hsa-mir-4647
miRBase:MI0017274
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miRBase:MI0017275
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miRBase:MI0017276
hsa-mir-4651
miRBase:MI0017279
hsa-mir-4652
miRBase:MI0017280
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miRBase:MI0017281
hsa-mir-4655
miRBase:MI0017283
hsa-mir-4656
miRBase:MI0017284
hsa-mir-4658
miRBase:MI0017286
hsa-mir-4661
miRBase:MI0017289
hsa-mir-4663
miRBase:MI0017292
hsa-mir-4664
miRBase:MI0017294
hsa-mir-4665
miRBase:MI0017295
hsa-mir-4666a
miRBase:MI0017296
hsa-mir-4668
miRBase:MI0017298
hsa-mir-4669
miRBase:MI0017300
hsa-mir-4670
miRBase:MI0017301
hsa-mir-4671
miRBase:MI0017302
hsa-mir-4673
miRBase:MI0017304
hsa-mir-4674
miRBase:MI0017305
hsa-mir-4675
miRBase:MI0017306
hsa-mir-4676
miRBase:MI0017307
hsa-mir-4678
miRBase:MI0017309
hsa-mir-4681
miRBase:MI0017313
hsa-mir-4682
miRBase:MI0017314
hsa-mir-4683
miRBase:MI0017315
hsa-mir-4684
miRBase:MI0017316
hsa-mir-4685
miRBase:MI0017317
hsa-mir-4686
miRBase:MI0017318
hsa-mir-4687
miRBase:MI0017319
hsa-mir-4688
miRBase:MI0017321
hsa-mir-4689
miRBase:MI0017322
hsa-mir-4690
miRBase:MI0017323
hsa-mir-4691
miRBase:MI0017324
hsa-mir-4692
miRBase:MI0017325
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miRBase:MI0017326
hsa-mir-4694
miRBase:MI0017327
hsa-mir-4695
miRBase:MI0017328
hsa-mir-4696
miRBase:MI0017329
hsa-mir-4697
miRBase:MI0017330
hsa-mir-4698
miRBase:MI0017331
hsa-mir-4699
miRBase:MI0017332
hsa-mir-4700
miRBase:MI0017333
hsa-mir-4701
miRBase:MI0017334
hsa-mir-4704
miRBase:MI0017337
hsa-mir-4705
miRBase:MI0017338
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miRBase:MI0017339
hsa-mir-4707
miRBase:MI0017340
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miRBase:MI0017341
hsa-mir-4709
miRBase:MI0017342
hsa-mir-4710
miRBase:MI0017344
hsa-mir-4711
miRBase:MI0017345
hsa-mir-4712
miRBase:MI0017346
hsa-mir-4713
miRBase:MI0017347
hsa-mir-4714
miRBase:MI0017348
hsa-mir-4715
miRBase:MI0017349
hsa-mir-4717
miRBase:MI0017352
hsa-mir-4718
miRBase:MI0017353
hsa-mir-4719
miRBase:MI0017354
hsa-mir-4720
miRBase:MI0017355
hsa-mir-4721
miRBase:MI0017356
hsa-mir-4722
miRBase:MI0017357
hsa-mir-4723
miRBase:MI0017359
hsa-mir-4724
miRBase:MI0017361
hsa-mir-4725
miRBase:MI0017362
hsa-mir-4726
miRBase:MI0017363
hsa-mir-4727
miRBase:MI0017364
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miRBase:MI0017365
hsa-mir-4729
miRBase:MI0017366
hsa-mir-4730
miRBase:MI0017367
hsa-mir-4731
miRBase:MI0017368
hsa-mir-4732
miRBase:MI0017369
hsa-mir-4733
miRBase:MI0017370
hsa-mir-4734
miRBase:MI0017371
hsa-mir-4735
miRBase:MI0017372
hsa-mir-4736
miRBase:MI0017373
hsa-mir-4737
miRBase:MI0017374
hsa-mir-4739
miRBase:MI0017377
hsa-mir-4740
miRBase:MI0017378
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miRBase:MI0017379
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miRBase:MI0017382
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miRBase:MI0017384
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miRBase:MI0017385
hsa-mir-4747
miRBase:MI0017386
hsa-mir-4748
miRBase:MI0017387
hsa-mir-4749
miRBase:MI0017388
hsa-mir-4750
miRBase:MI0017389
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miRBase:MI0017390
hsa-mir-4752
miRBase:MI0017391
hsa-mir-4753
miRBase:MI0017392
hsa-mir-4754
miRBase:MI0017394
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miRBase:MI0017395
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miRBase:MI0017396
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miRBase:MI0017397
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miRBase:MI0017398
hsa-mir-4758
miRBase:MI0017399
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miRBase:MI0017400
hsa-mir-4760
miRBase:MI0017401
hsa-mir-4761
miRBase:MI0017402
hsa-mir-4762
miRBase:MI0017403
hsa-mir-4763
miRBase:MI0017404
hsa-mir-4764
miRBase:MI0017405
hsa-mir-4765
miRBase:MI0017406
hsa-mir-4767
miRBase:MI0017408
hsa-mir-4768
miRBase:MI0017409
hsa-mir-4769
miRBase:MI0017410
hsa-mir-4770
miRBase:MI0017411
hsa-mir-4772
miRBase:MI0017414
hsa-mir-4775
miRBase:MI0017418
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miRBase:MI0017421
hsa-mir-4778
miRBase:MI0017422
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miRBase:MI0017423
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miRBase:MI0017424
hsa-mir-4781
miRBase:MI0017426
hsa-mir-4783
miRBase:MI0017428
hsa-mir-4784
miRBase:MI0017429
hsa-mir-4785
miRBase:MI0017430
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miRBase:MI0017432
hsa-mir-4786
miRBase:MI0017433
hsa-mir-4787
miRBase:MI0017434
hsa-mir-4789
miRBase:MI0017436
hsa-mir-4790
miRBase:MI0017437
hsa-mir-4792
miRBase:MI0017439
hsa-mir-4793
miRBase:MI0017440
hsa-mir-4794
miRBase:MI0017441
hsa-mir-4795
miRBase:MI0017442
hsa-mir-4797
miRBase:MI0017444
hsa-mir-4799
miRBase:MI0017446
hsa-mir-4800
miRBase:MI0017448
hsa-mir-4801
miRBase:MI0017449
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miRBase:MI0017450
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miRBase:MI0017452
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miRBase:MI0017865
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miRBase:MI0017866
hsa-mir-5001
miRBase:MI0017867
hsa-mir-5002
miRBase:MI0017868
hsa-mir-5003
miRBase:MI0017869
hsa-mir-5004
miRBase:MI0017870
hsa-mir-5006
miRBase:MI0017873
hsa-mir-5007
miRBase:MI0017874
hsa-mir-5008
miRBase:MI0017876
hsa-mir-5009
miRBase:MI0017877
hsa-mir-5010
miRBase:MI0017878
hsa-mir-5011
miRBase:MI0017879
hsa-mir-5047
miRBase:MI0017932
hsa-mir-5087
miRBase:MI0017976
hsa-mir-5088
miRBase:MI0017977
hsa-mir-5089
miRBase:MI0017978
hsa-mir-5090
miRBase:MI0017979
hsa-mir-5091
miRBase:MI0017980
hsa-mir-5092
miRBase:MI0017981
hsa-mir-5093
miRBase:MI0017982
hsa-mir-5094
miRBase:MI0017983
hsa-mir-5095
miRBase:MI0018001
hsa-mir-5096
miRBase:MI0018004
hsa-mir-5186
miRBase:MI0018165
hsa-mir-5187
miRBase:MI0018166
hsa-mir-5188
miRBase:MI0018167
hsa-mir-5189
miRBase:MI0018168
hsa-mir-5190
miRBase:MI0018169
hsa-mir-5191
miRBase:MI0018170
hsa-mir-5192
miRBase:MI0018171
hsa-mir-5193
miRBase:MI0018172
hsa-mir-5194
miRBase:MI0018173
hsa-mir-5195
miRBase:MI0018174
hsa-mir-5196
miRBase:MI0018175
hsa-mir-5197
miRBase:MI0018176
hsa-mir-5571
miRBase:MI0019115
hsa-mir-5100
miRBase:MI0019116
hsa-mir-5572
miRBase:MI0019117
hsa-mir-5579
miRBase:MI0019133
hsa-mir-5580
miRBase:MI0019135
hsa-mir-5581
miRBase:MI0019136
hsa-mir-5582
miRBase:MI0019138
hsa-mir-5584
miRBase:MI0019141
hsa-mir-5585
miRBase:MI0019142
hsa-mir-5586
miRBase:MI0019143
hsa-mir-5587
miRBase:MI0019144
hsa-mir-1295b
miRBase:MI0019146
hsa-mir-5588
miRBase:MI0019147
hsa-mir-5589
miRBase:MI0019148
hsa-mir-5590
miRBase:MI0019150
hsa-mir-5591
miRBase:MI0019151
hsa-mir-5680
miRBase:MI0019280
hsa-mir-5682
miRBase:MI0019282
hsa-mir-5683
miRBase:MI0019284
hsa-mir-5684
miRBase:MI0019285
hsa-mir-5685
miRBase:MI0019287
hsa-mir-5687
miRBase:MI0019291
hsa-mir-5688
miRBase:MI0019292
hsa-mir-5689
miRBase:MI0019294
hsa-mir-5690
miRBase:MI0019295
hsa-mir-5691
miRBase:MI0019296
hsa-mir-4666b
miRBase:MI0019299
hsa-mir-5693
miRBase:MI0019300
hsa-mir-5694
miRBase:MI0019301
hsa-mir-5695
miRBase:MI0019302
hsa-mir-5696
miRBase:MI0019303
hsa-mir-5698
miRBase:MI0019305
hsa-mir-5699
miRBase:MI0019306
hsa-mir-5700
miRBase:MI0019307
hsa-mir-5702
miRBase:MI0019309
hsa-mir-5703
miRBase:MI0019310
hsa-mir-5692b
miRBase:MI0019311
hsa-mir-5704
miRBase:MI0019312
hsa-mir-5705
miRBase:MI0019313
hsa-mir-5706
miRBase:MI0019314
hsa-mir-5707
miRBase:MI0019315
hsa-mir-5739
miRBase:MI0019412
hsa-mir-5787
miRBase:MI0019797
hsa-mir-6068
miRBase:MI0020345
hsa-mir-6069
miRBase:MI0020346
hsa-mir-6070
miRBase:MI0020347
hsa-mir-6071
miRBase:MI0020348
hsa-mir-6072
miRBase:MI0020349
hsa-mir-6073
miRBase:MI0020350
hsa-mir-6074
miRBase:MI0020351
hsa-mir-6075
miRBase:MI0020352
hsa-mir-6076
miRBase:MI0020353
hsa-mir-6077
miRBase:MI0020354
hsa-mir-6078
miRBase:MI0020355
hsa-mir-6079
miRBase:MI0020356
hsa-mir-6080
miRBase:MI0020357
hsa-mir-6081
miRBase:MI0020358
hsa-mir-6082
miRBase:MI0020359
hsa-mir-6083
miRBase:MI0020360
hsa-mir-6084
miRBase:MI0020361
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miRNA_gene_family
2015-05-16T19:25:41Z
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miRBase:MI0000727
hsa-mir-153-1
miRBase:MI0000463
hsa-mir-153-2
miRBase:MI0000464
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miRBase:MI0000298
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miRBase:MI0000299
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miRBase:MI0011285
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miRBase:MI0000292
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miRBase:MI0005569
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miRBase:MI0000488
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miRBase:MI0000732
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miRBase:MI0000253
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miRBase:MI0000462
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miRBase:MI0000811
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miRBase:MI0013006
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miRBase:MI0000809
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miRBase:MI0003772
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miRBase:MI0000285
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miRBase:MI0000481
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miRBase:MI0017299
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miRBase:MI0000767
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miRBase:MI0000769
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miRBase:MI0000290
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miRBase:MI0014136
hsa-mir-192
miRBase:MI0000234
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miRBase:MI0000291
hsa-mir-31
miRBase:MI0031510
hsa-mir-212
miRBase:MI0000288
hsa-mir-132
miRBase:MI0006657
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miRBase:MI0000273
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miRBase:MI0000300
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miRBase:MI0000779
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miRBase:MI0000780
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miRBase:MI0017393
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miRBase:MI0014253
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miRBase:MI0000091
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miRBase:MI0003646
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miRBase:MI0000738
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miRBase:MI0000772
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miRBase:MI0000773
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miRBase:MI0000774
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miRBase:MI0006418
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miRBase:MI0000098
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miRBase:MI0000252
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miRBase:MI0000473
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miRBase:MI0000111
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miRBase:MI0000112
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miRBase:MI0000455
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miRBase:MI0000476
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miRBase:MI0000486
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miRBase:MI0005545
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miRBase:MI0000293
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miRBase:MI0000274
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miRBase:MI0000461
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miRBase:MI0018003
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miRBase:MI0000487
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miRBase:MI0003137
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miRBase:MI0000458
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miRBase:MI0000456
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miRBase:MI0000286
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miRBase:MI0000301
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miRBase:MI0000240
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miRBase:MI0000776
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miRBase:MI0000784
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miRBase:MI0002466
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miRBase:MI0003529
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miRBase:MI0000460
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miRBase:MI0000459
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miRBase:MI0006318
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miRBase:MI0017383
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miRBase:MI0000814
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miRBase:MI0000097
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miRBase:MI0003516
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miRBase:MI0003685
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miRBase:MI0003758
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miRBase:MI0000475
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miRBase:MI0000477
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miRBase:MI0003129
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miRBase:MI0000262
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miRBase:MI0005544
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miRBase:MI0000454
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miRBase:MI0000283
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miRBase:MI0017343
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miRBase:MI0000483
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miRBase:MI0001725
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miRBase:MI0001726
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miRBase:MI0003135
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miRBase:MI0005565
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miRBase:MI0003124
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miRBase:MI0017320
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miRBase:MI0000484
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miRBase:MI0003205
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miRBase:MI0003684
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miRBase:MI0000783
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miRBase:MI0014197
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miRBase:MI0008195
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miRBase:MI0000261
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miRBase:MI0003130
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miRBase:MI0015977
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miRBase:MI0000787
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miRBase:MI0000788
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miRBase:MI0003675
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miRBase:MI0003757
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miRBase:MI0006656
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miRBase:MI0001652
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miRBase:MI0003187
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miRBase:MI0005531
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miRBase:MI0003513
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miRBase:MI0003127
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miRBase:MI0003140
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miRBase:MI0003141
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miRBase:MI0003191
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miRBase:MI0003192
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miRBase:MI0003193
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miRBase:MI0003194
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miRBase:MI0003195
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miRBase:MI0003196
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miRBase:MI0003197
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miRBase:MI0003198
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miRBase:MI0003199
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miRBase:MI0003200
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miRBase:MI0005530
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miRBase:MI0005717
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miRBase:MI0006648
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miRBase:MI0006649
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miRBase:MI0014251
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miRBase:MI0001648
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miRBase:MI0003673
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miRBase:MI0003823
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miRBase:MI0000791
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miRBase:MI0000764
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miRBase:MI0003184
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miRBase:MI0003185
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miRBase:MI0003186
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miRBase:MI0015903
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miRBase:MI0015983
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miRBase:MI0000808
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miRBase:MI0000824
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miRBase:MI0001729
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miRBase:MI0017360
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miRBase:MI0016849
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miRBase:MI0000681
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miRBase:MI0000747
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miRBase:MI0031514
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miRBase:MI0000542
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miRBase:MI0003776
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miRBase:MI0003778
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miRBase:MI0003839
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miRBase:MI0008190
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miRBase:MI0008191
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miRBase:MI0008192
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miRBase:MI0014234
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miRBase:MI0001446
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miRBase:MI0000813
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miRBase:MI0000778
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miRBase:MI0000786
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miRBase:MI0003840
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miRBase:MI0014154
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miRBase:MI0016749
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miRBase:MI0016750
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miRBase:MI0016008
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miRBase:MI0003183
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miRBase:MI0003820
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miRBase:MI0000251
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miRBase:MI0005570
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miRBase:MI0002467
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miRBase:MI0003188
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miRBase:MI0003686
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miRBase:MI0000744
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miRBase:MI0000826
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miRBase:MI0000825
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miRBase:MI0000805
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miRBase:MI0000802
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miRBase:MI0002464
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miRBase:MI0000815
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miRBase:MI0008336
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miRBase:MI0000806
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miRBase:MI0000816
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miRBase:MI0000479
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miRBase:MI0000812
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miRBase:MI0000803
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miRBase:MI0002469
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miRBase:MI0000482
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miRBase:MI0000804
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miRBase:MI0005775
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miRBase:MI0005523
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miRBase:MI0016014
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miRBase:MI0003133
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miRBase:MI0005539
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miRBase:MI0003190
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miRBase:MI0002468
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miRBase:MI0002470
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miRBase:MI0023622
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miRBase:MI0003125
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miRBase:MI0003132
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miRBase:MI0003138
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miRBase:MI0001448
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miRBase:MI0000478
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miRBase:MI0019114
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miRBase:MI0000782
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miRBase:MI0005566
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miRBase:MI0016684
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miRBase:MI0001145
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miRBase:MI0006442
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miRBase:MI0019134
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miRBase:MI0017297
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miRBase:MI0019593
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miRBase:MI0003586
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miRBase:MI0003593
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miRBase:MI0029321
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miRBase:MI0003598
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miRBase:MI0003612
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miRBase:MI0003616
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miRBase:MI0003630
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miRBase:MI0003668
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miRBase:MI0003671
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miRBase:MI0006344
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miRBase:MI0006345
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miRBase:MI0006354
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miRBase:MI0006361
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miRBase:MI0006374
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miRBase:MI0006375
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miRBase:MI0006376
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miRBase:MI0006377
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miRBase:MI0006378
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miRBase:MI0006395
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miRBase:MI0006399
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miRBase:MI0006411
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miRBase:MI0006412
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miRBase:MI0006413
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miRBase:MI0006414
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miRBase:MI0006420
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miRBase:MI0006421
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miRBase:MI0006422
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miRBase:MI0006423
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miRBase:MI0006424
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miRBase:MI0010637
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miRBase:MI0014141
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miRBase:MI0014164
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miRBase:MI0014168
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miRBase:MI0014174
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miRBase:MI0014222
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miRBase:MI0016833
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miRBase:MI0016595
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miRBase:MI0016688
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miRBase:MI0016689
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miRBase:MI0016690
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miRBase:MI0016746
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miRBase:MI0016751
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miRBase:MI0016752
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miRBase:MI0016762
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miRBase:MI0016770
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miRBase:MI0016779
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miRBase:MI0016780
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miRBase:MI0016793
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miRBase:MI0016794
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miRBase:MI0016796
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miRBase:MI0016813
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miRBase:MI0016814
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miRBase:MI0016815
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miRBase:MI0016833
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miRBase:MI0016840
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miRBase:MI0016851
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miRBase:MI0016904
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miRBase:MI0016907
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miRBase:MI0017871
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miRBase:MI0017875
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miRBase:MI0019130
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miRBase:MI0019131
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miRBase:MI0019132
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miRBase:MI0019137
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miRBase:MI0019145
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miRBase:MI0019152
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miRBase:MI0019283
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miRBase:MI0019286
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miRBase:MI0022210
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miRBase:MI0022212
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miRBase:MI0025747
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miRBase:MI0029321
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miRBase:MI0003123
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miRBase:MI0003126
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miRBase:MI0001445
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miRBase:MI0003667
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miRBase:MI0003600
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miRBase:MI0003601
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miRBase:MI0003762
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miRBase:MI0016686
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miRBase:MI0016687
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miRBase:MI0003604
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miRBase:MI0003628
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miRBase:MI0003906
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miRBase:MI0005118
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miRBase:MI0003761
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miRBase:MI0022548
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miRBase:MI0003556
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miRBase:MI0003575
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miRBase:MI0005416
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miRBase:MI0005528
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miRBase:MI0005533
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miRBase:MI0005537
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miRBase:MI0005538
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miRBase:MI0022560
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miRBase:MI0005763
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miRBase:MI0005764
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miRBase:MI0005765
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miRBase:MI0005766
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miRBase:MI0031520
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miRBase:MI0005564
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miRBase:MI0005561
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miRBase:MI0003610
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miRBase:MI0005567
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miRBase:MI0005543
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miRBase:MI0005532
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miRBase:MI0005563
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miRBase:MI0019293
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miRBase:MI0003676
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miRBase:MI0003589
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miRBase:MI0003602
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miRBase:MI0003581
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miRBase:MI0005524
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miRBase:MI0005534
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miRBase:MI0005541
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miRBase:MI0005542
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miRBase:MI0005559
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miRBase:MI0003674
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miRBase:MI0003515
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miRBase:MI0014159
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miRBase:MI0003189
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miRBase:MI0003764
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miRBase:MI0006313
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miRBase:MI0006311
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miRBase:MI0006316
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miRBase:MI0015980
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miRBase:MI0006363
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miRBase:MI0006364
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miRBase:MI0006365
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miRBase:MI0006366
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miRBase:MI0006367
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miRBase:MI0006368
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miRBase:MI0006369
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miRBase:MI0015978
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miRBase:MI0015979
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miRBase:MI0015980
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miRBase:MI0022217
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miRBase:MI0003672
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miRBase:MI0006336
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miRBase:MI0003142
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miRBase:MI0021274
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miRBase:MI0003669
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miRBase:MI0003588
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miRBase:MI0003594
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miRBase:MI0003657
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miRBase:MI0016685
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miRBase:MI0005760
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miRBase:MI0003679
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miRBase:MI0016436
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miRBase:MI0003640
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miRBase:MI0003562
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miRBase:MI0003663
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miRBase:MI0003585
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miRBase:MI0025513
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miRBase:MI0003609
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miRBase:MI0003620
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miRBase:MI0003590
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miRBase:MI0003814
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miRBase:MI0003613
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miRBase:MI0003653
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miRBase:MI0003558
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miRBase:MI0003658
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miRBase:MI0005761
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miRBase:MI0003670
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miRBase:MI0003583
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miRBase:MI0003655
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miRBase:MI0005712
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miRBase:MI0003599
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miRBase:MI0003681
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miRBase:MI0003131
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miRBase:MI0000781
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miRBase:MI0003557
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miRBase:MI0003611
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miRBase:MI0003605
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miRBase:MI0005755
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miRBase:MI0006389
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miRBase:MI0006435
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miRBase:MI0006436
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miRBase:MI0003629
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miRBase:MI0003645
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miRBase:MI0005767
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miRBase:MI0003568
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miRBase:MI0005716
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miRBase:MI0005540
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miRBase:MI0003587
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miRBase:MI0003622
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miRBase:MI0005758
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miRBase:MI0003569
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miRBase:MI0003563
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miRBase:MI0003614
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miRBase:MI0003638
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miRBase:MI0003651
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miRBase:MI0003647
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miRBase:MI0003618
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miRBase:MI0003642
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miRBase:MI0003584
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miRBase:MI0006443
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miRBase:MI0005560
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miRBase:MI0003591
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miRBase:MI0003639
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miRBase:MI0019304
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miRBase:MI0005714
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miRBase:MI0003579
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miRBase:MI0019140
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miRBase:MI0003624
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miRBase:MI0005762
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miRBase:MI0005769
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miRBase:MI0005756
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miRBase:MI0005116
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miRBase:MI0003648
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miRBase:MI0003664
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miRBase:MI0001444
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miRBase:MI0003654
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miRBase:MI0003641
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miRBase:MI0003559
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miRBase:MI0003763
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miRBase:MI0003632
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miRBase:MI0005562
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miRBase:MI0003573
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miRBase:MI0003659
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miRBase:MI0003633
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miRBase:MI0006444
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miRBase:MI0006346
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miRBase:MI0006347
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miRBase:MI0005759
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miRBase:MI0003580
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miRBase:MI0003617
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miRBase:MI0003595
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miRBase:MI0006379
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miRBase:MI0015974
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miRBase:MI0015975
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miRBase:MI0031511
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miRBase:MI0003572
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miRBase:MI0006323
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miRBase:MI0015973
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miRBase:MI0006409
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miRBase:MI0014254
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miRBase:MI0016059
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miRBase:MI0018002
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miRBase:MI0018003
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miRBase:MI0003561
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miRBase:MI0006358
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miRBase:MI0006327
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miRBase:MI0003582
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miRBase:MI0006429
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miRBase:MI0006657
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miRBase:MI0021279
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miRBase:MI0006425
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miRBase:MI0006277
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miRBase:MI0015971
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miRBase:MI0015972
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miRBase:MI0006390
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miRBase:MI0006397
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miRBase:MI0006340
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miRBase:MI0003652
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miRBase:MI0003938
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miRBase:MI0006353
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miRBase:MI0003649
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miRBase:MI0006271
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miRBase:MI0006356
hsa-mir-1284
miRBase:MI0006431
hsa-mir-646
miRBase:MI0003661
hsa-mir-935
miRBase:MI0005757
hsa-mir-1303
miRBase:MI0006370
hsa-mir-1205
miRBase:MI0006338
hsa-mir-1290
miRBase:MI0006352
hsa-mir-1253
miRBase:MI0006387
hsa-mir-564
miRBase:MI0003570
hsa-mir-1202
miRBase:MI0006334
hsa-mir-1254-1
miRBase:MI0006388
hsa-mir-1254-2
miRBase:MI0016747
hsa-mir-1266
miRBase:MI0006403
hsa-mir-1323
miRBase:MI0003786
hsa-mir-622
miRBase:MI0003636
hsa-mir-1245a
miRBase:MI0006380
hsa-mir-1245b
miRBase:MI0017431
hsa-mir-1251
miRBase:MI0006386
hsa-mir-1248
miRBase:MI0006383
hsa-mir-561
miRBase:MI0003567
hsa-mir-762
miRBase:MI0003892
hsa-mir-1299
miRBase:MI0006359
hsa-mir-1289-1
miRBase:MI0006350
hsa-mir-1289-2
miRBase:MI0006351
hsa-mir-1246
miRBase:MI0006381
hsa-mir-1208
miRBase:MI0006341
hsa-mir-621
miRBase:MI0003635
hsa-mir-1179
miRBase:MI0006272
hsa-mir-1203
miRBase:MI0006335
hsa-mir-1206
miRBase:MI0006339
hsa-mir-1267
miRBase:MI0006404
hsa-mir-591
miRBase:MI0003603
hsa-mir-658
miRBase:MI0003682
hsa-mir-1272
miRBase:MI0006408
hsa-mir-1827
miRBase:MI0008195
hsa-mir-614
miRBase:MI0003627
hsa-mir-1296
miRBase:MI0003780
hsa-mir-595
miRBase:MI0003607
hsa-mir-1276
miRBase:MI0006416
hsa-mir-630
miRBase:MI0003644
hsa-mir-559
miRBase:MI0003565
hsa-mir-645
miRBase:MI0003660
hsa-mir-302e
miRBase:MI0006417
hsa-mir-1288
miRBase:MI0006432
hsa-mir-610
miRBase:MI0003623
hsa-mir-635
miRBase:MI0003650
hsa-mir-1322
miRBase:MI0006653
hsa-mir-1181
miRBase:MI0006274
hsa-mir-1249
miRBase:MI0006384
hsa-mir-1183
miRBase:MI0006276
hsa-mir-1247
miRBase:MI0006382
hsa-mir-1825
miRBase:MI0008193
hsa-mir-1204
miRBase:MI0006337
hsa-mir-617
miRBase:MI0003631
hsa-mir-1182
miRBase:MI0006275
hsa-mir-1275
miRBase:MI0006415
hsa-mir-1292
miRBase:MI0006433
hsa-mir-1295a
miRBase:MI0006357
hsa-mir-766
miRBase:MI0003836
hsa-mir-641
miRBase:MI0003656
hsa-mir-588
miRBase:MI0003597
hsa-mir-1286
miRBase:MI0006348
hsa-mir-1258
miRBase:MI0006392
hsa-mir-1263
miRBase:MI0006398
hsa-mir-1265
miRBase:MI0006401
hsa-mir-1236
miRBase:MI0006326
hsa-mir-943
miRBase:MI0005768
hsa-mir-1293
miRBase:MI0006355
hsa-mir-1281
miRBase:MI0006428
hsa-mir-1250
miRBase:MI0006385
hsa-mir-759
miRBase:MI0004065
hsa-mir-764
miRBase:MI0024976
hsa-mir-761
miRBase:MI0003941
hsa-mir-1193
miRBase:MI0014205
hsa-mir-718
miRBase:MI0012489
hsa-mir-1287
miRBase:MI0006349
hsa-mir-769
miRBase:MI0003834
hsa-mir-670
miRBase:MI0003933
hsa-mir-1301
miRBase:MI0003815
hsa-mir-711
miRBase:MI0012488
hsa-mir-571
miRBase:MI0003578
hsa-mir-602
miRBase:MI0003615
hsa-mir-1912
miRBase:MI0008333
hsa-mir-1468
miRBase:MI0003782
hsa-mir-606
miRBase:MI0003619
hsa-mir-1180
miRBase:MI0006273
hsa-mir-623
miRBase:MI0003637
hsa-mir-1261
miRBase:MI0006396
hsa-mir-596
miRBase:MI0003608
hsa-mir-3130-1
miRBase:MI0014147
hsa-mir-3130-2
miRBase:MI0014148
hsa-mir-3202-1
miRBase:MI0014252
hsa-mir-3202-2
miRBase:MI0014253
hsa-mir-1270
miRBase:MI0006407
hsa-mir-3156-1
miRBase:MI0014184
hsa-mir-3156-2
miRBase:MI0014230
hsa-mir-3156-3
miRBase:MI0014242
hsa-mir-3180-1
miRBase:MI0014214
hsa-mir-3180-2
miRBase:MI0014215
hsa-mir-3180-3
miRBase:MI0014217
hsa-mir-3180-4
miRBase:MI0016408
hsa-mir-3180-5
miRBase:MI0016409
hsa-mir-3179-1
miRBase:MI0014213
hsa-mir-3179-2
miRBase:MI0014216
hsa-mir-3179-3
miRBase:MI0014221
hsa-mir-3179-4
miRBase:MI0031510
hsa-mir-1538
miRBase:MI0007259
hsa-mir-1537
miRBase:MI0007258
hsa-mir-4283-1
miRBase:MI0015892
hsa-mir-4283-2
miRBase:MI0015982
hsa-mir-1228
miRBase:MI0006318
hsa-mir-2355
miRBase:MI0015873
hsa-mir-647
miRBase:MI0003662
hsa-mir-1238
miRBase:MI0006328
hsa-mir-1268a
miRBase:MI0006405
hsa-mir-2861
miRBase:MI0013006
hsa-mir-1305
miRBase:MI0006372
hsa-mir-1252
miRBase:MI0006434
hsa-mir-3119-1
miRBase:MI0014134
hsa-mir-3119-2
miRBase:MI0014135
hsa-mir-608
miRBase:MI0023563
hsa-mir-1909
miRBase:MI0008330
hsa-mir-1469
miRBase:MI0007074
hsa-mir-921
miRBase:MI0005713
hsa-mir-1269a
miRBase:MI0006406
hsa-mir-1910
miRBase:MI0008331
hsa-mir-1257
miRBase:MI0006391
hsa-mir-3116-1
miRBase:MI0014128
hsa-mir-3116-2
miRBase:MI0014129
hsa-mir-1913
miRBase:MI0008334
hsa-mir-1260a
miRBase:MI0006394
hsa-mir-1908
miRBase:MI0008329
hsa-mir-1972-1
miRBase:MI0009982
hsa-mir-1972-2
miRBase:MI0015977
hsa-mir-5708
miRBase:MI0019316
hsa-mir-3199-1
miRBase:MI0014247
hsa-mir-3199-2
miRBase:MI0014248
hsa-mir-3160-1
miRBase:MI0014189
hsa-mir-3160-2
miRBase:MI0014190
hsa-mir-4315-1
miRBase:MI0015844
hsa-mir-4315-2
miRBase:MI0015983
hsa-mir-1200
miRBase:MI0006332
hsa-mir-1915
miRBase:MI0008336
hsa-mir-1914
miRBase:MI0008335
hsa-mir-1304
miRBase:MI0006371
hsa-mir-3158-1
miRBase:MI0014186
hsa-mir-3158-2
miRBase:MI0014187
hsa-mir-1471
miRBase:MI0007076
hsa-mir-3150a
miRBase:MI0014177
hsa-mir-3150b
miRBase:MI0016426
hsa-mir-3074
miRBase:MI0014181
hsa-mir-3065
miRBase:MI0014228
hsa-mir-3926-1
miRBase:MI0016434
hsa-mir-3926-2
miRBase:MI0016437
hsa-mir-3913-1
miRBase:MI0016417
hsa-mir-3913-2
miRBase:MI0016418
hsa-mir-3689a
miRBase:MI0016090
hsa-mir-3689b
miRBase:MI0016411
hsa-mir-3689c
miRBase:MI0016832
hsa-mir-3689d-1
miRBase:MI0016834
hsa-mir-3689d-2
miRBase:MI0016835
hsa-mir-3689e
miRBase:MI0016836
hsa-mir-3689f
miRBase:MI0016837
hsa-mir-3910-1
miRBase:MI0016414
hsa-mir-3910-2
miRBase:MI0016431
hsa-mir-3914-1
miRBase:MI0016419
hsa-mir-3914-2
miRBase:MI0016421
hsa-mir-3622a
miRBase:MI0016013
hsa-mir-3622b
miRBase:MI0016014
hsa-mir-1343
miRBase:MI0017320
hsa-mir-4509-1
miRBase:MI0016873
hsa-mir-4509-2
miRBase:MI0016874
hsa-mir-4509-3
miRBase:MI0016875
hsa-mir-4776-1
miRBase:MI0017419
hsa-mir-4776-2
miRBase:MI0017420
hsa-mir-3198-1
miRBase:MI0014246
hsa-mir-3198-2
miRBase:MI0017335
hsa-mir-3135a
miRBase:MI0014156
hsa-mir-3135b
miRBase:MI0016809
hsa-mir-4435-1
miRBase:MI0016775
hsa-mir-4435-2
miRBase:MI0016777
hsa-mir-4679-1
miRBase:MI0017310
hsa-mir-4679-2
miRBase:MI0017311
hsa-mir-4650-1
miRBase:MI0017277
hsa-mir-4650-2
miRBase:MI0017278
hsa-mir-4436a
miRBase:MI0016776
hsa-mir-4436b-1
miRBase:MI0017425
hsa-mir-4436b-2
miRBase:MI0019110
hsa-mir-3064
miRBase:MI0017375
hsa-mir-3155a
miRBase:MI0014183
hsa-mir-3155b
miRBase:MI0016839
hsa-mir-4662a
miRBase:MI0017290
hsa-mir-4662b
miRBase:MI0017293
hsa-mir-4773-1
miRBase:MI0017415
hsa-mir-4773-2
miRBase:MI0017416
hsa-mir-3190
miRBase:MI0014235
hsa-mir-3191
miRBase:MI0014236
hsa-mir-4659a
miRBase:MI0017287
hsa-mir-4659b
miRBase:MI0017291
hsa-mir-4771-1
miRBase:MI0017412
hsa-mir-4771-2
miRBase:MI0017413
hsa-mir-3529
miRBase:MI0017351
hsa-mir-3688-1
miRBase:MI0016089
hsa-mir-3688-2
miRBase:MI0017447
hsa-mir-3960
miRBase:MI0016964
hsa-mir-4520-1
miRBase:MI0016886
hsa-mir-4520-2
miRBase:MI0017358
hsa-mir-4477a
miRBase:MI0016829
hsa-mir-4477b
miRBase:MI0016830
hsa-mir-1231
miRBase:MI0006321
hsa-mir-4444-1
miRBase:MI0016787
hsa-mir-4444-2
miRBase:MI0019111
hsa-mir-4536-1
miRBase:MI0016906
hsa-mir-4536-2
miRBase:MI0019149
hsa-mir-5701-1
miRBase:MI0019308
hsa-mir-5701-2
miRBase:MI0019593
hsa-mir-4524a
miRBase:MI0016891
hsa-mir-4524b
miRBase:MI0019114
hsa-mir-3680-1
miRBase:MI0016081
hsa-mir-3680-2
miRBase:MI0019113
hsa-mir-3670-1
miRBase:MI0016071
hsa-mir-3670-2
miRBase:MI0019112
hsa-mir-3670-3
miRBase:MI0031513
hsa-mir-3670-4
miRBase:MI0031514
hsa-mir-5681a
miRBase:MI0019281
hsa-mir-5681b
miRBase:MI0019293
hsa-mir-5692c-1
miRBase:MI0019288
hsa-mir-5692c-2
miRBase:MI0019289
hsa-mir-5692a-1
miRBase:MI0019297
hsa-mir-5692a-2
miRBase:MI0019298
hsa-mir-5583-1
miRBase:MI0019139
hsa-mir-5583-2
miRBase:MI0019140
hsa-mir-1260b
miRBase:MI0014197
hsa-mir-6511a-1
miRBase:MI0022223
hsa-mir-6511b-1
miRBase:MI0022552
hsa-mir-6511b-2
miRBase:MI0023431
hsa-mir-6511a-2
miRBase:MI0023564
hsa-mir-6511a-3
miRBase:MI0023565
hsa-mir-6511a-4
miRBase:MI0023566
hsa-mir-3173
miRBase:MI0014204
hsa-mir-4743
miRBase:MI0017381
hsa-mir-4446
miRBase:MI0016789
hsa-mir-3154
miRBase:MI0014182
hsa-mir-4667
miRBase:MI0017297
hsa-mir-3151
miRBase:MI0014178
hsa-mir-3660
miRBase:MI0016061
hsa-mir-2110
miRBase:MI0010629
hsa-mir-3943
miRBase:MI0016600
hsa-mir-3193
miRBase:MI0014238
hsa-mir-4796
miRBase:MI0017443
hsa-mir-6127
miRBase:MI0021271
hsa-mir-3613
miRBase:MI0016003
hsa-mir-6131
miRBase:MI0021276
hsa-mir-6130
miRBase:MI0021275
hsa-mir-6133
miRBase:MI0021278
hsa-mir-3121
miRBase:MI0014137
hsa-mir-6129
miRBase:MI0021274
hsa-mir-3145
miRBase:MI0014170
hsa-mir-3138
miRBase:MI0014161
hsa-mir-23c
miRBase:MI0016010
hsa-mir-6132
miRBase:MI0021277
hsa-mir-3127
miRBase:MI0014144
hsa-mir-4484
miRBase:MI0016845
hsa-mir-3200
miRBase:MI0014249
hsa-mir-6128
miRBase:MI0021272
hsa-mir-6134
miRBase:MI0021279
hsa-mir-4529
miRBase:MI0016896
hsa-mir-3129
miRBase:MI0014146
hsa-mir-4660
miRBase:MI0017288
hsa-mir-3927
miRBase:MI0016435
hsa-mir-378j
miRBase:MI0021273
hsa-mir-2114
miRBase:MI0010633
hsa-mir-4510
miRBase:MI0016876
hsa-mir-4429
miRBase:MI0016768
hsa-mir-4716
miRBase:MI0017350
hsa-mir-3617
miRBase:MI0016007
hsa-mir-1273c
miRBase:MI0014171
hsa-mir-3188
miRBase:MI0014232
hsa-mir-3937
miRBase:MI0016593
hsa-mir-3117
miRBase:MI0014130
hsa-mir-4654
miRBase:MI0017282
hsa-mir-4504
miRBase:MI0016867
hsa-mir-3132
miRBase:MI0014152
hsa-mir-6089-1
miRBase:MI0020366
hsa-mir-6089-2
miRBase:MI0023563
hsa-mir-4803
miRBase:MI0017451
hsa-mir-4515
miRBase:MI0016881
hsa-mir-3664
miRBase:MI0016065
hsa-mir-3612
miRBase:MI0016002
hsa-mir-3938
miRBase:MI0016594
hsa-mir-4738
miRBase:MI0017376
hsa-mir-2278
miRBase:MI0011285
hsa-mir-3126
miRBase:MI0014143
hsa-mir-3923
miRBase:MI0016430
hsa-mir-4791
miRBase:MI0017438
hsa-mir-3661
miRBase:MI0016062
hsa-mir-3615
miRBase:MI0016005
hsa-mir-4526
miRBase:MI0016893
hsa-mir-4782
miRBase:MI0017427
hsa-mir-4421
miRBase:MI0016758
hsa-mir-6500
miRBase:MI0022211
hsa-mir-3122
miRBase:MI0014138
hsa-mir-4672
miRBase:MI0017303
hsa-mir-4742
miRBase:MI0017380
hsa-mir-629
miRBase:MI0003643
hsa-mir-3607
miRBase:MI0015997
hsa-mir-3174
miRBase:MI0014208
hsa-mir-4788
miRBase:MI0017435
hsa-mir-4798
miRBase:MI0017445
hsa-mir-3136
miRBase:MI0014158
hsa-mir-4774
miRBase:MI0017417
hsa-mir-4451
miRBase:MI0016797
hsa-mir-3934
miRBase:MI0016590
hsa-mir-4637
miRBase:MI0017264
hsa-mir-4423
miRBase:MI0016760
hsa-mir-3192
miRBase:MI0014237
hsa-mir-3940
miRBase:MI0016597
hsa-mir-3912
miRBase:MI0016416
hsa-mir-2392
miRBase:MI0016870
hsa-mir-3140
miRBase:MI0014163
hsa-mir-3690-1
miRBase:MI0016091
hsa-mir-3690-2
miRBase:MI0023561
hsa-mir-4488
miRBase:MI0016849
hsa-mir-3146
miRBase:MI0014172
hsa-mir-4428
miRBase:MI0016767
hsa-mir-1976
miRBase:MI0009986
hsa-mir-3165
miRBase:MI0014195
hsa-mir-3170
miRBase:MI0014201
hsa-mir-3605
miRBase:MI0015995
hsa-mir-4427
miRBase:MI0016766
hsa-mir-1199
miRBase:MI0020340
hsa-mir-6516
miRBase:MI0025513
hsa-mir-6770-1
miRBase:MI0022615
hsa-mir-6770-2
miRBase:MI0026418
hsa-mir-6770-3
miRBase:MI0026419
hsa-mir-7973-1
miRBase:MI0025748
hsa-mir-7973-2
miRBase:MI0025749
hsa-mir-6859-1
miRBase:MI0022705
hsa-mir-6859-2
miRBase:MI0026420
hsa-mir-6859-3
miRBase:MI0026421
hsa-mir-6859-4
miRBase:MI0031521
hsa-mir-6715a
miRBase:MI0022548
hsa-mir-3618
miRBase:MI0016008
hsa-mir-6794
miRBase:MI0022639
hsa-mir-6827
miRBase:MI0022672
hsa-mir-5697
miRBase:MI0019304
hsa-mir-4703
miRBase:MI0017336
hsa-mir-4766
miRBase:MI0017407
hsa-mir-1911
miRBase:MI0008332
hsa-mir-8071-1
miRBase:MI0025907
hsa-mir-8071-2
miRBase:MI0026417
hsa-mir-6505
miRBase:MI0022217
hsa-mir-6790
miRBase:MI0022635
hsa-mir-1243
miRBase:MI0006373
hsa-mir-3167
miRBase:MI0014198
hsa-mir-7641-1
miRBase:MI0024975
hsa-mir-7641-2
miRBase:MI0024976
hsa-mir-4433a
miRBase:MI0016773
hsa-mir-4433b
miRBase:MI0025511
hsa-mir-4677
miRBase:MI0017308
hsa-mir-6862-1
miRBase:MI0022709
hsa-mir-6862-2
miRBase:MI0026415
hsa-mir-6724-1
miRBase:MI0022559
hsa-mir-6724-2
miRBase:MI0031516
hsa-mir-6724-3
miRBase:MI0031517
hsa-mir-6724-4
miRBase:MI0031518
hsa-mir-3118-1
miRBase:MI0014131
hsa-mir-3118-2
miRBase:MI0014132
hsa-mir-3118-3
miRBase:MI0014133
hsa-mir-3149
miRBase:MI0014176
hsa-mir-1277
miRBase:MI0006419
hsa-mir-3648-1
miRBase:MI0016048
hsa-mir-3648-2
miRBase:MI0031512
hsa-mir-4680
miRBase:MI0017312
hsa-mir-4657
miRBase:MI0017285
hsa-mir-8069-1
miRBase:MI0025905
hsa-mir-8069-2
miRBase:MI0031519
hsa-mir-3687-1
miRBase:MI0016088
hsa-mir-3687-2
miRBase:MI0031515
hsa-mir-4449
miRBase:MI0016792
hsa-mir-4523
miRBase:MI0016890
mir-17
miRBase:MIPF0000001
let-7
miRBase:MIPF0000002
mir-30
miRBase:MIPF0000005
mir-15
miRBase:MIPF0000006
mir-181
miRBase:MIPF0000007
mir-29
miRBase:MIPF0000009
mir-19
miRBase:MIPF0000011
mir-25
miRBase:MIPF0000013
mir-9
miRBase:MIPF0000014
mir-154
miRBase:MIPF0000018
mir-8
miRBase:MIPF0000019
mir-515
miRBase:MIPF0000020
mir-124
miRBase:MIPF0000021
mir-7
miRBase:MIPF0000022
mir-103
miRBase:MIPF0000024
mir-218
miRBase:MIPF0000026
mir-23
miRBase:MIPF0000027
mir-135
miRBase:MIPF0000028
mir-133
miRBase:MIPF0000029
mir-196
miRBase:MIPF0000031
mir-10
miRBase:MIPF0000033
mir-130
miRBase:MIPF0000034
mir-27
miRBase:MIPF0000036
mir-1
miRBase:MIPF0000038
mir-34
miRBase:MIPF0000039
mir-199
miRBase:MIPF0000040
mir-24
miRBase:MIPF0000041
mir-204
miRBase:MIPF0000042
mir-26
miRBase:MIPF0000043
mir-219
miRBase:MIPF0000044
mir-101
miRBase:MIPF0000046
mir-128
miRBase:MIPF0000048
mir-153
miRBase:MIPF0000050
mir-221
miRBase:MIPF0000051
mir-22
miRBase:MIPF0000053
mir-216
miRBase:MIPF0000054
mir-194
miRBase:MIPF0000055
mir-148
miRBase:MIPF0000056
mir-28
miRBase:MIPF0000057
mir-205
miRBase:MIPF0000058
mir-184
miRBase:MIPF0000059
mir-21
miRBase:MIPF0000060
mir-365
miRBase:MIPF0000061
mir-214
miRBase:MIPF0000062
mir-192
miRBase:MIPF0000063
mir-31
miRBase:MIPF0000064
mir-132
miRBase:MIPF0000065
mir-183
miRBase:MIPF0000066
mir-223
miRBase:MIPF0000067
mir-290
miRBase:MIPF0000068
mir-32
miRBase:MIPF0000069
mir-33
miRBase:MIPF0000070
mir-302
miRBase:MIPF0000071
mir-96
miRBase:MIPF0000072
mir-129
miRBase:MIPF0000073
mir-105
miRBase:MIPF0000074
mir-138
miRBase:MIPF0000075
mir-190
miRBase:MIPF0000076
mir-217
miRBase:MIPF0000077
mir-187
miRBase:MIPF0000078
mir-145
miRBase:MIPF0000079
mir-127
miRBase:MIPF0000080
mir-193
miRBase:MIPF0000082
mir-142
miRBase:MIPF0000084
mir-140
miRBase:MIPF0000085
mir-210
miRBase:MIPF0000086
mir-224
miRBase:MIPF0000088
mir-198
miRBase:MIPF0000090
mir-368
miRBase:MIPF0000091
mir-144
miRBase:MIPF0000093
mir-143
miRBase:MIPF0000094
mir-122
miRBase:MIPF0000095
mir-338
miRBase:MIPF0000097
mir-95
miRBase:MIPF0000098
mir-136
miRBase:MIPF0000099
mir-146
miRBase:MIPF0000103
mir-147
miRBase:MIPF0000105
mir-137
miRBase:MIPF0000106
mir-203
miRBase:MIPF0000108
mir-186
miRBase:MIPF0000109
mir-329
miRBase:MIPF0000110
mir-489
miRBase:MIPF0000111
mir-134
miRBase:MIPF0000112
mir-188
miRBase:MIPF0000113
mir-375
miRBase:MIPF0000114
mir-126
miRBase:MIPF0000115
mir-182
miRBase:MIPF0000116
mir-139
miRBase:MIPF0000117
mir-202
miRBase:MIPF0000121
mir-197
miRBase:MIPF0000123
mir-379
miRBase:MIPF0000126
mir-450
miRBase:MIPF0000128
mir-455
miRBase:MIPF0000129
mir-506
miRBase:MIPF0000130
mir-449
miRBase:MIPF0000133
mir-383
miRBase:MIPF0000137
mir-363
miRBase:MIPF0000138
mir-500
miRBase:MIPF0000139
mir-431
miRBase:MIPF0000142
mir-326
miRBase:MIPF0000143
mir-325
miRBase:MIPF0000147
mir-451
miRBase:MIPF0000148
mir-448
miRBase:MIPF0000149
mir-155
miRBase:MIPF0000157
mir-296
miRBase:MIPF0000159
mir-367
miRBase:MIPF0000162
mir-320
miRBase:MIPF0000163
mir-322
miRBase:MIPF0000164
mir-324
miRBase:MIPF0000165
mir-370
miRBase:MIPF0000167
mir-378
miRBase:MIPF0000168
mir-361
miRBase:MIPF0000172
mir-499
miRBase:MIPF0000173
mir-454
miRBase:MIPF0000174
mir-433
miRBase:MIPF0000177
mir-208
miRBase:MIPF0000178
mir-483
miRBase:MIPF0000180
mir-503
miRBase:MIPF0000183
mir-542
miRBase:MIPF0000185
mir-299
miRBase:MIPF0000186
mir-346
miRBase:MIPF0000188
mir-345
miRBase:MIPF0000189
mir-342
miRBase:MIPF0000190
mir-340
miRBase:MIPF0000191
mir-412
miRBase:MIPF0000192
mir-339
miRBase:MIPF0000193
mir-191
miRBase:MIPF0000194
mir-337
miRBase:MIPF0000195
mir-335
miRBase:MIPF0000196
mir-150
miRBase:MIPF0000197
mir-331
miRBase:MIPF0000199
mir-330
miRBase:MIPF0000200
mir-485
miRBase:MIPF0000201
mir-185
miRBase:MIPF0000202
mir-328
miRBase:MIPF0000203
mir-297
miRBase:MIPF0000204
mir-298
miRBase:MIPF0000206
mir-362
miRBase:MIPF0000209
mir-432
miRBase:MIPF0000211
mir-541
miRBase:MIPF0000213
mir-505
miRBase:MIPF0000217
mir-484
miRBase:MIPF0000219
mir-486
miRBase:MIPF0000220
mir-490
miRBase:MIPF0000229
mir-493
miRBase:MIPF0000230
mir-497
miRBase:MIPF0000231
mir-425
miRBase:MIPF0000242
mir-149
miRBase:MIPF0000274
mir-452
miRBase:MIPF0000287
mir-374
miRBase:MIPF0000288
mir-384
miRBase:MIPF0000289
mir-664
miRBase:MIPF0000300
mir-467
miRBase:MIPF0000316
mir-548
miRBase:MIPF0000317
mir-488
miRBase:MIPF0000318
mir-491
miRBase:MIPF0000319
mir-423
miRBase:MIPF0000329
mir-652
miRBase:MIPF0000333
mir-550
miRBase:MIPF0000334
mir-592
miRBase:MIPF0000340
mir-615
miRBase:MIPF0000342
mir-802
miRBase:MIPF0000353
mir-770
miRBase:MIPF0000355
mir-668
miRBase:MIPF0000357
mir-671
miRBase:MIPF0000358
mir-551
miRBase:MIPF0000360
mir-675
miRBase:MIPF0000365
mir-743
miRBase:MIPF0000386
mir-941
miRBase:MIPF0000387
mir-873
miRBase:MIPF0000390
mir-877
miRBase:MIPF0000392
mir-598
miRBase:MIPF0000393
mir-760
miRBase:MIPF0000395
mir-708
miRBase:MIPF0000397
mir-874
miRBase:MIPF0000401
mir-665
miRBase:MIPF0000404
mir-568
miRBase:MIPF0000408
mir-654
miRBase:MIPF0000409
mir-582
miRBase:MIPF0000417
mir-590
miRBase:MIPF0000418
mir-574
miRBase:MIPF0000419
mir-891
miRBase:MIPF0000420
mir-875
miRBase:MIPF0000424
mir-876
miRBase:MIPF0000430
mir-744
miRBase:MIPF0000431
mir-653
miRBase:MIPF0000435
mir-544
miRBase:MIPF0000436
mir-504
miRBase:MIPF0000437
mir-1224
miRBase:MIPF0000440
mir-1226
miRBase:MIPF0000444
mir-1225
miRBase:MIPF0000445
mir-1227
miRBase:MIPF0000454
mir-1302
miRBase:MIPF0000456
mir-650
miRBase:MIPF0000457
mir-663
miRBase:MIPF0000462
mir-498
miRBase:MIPF0000463
mir-612
miRBase:MIPF0000464
mir-661
miRBase:MIPF0000465
mir-581
miRBase:MIPF0000466
mir-586
miRBase:MIPF0000467
mir-642
miRBase:MIPF0000468
mir-938
miRBase:MIPF0000469
mir-549
miRBase:MIPF0000470
mir-676
miRBase:MIPF0000471
mir-626
miRBase:MIPF0000474
mir-556
miRBase:MIPF0000475
mir-648
miRBase:MIPF0000476
mir-578
miRBase:MIPF0000477
mir-651
miRBase:MIPF0000478
mir-597
miRBase:MIPF0000479
mir-607
miRBase:MIPF0000480
mir-583
miRBase:MIPF0000482
mir-1271
miRBase:MIPF0000483
mir-600
miRBase:MIPF0000484
mir-638
miRBase:MIPF0000486
mir-553
miRBase:MIPF0000487
mir-643
miRBase:MIPF0000488
mir-939
miRBase:MIPF0000490
mir-662
miRBase:MIPF0000492
mir-576
miRBase:MIPF0000493
mir-640
miRBase:MIPF0000494
mir-920
miRBase:MIPF0000495
mir-589
miRBase:MIPF0000496
mir-657
miRBase:MIPF0000498
mir-492
miRBase:MIPF0000499
mir-373
miRBase:MIPF0000500
mir-552
miRBase:MIPF0000501
mir-599
miRBase:MIPF0000502
mir-593
miRBase:MIPF0000503
mir-933
miRBase:MIPF0000505
mir-1255
miRBase:MIPF0000506
mir-616
miRBase:MIPF0000507
mir-631
miRBase:MIPF0000508
mir-942
miRBase:MIPF0000511
mir-562
miRBase:MIPF0000512
mir-924
miRBase:MIPF0000513
mir-889
miRBase:MIPF0000514
mir-580
miRBase:MIPF0000515
mir-609
miRBase:MIPF0000516
mir-936
miRBase:MIPF0000517
mir-563
miRBase:MIPF0000519
mir-557
miRBase:MIPF0000520
mir-601
miRBase:MIPF0000522
mir-624
miRBase:MIPF0000523
mir-636
miRBase:MIPF0000524
mir-632
miRBase:MIPF0000527
mir-605
miRBase:MIPF0000528
mir-628
miRBase:MIPF0000529
mir-577
miRBase:MIPF0000530
mir-1306
miRBase:MIPF0000531
mir-885
miRBase:MIPF0000532
mir-584
miRBase:MIPF0000533
mir-625
miRBase:MIPF0000534
mir-569
miRBase:MIPF0000535
mir-922
miRBase:MIPF0000536
mir-572
miRBase:MIPF0000537
mir-558
miRBase:MIPF0000538
mir-611
miRBase:MIPF0000539
mir-940
miRBase:MIPF0000540
mir-944
miRBase:MIPF0000541
mir-934
miRBase:MIPF0000542
mir-765
miRBase:MIPF0000545
mir-633
miRBase:MIPF0000546
mir-649
miRBase:MIPF0000547
mir-422
miRBase:MIPF0000548
mir-639
miRBase:MIPF0000549
mir-627
miRBase:MIPF0000550
mir-554
miRBase:MIPF0000551
mir-767
miRBase:MIPF0000552
mir-618
miRBase:MIPF0000553
mir-887
miRBase:MIPF0000554
mir-567
miRBase:MIPF0000555
mir-644
miRBase:MIPF0000556
mir-619
miRBase:MIPF0000557
mir-1307
miRBase:MIPF0000558
mir-1285
miRBase:MIPF0000559
mir-937
miRBase:MIPF0000560
mir-573
miRBase:MIPF0000561
mir-604
miRBase:MIPF0000562
mir-587
miRBase:MIPF0000563
mir-1244
miRBase:MIPF0000569
mir-566
miRBase:MIPF0000576
mir-1233
miRBase:MIPF0000578
mir-1273
miRBase:MIPF0000579
mir-555
miRBase:MIPF0000583
mir-1297
miRBase:MIPF0000584
mir-1237
miRBase:MIPF0000585
mir-575
miRBase:MIPF0000586
mir-1282
miRBase:MIPF0000587
mir-1324
miRBase:MIPF0000589
mir-613
miRBase:MIPF0000590
mir-1278
miRBase:MIPF0000591
mir-1184
miRBase:MIPF0000592
mir-1256
miRBase:MIPF0000594
mir-1262
miRBase:MIPF0000595
mir-1207
miRBase:MIPF0000596
mir-637
miRBase:MIPF0000597
mir-1298
miRBase:MIPF0000598
mir-1291
miRBase:MIPF0000599
mir-634
miRBase:MIPF0000600
mir-1178
miRBase:MIPF0000601
mir-1294
miRBase:MIPF0000603
mir-1284
miRBase:MIPF0000604
mir-646
miRBase:MIPF0000605
mir-935
miRBase:MIPF0000606
mir-1303
miRBase:MIPF0000608
mir-1205
miRBase:MIPF0000609
mir-1290
miRBase:MIPF0000610
mir-1253
miRBase:MIPF0000611
mir-564
miRBase:MIPF0000612
mir-1202
miRBase:MIPF0000613
mir-1254
miRBase:MIPF0000614
mir-1266
miRBase:MIPF0000615
mir-1323
miRBase:MIPF0000617
mir-622
miRBase:MIPF0000619
mir-1245
miRBase:MIPF0000620
mir-1251
miRBase:MIPF0000621
mir-1248
miRBase:MIPF0000622
mir-561
miRBase:MIPF0000623
mir-762
miRBase:MIPF0000624
mir-1299
miRBase:MIPF0000625
mir-1289
miRBase:MIPF0000626
mir-1246
miRBase:MIPF0000627
mir-1208
miRBase:MIPF0000628
mir-621
miRBase:MIPF0000631
mir-1179
miRBase:MIPF0000632
mir-1203
miRBase:MIPF0000633
mir-1206
miRBase:MIPF0000634
mir-1267
miRBase:MIPF0000640
mir-591
miRBase:MIPF0000641
mir-658
miRBase:MIPF0000643
mir-1272
miRBase:MIPF0000645
mir-1827
miRBase:MIPF0000646
mir-614
miRBase:MIPF0000647
mir-1296
miRBase:MIPF0000649
mir-595
miRBase:MIPF0000651
mir-1276
miRBase:MIPF0000652
mir-630
miRBase:MIPF0000653
mir-559
miRBase:MIPF0000656
mir-645
miRBase:MIPF0000657
mir-302_2
miRBase:MIPF0000658
mir-1288
miRBase:MIPF0000660
mir-610
miRBase:MIPF0000661
mir-635
miRBase:MIPF0000662
mir-1322
miRBase:MIPF0000663
mir-1181
miRBase:MIPF0000665
mir-1249
miRBase:MIPF0000667
mir-1183
miRBase:MIPF0000668
mir-1247
miRBase:MIPF0000669
mir-1825
miRBase:MIPF0000670
mir-1204
miRBase:MIPF0000671
mir-617
miRBase:MIPF0000672
mir-1182
miRBase:MIPF0000673
mir-1275
miRBase:MIPF0000674
mir-1292
miRBase:MIPF0000675
mir-1295
miRBase:MIPF0000676
mir-766
miRBase:MIPF0000677
mir-641
miRBase:MIPF0000679
mir-588
miRBase:MIPF0000681
mir-1286
miRBase:MIPF0000682
mir-1258
miRBase:MIPF0000684
mir-1263
miRBase:MIPF0000687
mir-1265
miRBase:MIPF0000688
mir-1236
miRBase:MIPF0000689
mir-943
miRBase:MIPF0000690
mir-1293
miRBase:MIPF0000691
mir-1281
miRBase:MIPF0000695
mir-1250
miRBase:MIPF0000696
mir-759
miRBase:MIPF0000706
mir-764
miRBase:MIPF0000707
mir-761
miRBase:MIPF0000709
mir-1193
miRBase:MIPF0000714
mir-718
miRBase:MIPF0000721
mir-1287
miRBase:MIPF0000725
mir-769
miRBase:MIPF0000727
mir-670
miRBase:MIPF0000734
mir-1301
miRBase:MIPF0000742
mir-711
miRBase:MIPF0000748
mir-571
miRBase:MIPF0000757
mir-602
miRBase:MIPF0000767
mir-1912
miRBase:MIPF0000768
mir-1468
miRBase:MIPF0000777
mir-606
miRBase:MIPF0000780
mir-1180
miRBase:MIPF0000789
mir-623
miRBase:MIPF0000798
mir-1261
miRBase:MIPF0000802
mir-596
miRBase:MIPF0000808
mir-3130
miRBase:MIPF0000845
mir-3202
miRBase:MIPF0000846
mir-1270
miRBase:MIPF0000877
mir-3156
miRBase:MIPF0000891
mir-3180
miRBase:MIPF0000894
mir-3179
miRBase:MIPF0000900
mir-1538
miRBase:MIPF0000903
mir-1537
miRBase:MIPF0000917
mir-4283
miRBase:MIPF0000919
mir-1228
miRBase:MIPF0000924
mir-2355
miRBase:MIPF0000938
mir-647
miRBase:MIPF0000939
mir-1238
miRBase:MIPF0000941
mir-1268
miRBase:MIPF0000946
mir-2861
miRBase:MIPF0000963
mir-1305
miRBase:MIPF0000965
mir-1252
miRBase:MIPF0000968
mir-3119
miRBase:MIPF0000971
mir-608
miRBase:MIPF0000972
mir-1909
miRBase:MIPF0000973
mir-1469
miRBase:MIPF0000979
mir-921
miRBase:MIPF0000982
mir-1269
miRBase:MIPF0000984
mir-1910
miRBase:MIPF0000987
mir-1257
miRBase:MIPF0000998
mir-3116
miRBase:MIPF0001002
mir-1913
miRBase:MIPF0001015
mir-1260a
miRBase:MIPF0001020
mir-1908
miRBase:MIPF0001021
mir-1972
miRBase:MIPF0001025
mir-3199
miRBase:MIPF0001026
mir-3160
miRBase:MIPF0001028
mir-4315
miRBase:MIPF0001033
mir-1200
miRBase:MIPF0001036
mir-1915
miRBase:MIPF0001037
mir-1914
miRBase:MIPF0001040
mir-1304
miRBase:MIPF0001064
mir-3158
miRBase:MIPF0001065
mir-1471
miRBase:MIPF0001069
mir-3150
miRBase:MIPF0001102
mir-3074
miRBase:MIPF0001103
mir-3065
miRBase:MIPF0001105
mir-3926
miRBase:MIPF0001118
mir-3913
miRBase:MIPF0001134
mir-3689
miRBase:MIPF0001144
mir-3910
miRBase:MIPF0001148
mir-3914
miRBase:MIPF0001169
mir-3622
miRBase:MIPF0001179
mir-1343
miRBase:MIPF0001206
mir-4509
miRBase:MIPF0001207
mir-4776
miRBase:MIPF0001210
mir-3198
miRBase:MIPF0001216
mir-3135
miRBase:MIPF0001219
mir-4435
miRBase:MIPF0001220
mir-4679
miRBase:MIPF0001228
mir-4650
miRBase:MIPF0001234
mir-4436
miRBase:MIPF0001236
mir-3064
miRBase:MIPF0001238
mir-3155
miRBase:MIPF0001242
mir-4662
miRBase:MIPF0001245
mir-4773
miRBase:MIPF0001250
mir-3190
miRBase:MIPF0001251
mir-4659
miRBase:MIPF0001256
mir-4771
miRBase:MIPF0001258
mir-3529
miRBase:MIPF0001261
mir-3688
miRBase:MIPF0001263
mir-3960
miRBase:MIPF0001271
mir-4520
miRBase:MIPF0001272
mir-4477
miRBase:MIPF0001274
mir-1231
miRBase:MIPF0001309
mir-4444
miRBase:MIPF0001310
mir-4536
miRBase:MIPF0001319
mir-5701
miRBase:MIPF0001325
mir-4524
miRBase:MIPF0001330
mir-3680
miRBase:MIPF0001338
mir-3670
miRBase:MIPF0001340
mir-5681
miRBase:MIPF0001343
mir-5692
miRBase:MIPF0001351
mir-5583
miRBase:MIPF0001356
mir-1260b
miRBase:MIPF0001381
mir-6511
miRBase:MIPF0001382
mir-3173
miRBase:MIPF0001383
mir-4743
miRBase:MIPF0001384
mir-4446
miRBase:MIPF0001385
mir-3154
miRBase:MIPF0001387
mir-4667
miRBase:MIPF0001390
mir-3151
miRBase:MIPF0001394
mir-3660
miRBase:MIPF0001397
mir-2110
miRBase:MIPF0001399
mir-3943
miRBase:MIPF0001400
mir-3193
miRBase:MIPF0001401
mir-4796
miRBase:MIPF0001402
mir-6127
miRBase:MIPF0001405
mir-3613
miRBase:MIPF0001411
mir-6131
miRBase:MIPF0001412
mir-6130
miRBase:MIPF0001413
mir-6133
miRBase:MIPF0001415
mir-3121
miRBase:MIPF0001417
mir-6129
miRBase:MIPF0001423
mir-3145
miRBase:MIPF0001427
mir-3138
miRBase:MIPF0001428
mir-23c
miRBase:MIPF0001429
mir-6132
miRBase:MIPF0001438
mir-3127
miRBase:MIPF0001439
mir-4484
miRBase:MIPF0001440
mir-3200
miRBase:MIPF0001441
mir-6128
miRBase:MIPF0001442
mir-6134
miRBase:MIPF0001445
mir-4529
miRBase:MIPF0001451
mir-3129
miRBase:MIPF0001458
mir-4660
miRBase:MIPF0001460
mir-3927
miRBase:MIPF0001462
mir-378_2
miRBase:MIPF0001463
mir-2114
miRBase:MIPF0001464
mir-4510
miRBase:MIPF0001467
mir-4429
miRBase:MIPF0001474
mir-4716
miRBase:MIPF0001476
mir-3617
miRBase:MIPF0001477
mir-1273c
miRBase:MIPF0001481
mir-3188
miRBase:MIPF0001488
mir-3937
miRBase:MIPF0001500
mir-3117
miRBase:MIPF0001506
mir-4654
miRBase:MIPF0001507
mir-4504
miRBase:MIPF0001508
mir-3132
miRBase:MIPF0001509
mir-6089
miRBase:MIPF0001510
mir-4803
miRBase:MIPF0001511
mir-4515
miRBase:MIPF0001512
mir-3664
miRBase:MIPF0001518
mir-3612
miRBase:MIPF0001519
mir-3938
miRBase:MIPF0001520
mir-4738
miRBase:MIPF0001521
mir-2278
miRBase:MIPF0001522
mir-3126
miRBase:MIPF0001525
mir-3923
miRBase:MIPF0001527
mir-4791
miRBase:MIPF0001529
mir-3661
miRBase:MIPF0001530
mir-3615
miRBase:MIPF0001540
mir-4526
miRBase:MIPF0001545
mir-4782
miRBase:MIPF0001546
mir-4421
miRBase:MIPF0001548
mir-3122
miRBase:MIPF0001549
mir-4672
miRBase:MIPF0001551
mir-4742
miRBase:MIPF0001552
mir-629
miRBase:MIPF0001555
mir-3607
miRBase:MIPF0001566
mir-3174
miRBase:MIPF0001569
mir-4788
miRBase:MIPF0001573
mir-4798
miRBase:MIPF0001574
mir-3136
miRBase:MIPF0001575
mir-4774
miRBase:MIPF0001578
mir-4451
miRBase:MIPF0001582
mir-3934
miRBase:MIPF0001584
mir-4637
miRBase:MIPF0001586
mir-4423
miRBase:MIPF0001587
mir-3192
miRBase:MIPF0001597
mir-3940
miRBase:MIPF0001599
mir-3912
miRBase:MIPF0001601
mir-2392
miRBase:MIPF0001614
mir-3140
miRBase:MIPF0001615
mir-3690
miRBase:MIPF0001618
mir-4488
miRBase:MIPF0001623
mir-3146
miRBase:MIPF0001626
mir-4428
miRBase:MIPF0001630
mir-1976
miRBase:MIPF0001633
mir-3165
miRBase:MIPF0001635
mir-3170
miRBase:MIPF0001637
mir-3605
miRBase:MIPF0001639
mir-4427
miRBase:MIPF0001640
mir-1199
miRBase:MIPF0001659
mir-6516
miRBase:MIPF0001672
mir-6770
miRBase:MIPF0001692
mir-7973
miRBase:MIPF0001693
mir-6859
miRBase:MIPF0001698
mir-6715
miRBase:MIPF0001708
mir-3618
miRBase:MIPF0001710
mir-6794
miRBase:MIPF0001726
mir-6827
miRBase:MIPF0001747
mir-5697
miRBase:MIPF0001748
mir-4703
miRBase:MIPF0001759
mir-4766
miRBase:MIPF0001764
mir-1911
miRBase:MIPF0001787
mir-8071
miRBase:MIPF0001799
mir-6505
miRBase:MIPF0001805
mir-6790
miRBase:MIPF0001811
mir-1243
miRBase:MIPF0001821
mir-3167
miRBase:MIPF0001823
mir-7641
miRBase:MIPF0001825
mir-4433
miRBase:MIPF0001826
mir-4677
miRBase:MIPF0001848
mir-6862
miRBase:MIPF0001855
mir-6724
miRBase:MIPF0001920
mir-3118
miRBase:MIPF0001928
mir-3149
miRBase:MIPF0001935
mir-1277
miRBase:MIPF0001937
mir-3648
miRBase:MIPF0001984
mir-4680
miRBase:MIPF0001988
mir-4657
miRBase:MIPF0002009
mir-8069
miRBase:MIPF0002050
mir-3687
miRBase:MIPF0002051
mir-4449
miRBase:MIPF0002103
mir-4523
miRBase:MIPF0002104
hsa-miR-125b-5p
miRBase:MIMAT0000423
hsa-miR-125b-1-3p
miRBase:MIMAT0004592
hsa-miR-125b-2-3p
miRBase:MIMAT0004603
non-coding RNA
A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein.
Alan Ruttenberg
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
Alan Ruttenberg
TODO: Add axiom linking GO transcription
synthesized non-coding RNA
Alan Ruttenberg
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
Alan Ruttenberg
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
Alan Ruttenberg
Should requested and then imported from ChEBI
WEB:https://en.wikipedia.org/w/index.php?title=Special:CiteThisPage&page=Small_interfering_RNA&id=685334024#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.
PERSON: Alan Ruttenberg
processed material
organism
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')
GROUP: OBI Biomaterial Branch
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
organism
plant
virus
cultured cell population
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
PERSON:Matthew Brush
PERSON:Matthew Brush
cultured cell population
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.
cell culture sample
protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
amino acid chain
A molecular entity that is a polymer of amino acids residues linked by peptide bonds.
region
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.
sequence
sequence_secondary_structure
A folded sequence.
sequence secondary structure
linkage_group
A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.
http://en.wikipedia.org/wiki/Linkage_group
linkage group
nuclear_gene
A gene from nuclear sequence.
http://en.wikipedia.org/wiki/Nuclear_gene
nuclear gene
mt_gene
A gene located in mitochondrial sequence.
http://en.wikipedia.org/wiki/Mitochondrial_gene
mitochondrial gene
mt gene
kinetoplast_gene
A gene located in kinetoplast sequence.
kinetoplast gene
plastid_gene
A gene from plastid sequence.
plastid gene
apicoplast_gene
A gene from apicoplast sequence.
apicoplast gene
ct_gene
A gene from chloroplast sequence.
chloroplast gene
ct gene
chromoplast_gene
A gene from chromoplast_sequence.
chromoplast gene
cyanelle_gene
A gene from cyanelle sequence.
cyanelle gene
leucoplast_gene
A plastid gene from leucoplast sequence.
leucoplast gene
proplastid_gene
A gene from proplastid sequence.
proplastid gene
nucleomorph_gene
A gene from nucleomorph sequence.
nucleomorph gene
plasmid_gene
A gene from plasmid sequence.
plasmid gene
proviral_gene
A gene from proviral sequence.
proviral gene
endogenous_retroviral_gene
A proviral gene with origin endogenous retrovirus.
endogenous retroviral gene
transposable_element
A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
http://en.wikipedia.org/wiki/Transposable_element
transposable element
transposon
polypeptide
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
http://en.wikipedia.org/wiki/Polypeptide
protein
mRNA_with_frameshift
An mRNA with a frameshift.
frameshifted mRNA
mRNA with frameshift
sequence_feature
Any extent of continuous biological sequence.
located_sequence_feature
sequence feature
transposable_element_gene
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.
transposable element gene
silenced_gene
A gene that is silenced.
silenced gene
gene_silenced_by_DNA_modification
A gene that is silenced by DNA modification.
gene silenced by DNA modification
gene_silenced_by_DNA_methylation
A gene that is silenced by DNA methylation.
gene silenced by DNA methylation
methylation-silenced gene
gene_rearranged_at_DNA_level
An epigenetically modified gene, rearranged at the DNA level.
gene rearranged at DNA level
deletion
The point at which one or more contiguous nucleotides were excised.
deleted_sequence
http://en.wikipedia.org/wiki/Nucleotide_deletion
loinc:LA6692-3
nucleotide deletion
nucleotide_deletion
promoter
A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
http://en.wikipedia.org/wiki/Promoter
promoter sequence
RNApol_I_promoter
A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.
RNA polymerase A promoter
RNApol I promoter
pol I promoter
polymerase I promoter
RNApol_II_promoter
A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
RNA polymerase B promoter
RNApol II promoter
polymerase II promoter
RNApol_III_promoter
A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.
RNA polymerase C promoter
RNApol III promoter
pol III promoter
polymerase III promoter
primary_transcript
A transcript that in its initial state requires modification to be functional.
http://en.wikipedia.org/wiki/Primary_transcript
precursor RNA
primary transcript
mature_transcript
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.
http://en.wikipedia.org/wiki/Mature_transcript
mature transcript
mRNA
Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
http://en.wikipedia.org/wiki/MRNA
messenger RNA
flanking_region
The sequences extending on either side of a specific region.
flanking region
miRNA
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.
http://en.wikipedia.org/wiki/MiRNA
http://en.wikipedia.org/wiki/StRNA
micro RNA
microRNA
small temporal RNA
stRNA
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
engineered_gene
A gene that is engineered.
engineered gene
engineered_foreign_gene
A gene that is engineered and foreign.
engineered foreign gene
mRNA_with_minus_1_frameshift
An mRNA with a minus 1 frameshift.
mRNA with minus 1 frameshift
engineered_foreign_transposable_element_gene
A transposable_element that is engineered and foreign.
engineered foreign transposable element gene
foreign_gene
A gene that is foreign.
foreign gene
fusion_gene
A gene that is a fusion.
fusion gene
http://en.wikipedia.org/wiki/Fusion_gene
engineered_fusion_gene
A fusion gene that is engineered.
engineered fusion gene
origin_of_replication
The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
http://en.wikipedia.org/wiki/Origin_of_replication
ori
origin of replication
recombination_feature
recombination feature
CpG_island
CG island
CpG island
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.
http://en.wikipedia.org/wiki/CpG_island
mRNA_with_plus_1_frameshift
An mRNA with a plus 1 frameshift.
mRNA with plus 1 frameshift
mRNA_with_plus_2_frameshift
An mRNA with a plus 2 frameshift.
mRNA with plus 2 frameshift
mRNA_with_minus_2_frameshift
A mRNA with a minus 2 frameshift.
mRNA with minus 2 frameshift
pseudogene
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).
http://en.wikipedia.org/wiki/Pseudogene
floxed_gene
A transgene that is floxed.
floxed gene
transposable_element_flanking_region
The region of sequence surrounding a transposable element.
transposable element flanking region
insertion_site
The junction where an insertion occurred.
insertion site
transposable_element_insertion_site
The junction in a genome where a transposable_element has inserted.
transposable element insertion site
small_regulatory_ncRNA
A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
small regulatory ncRNA
recombinationally_inverted_gene
A recombinationally rearranged gene by inversion.
recombinationally inverted gene
RNA_6S
6S RNA
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.
RNA 6S
http://en.wikipedia.org/wiki/6S_RNA
CsrB_RsmB_RNA
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.
CsrB RsmB RNA
CsrB-RsmB RNA
DsrA_RNA
DsrA RNA
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.
http://en.wikipedia.org/wiki/DsrA_RNA
OxyS_RNA
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.
OxyS RNA
http://en.wikipedia.org/wiki/OxyS_RNA
RprA_RNA
RprA RNA
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.
http://en.wikipedia.org/wiki/RprA_RNA
RRE_RNA
RRE RNA
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.
spot_42_RNA
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.
http://en.wikipedia.org/wiki/Spot_42_RNA
spot-42 RNA
binding_site
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.
binding_or_interaction_site
http://en.wikipedia.org/wiki/Binding_site
gene_with_polyadenylated_mRNA
A gene that encodes a polyadenylated mRNA.
gene with polyadenylated mRNA
gene_with_mRNA_with_frameshift
A gene that encodes an mRNA with a frameshift.
gene with mRNA with frameshift
recombinationally_rearranged_gene
A gene that is recombinationally rearranged.
recombinationally rearranged gene
gene_with_trans_spliced_transcript
A gene with a transcript that is trans-spliced.
gene with trans spliced transcript
pseudogenic_region
A non-functional descendant of a functional entity.
pseudogenic region
nc_primary_transcript
A primary transcript that is never translated into a protein.
nc primary transcript
noncoding primary transcript
gene_with_edited_transcript
A gene that encodes a transcript that is edited.
gene with edited transcript
bidirectional_promoter
An unregulated promoter that allows continuous expression.
bidirectional promoter
cap
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.
http://en.wikipedia.org/wiki/5%27_cap
tmRNA
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.
http://en.wikipedia.org/wiki/TmRNA
intergenic_region
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.
http://en.wikipedia.org/wiki/Intergenic_region
intergenic region
oligo_U_tail
The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).
oligo U tail
polyA_sequence
Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
polyA sequence
bacterial_RNApol_promoter
A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
bacterial RNApol promoter
RNApol_III_promoter_type_1
RNApol III promoter type 1
RNApol_III_promoter_type_2
RNApol III promoter type 2
RNApol_III_promoter_type_3
RNApol III promoter type 3
insulator
A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
http://en.wikipedia.org/wiki/Insulator_(genetics)
insulator element
monocistronic_mRNA
An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
http://en.wikipedia.org/wiki/Monocistronic_mRNA
monocistronic mRNA
monocistronic processed transcript
polycistronic_mRNA
An mRNA that encodes multiple proteins from at least two non-overlapping regions.
http://en.wikipedia.org/wiki/Polycistronic_mRNA
polycistronic mRNA
miRNA_primary_transcript
A primary transcript encoding a micro RNA.
miRNA primary transcript
micro RNA primary transcript
small temporal RNA primary transcript
stRNA primary transcript
stRNA_primary_transcript
maxicircle_gene
A mitochondrial gene located in a maxicircle.
maxi-circle gene
maxicircle gene
ncRNA
An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
http://en.wikipedia.org/wiki/NcRNA
noncoding RNA
repeat_region
A region of sequence containing one or more repeat units.
repeat region
insertion
The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
insertion
loinc:LA6687-3
nucleotide insertion
nucleotide_insertion
transcript
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
http://en.wikipedia.org/wiki/RNA
gene_with_polycistronic_transcript
A gene that encodes a polycistronic transcript.
gene with polycistronic transcript
gene_with_dicistronic_transcript
A gene that encodes a dicistronic transcript.
gene with dicistronic transcript
gene_with_recoded_mRNA
A gene that encodes an mRNA that is recoded.
gene with recoded mRNA
gene_with_stop_codon_read_through
A gene that encodes a transcript with stop codon readthrough.
gene with stop codon read through
gene_with_stop_codon_redefined_as_pyrrolysine
A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.
gene with stop codon redefined as pyrrolysine
junction
A sequence_feature with an extent of zero.
boundary
breakpoint
gene
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.
http://en.wikipedia.org/wiki/Gene
gene_with_stop_codon_redefined_as_selenocysteine
A gene encoding an mRNA that has the stop codon redefined as selenocysteine.
gene with stop codon redefined as selenocysteine
gene_with_mRNA_recoded_by_translational_bypass
A gene with mRNA recoded by translational bypass.
gene with mRNA recoded by translational bypass
gene_with_transcript_with_translational_frameshift
A gene encoding a transcript that has a translational frameshift.
gene with transcript with translational frameshift
dicistronic_mRNA
An mRNA that has the quality dicistronic.
dicistronic mRNA
foreign_transposable_element
A transposable element that is foreign.
foreign transposable element
gene_with_dicistronic_primary_transcript
A gene that encodes a dicistronic primary transcript.
gene with dicistronic primary transcript
gene_with_dicistronic_mRNA
A gene that encodes a polycistronic mRNA.
gene with dicistronic mRNA
gene with dicistronic processed transcript
repeat_unit
The simplest repeated component of a repeat region. A single repeat.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
repeat unit
CRM
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.
TF module
cis regulatory module
transcription factor module
exemplar_mRNA
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.
exemplar mRNA
QTL
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.
quantitative trait locus
natural_transposable_element
TE that exists (or existed) in nature.
natural transposable element
engineered_transposable_element
TE that has been modified by manipulations in vitro.
engineered transposable element
rescue_gene
A gene that rescues.
rescue gene
wild_type_rescue_gene
A gene that rescues.
wild type rescue gene
chromosome_part
A region of a chromosome.
chromosome part
gene_member_region
A region of a gene.
gene member region
transcript_region
A region of a transcript.
transcript region
polypeptide_region
Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
gene_component_region
gene component region
capped_mRNA
An mRNA that is capped.
capped mRNA
polyadenylated_mRNA
An mRNA that is polyadenylated.
polyadenylated mRNA
trans_spliced_mRNA
An mRNA that is trans-spliced.
trans-spliced mRNA
maternally_imprinted_gene
A gene that is maternally_imprinted.
maternally imprinted gene
paternally_imprinted_gene
A gene that is paternally imprinted.
paternally imprinted gene
post_translationally_regulated_gene
A gene that is post translationally regulated.
post translationally regulated gene
negatively_autoregulated_gene
A gene that is negatively autoreguated.
negatively autoregulated gene
positively_autoregulated_gene
A gene that is positively autoregulated.
positively autoregulated gene
translationally_regulated_gene
A gene that is translationally regulated.
translationally regulated gene
allelically_excluded_gene
A gene that is allelically_excluded.
allelically excluded gene
epigenetically_modified_gene
A gene that is epigenetically modified.
epigenetically modified gene
transgene
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.
http://en.wikipedia.org/wiki/Transgene
edited_mRNA
An mRNA that is edited.
edited mRNA
recombinationally_rearranged_vertebrate_immune_system_gene
A recombinationally rearranged gene of the vertebrate immune system.
recombinationally rearranged vertebrate immune system gene
minicircle_gene
minicircle gene
consensus_mRNA
consensus mRNA
predicted_gene
predicted gene
mobile_genetic_element
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.
MGE
http://en.wikipedia.org/wiki/Mobile_genetic_element
mobile genetic element
transcriptional_cis_regulatory_region
A regulatory_region that modulates the transcription of a gene or genes.
transcription-control region
transcriptional cis regulatory region
promoter_targeting_sequence
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.
promoter targeting sequence
RNA_polymerase_promoter
A region (DNA) to which RNA polymerase binds, to begin transcription.
RNA polymerase promoter
Phage_RNA_Polymerase_Promoter
A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
Phage RNA Polymerase Promoter
SP6_RNA_Polymerase_Promoter
A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.
SP6 RNA Polymerase Promoter
T3_RNA_Polymerase_Promoter
A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.
T3 RNA Polymerase Promoter
T7_RNA_Polymerase_Promoter
A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.
T7 RNA Polymerase Promoter
protein_coding_gene
protein coding gene
retrogene
gene_silenced_by_RNA_interference
A gene that is silenced by RNA interference.
RNA interference silenced gene
RNAi silenced gene
gene silenced by RNA interference
gene_silenced_by_histone_modification
A gene that is silenced by histone modification.
gene silenced by histone modification
gene_silenced_by_histone_methylation
A gene that is silenced by histone methylation.
gene silenced by histone methylation
gene_silenced_by_histone_deacetylation
A gene that is silenced by histone deacetylation.
gene silenced by histone deacetylation
replicon
A region containing at least one unique origin of replication and a unique termination site.
http://en.wikipedia.org/wiki/Replicon_(genetics)
base
A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
http://en.wikipedia.org/wiki/Nucleobase
amino_acid
A sequence feature that corresponds to a single amino acid residue in a polypeptide.
amino acid
http://en.wikipedia.org/wiki/Amino_acid
ncRNA_gene
ncRNA gen
ncRNA gene
gRNA_gene
gRNA gene
miRNA_gene
miRNA gene
stRNA gene
stRNA_gene
scRNA_gene
scRNA gene
snoRNA_gene
snoRNA gene
snRNA_gene
snRNA gene
SRP_RNA_gene
SRP RNA gene
tmRNA_gene
tmRNA gene
tRNA_gene
tRNA gene
biological_region
A region defined by its disposition to be involved in a biological process.
biological region
topologically_defined_region
A region that is defined according to its relations with other regions within the same sequence.
topologically defined region
cryptic_gene
A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.
cryptic gene
rRNA_gene
A gene that encodes for ribosomal RNA.
rDNA
rRNA gene
piRNA_gene
A gene that encodes for an piwi associated RNA.
piRNA gene
RNase_P_RNA_gene
A gene that encodes an RNase P RNA.
RNase P RNA gene
RNase_MRP_RNA_gene
A gene that encodes a RNase_MRP_RNA.
lincRNA_gene
A gene that encodes large intervening non-coding RNA.
lincRNA gene
telomerase_RNA_gene
A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.
TERC
Telomerase RNA component
http:http://en.wikipedia.org/wiki/Telomerase_RNA_component
telomerase RNA gene
genetic_marker
A measurable sequence feature that varies within a population.
RNApol_II_core_promoter
RNApol II core promoter
The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.
bacterial_RNApol_promoter_sigma_70
bacterial RNA polymerase promoter sigma 70
bacterial_RNApol_promoter_sigma54
bacterial RNA polymerase promoter sigma54
transcription_regulatory_region
A regulatory region that is involved in the control of the process of transcription.
transcription regulatory region
sequence_motif
A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
http://en.wikipedia.org/wiki/Sequence_motif
restriction_enzyme_recognition_site
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
restriction enzyme recognition site
restriction_enzyme_single_strand_overhang
A terminal region of DNA sequence where the end of the region is not blunt ended.
single strand overhang
ISRE
An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.
interferon stimulated response element
epigenetically_modified_region
A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence.
gene_with_non_canonical_start_codon
A gene with a start codon other than AUG.
gene with non canonical start codon
gene_with_start_codon_CUG
A gene with a translational start codon of CUG.
gene with start codon CUG
open_chromatin_region
A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA.
open chromatin region
candidate_gene
A gene suspected of being involved in the expression of a trait.
candidate gene
target gene
positional_candidate_gene
A candidate gene whose association with a trait is based on the gene's location on a chromosome.
positional candidate gene
functional_candidate_gene
A candidate gene whose function has something in common biologically with the trait under investigation.
functional candidate gene
functional target gene
rearrangement_region
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.
rearrangement region
transposable_element_CDS
A CDS that is part of a transposable element.
transposable element CDS
transposable_element_pseudogene
A pseudogene contained within a transposable element.
transposable element pseudogene
bacterial_RNApol_promoter_sigma_ecf
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.
bacterial RNApol promoter sigma ecf
regulatory_region
A region of sequence that is involved in the control of a biological process.
http://en.wikipedia.org/wiki/Regulatory_region
regulatory region
gene_cassette
A gene that can be substituted for a related gene at a different site in the genome.
gene cassette
http://en.wikipedia.org/wiki/Gene_cassette
gene_group
A collection of related genes.
gene group
substitution
A sequence alteration where the length of the change in the variant is the same as that of the reference.
loinc:LA6690-7
inversion
A continuous nucleotide sequence is inverted in the same position.
inversion
loinc:LA6689-9
cryptogene
A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence.
recoded_mRNA
The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.
recoded mRNA
mRNA_recoded_by_translational_bypass
A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.
mRNA recoded by translational bypass
mRNA_recoded_by_codon_redefinition
A recoded_mRNA that was modified by an alteration of codon meaning.
mRNA recoded by codon redefinition
retron
Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes.
anatomical structure
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
TAO:0000037
TGMA:0001823
VHOG:0001759
WBbt:0000100
XAO:0003000
ZFA:0000037
biological structure
connected biological structure
organ
Anatomical structure that performs a specific function or group of functions [WP].
CARO:0020004
EFO:0000634
EMAPA:35949
ENVO:01000162
FMA:67498
MA:0003001
OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
UMLS:C0178784
WBbt:0003760
material anatomical entity
AAO:0010264
AEO:0000006
Anatomical entity that has mass.
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
tissue
AAO:0000607
AAO:0010054
AEO:0000043
BILA:0000043
CALOHA:TS-2090
CARO:0000043
EHDAA2:0003043
EMAPA:35868
FBbt:00007003
FMA:9637
HAO:0000043
MA:0003002
MESH:D014024
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.
TAO:0001477
TGMA:0001844
UMLS:C0040300
VHOG:0001757
WBbt:0005729
XAO:0003040
ZFA:0001477
galen:Tissue
portion of tissue
tissue portion
example to be eventually removed
failed exploratory term
Person:Alan Ruttenberg
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
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.
universal
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
Alan Ruttenberg
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.
defined class
"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
Alan Ruttenberg
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
Alan Ruttenberg
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
Alan Ruttenberg
Terms with this status should eventually replaced with a term from another ontology.
group:OBI
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.
Alan Ruttenberg
group:OBI
Person:Alan Ruttenberg
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])
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])